PARADIGM pathway analysis of mRNASeq expression and copy number data
Lung Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1PG1Q5D
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1PG1Q5D
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 32 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Angiopoietin receptor Tie2-mediated signaling 160
Signaling events mediated by the Hedgehog family 144
Endothelins 98
Fc-epsilon receptor I signaling in mast cells 66
Thromboxane A2 receptor signaling 59
IL4-mediated signaling events 56
Aurora B signaling 56
Signaling mediated by p38-alpha and p38-beta 55
amb2 Integrin signaling 54
TCGA08_retinoblastoma 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
Angiopoietin receptor Tie2-mediated signaling 0.3320 160 14097 88 -0.71 0.075 1000 -1000 -0.067 -1000
Signaling events mediated by the Hedgehog family 0.2988 144 7506 52 -0.44 0.23 1000 -1000 -0.035 -1000
Endothelins 0.2033 98 9437 96 -0.38 0.11 1000 -1000 -0.045 -1000
Fc-epsilon receptor I signaling in mast cells 0.1369 66 6448 97 -0.15 0.023 1000 -1000 -0.057 -1000
Thromboxane A2 receptor signaling 0.1224 59 6235 105 -0.2 0.055 1000 -1000 -0.044 -1000
IL4-mediated signaling events 0.1162 56 5135 91 -0.8 0.48 1000 -1000 -0.12 -1000
Aurora B signaling 0.1162 56 3779 67 -0.3 0.29 1000 -1000 -0.039 -1000
Signaling mediated by p38-alpha and p38-beta 0.1141 55 2429 44 -0.11 0.023 1000 -1000 -0.029 -1000
amb2 Integrin signaling 0.1120 54 4505 82 -0.5 0.036 1000 -1000 -0.045 -1000
TCGA08_retinoblastoma 0.1120 54 434 8 -0.009 0.096 1000 -1000 -0.002 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.1058 51 2671 52 -0.26 0.049 1000 -1000 -0.043 -1000
Aurora C signaling 0.1017 49 349 7 0 0.15 1000 -1000 -0.016 -1000
Signaling events regulated by Ret tyrosine kinase 0.0975 47 3911 82 -0.11 0.055 1000 -1000 -0.05 -1000
BMP receptor signaling 0.0768 37 3070 81 -0.27 0.15 1000 -1000 -0.045 -1000
Nongenotropic Androgen signaling 0.0768 37 1971 52 -0.11 0.076 1000 -1000 -0.037 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0768 37 2927 78 -0.16 0.051 1000 -1000 -0.063 -1000
Integrins in angiogenesis 0.0747 36 3028 84 -0.33 0.13 1000 -1000 -0.042 -1000
Calcium signaling in the CD4+ TCR pathway 0.0726 35 1098 31 -0.17 0.024 1000 -1000 -0.035 -1000
Arf6 signaling events 0.0705 34 2125 62 -0.14 0.043 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 0.0685 33 1266 38 -0.041 0.13 1000 -1000 -0.029 -1000
PLK1 signaling events 0.0664 32 2796 85 -0.028 0.16 1000 -1000 -0.038 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0643 31 2110 68 -0.18 0.04 1000 -1000 -0.075 -1000
Canonical Wnt signaling pathway 0.0622 30 1538 51 -0.34 0.16 1000 -1000 -0.054 -1000
Reelin signaling pathway 0.0581 28 1571 56 -0.07 0.059 1000 -1000 -0.043 -1000
IL23-mediated signaling events 0.0581 28 1704 60 -0.2 0.023 1000 -1000 -0.093 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0560 27 2362 85 -0.1 0.031 1000 -1000 -0.04 -1000
Presenilin action in Notch and Wnt signaling 0.0560 27 1648 61 -0.34 0.16 1000 -1000 -0.041 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0560 27 3407 125 -0.13 0.051 1000 -1000 -0.054 -1000
IL6-mediated signaling events 0.0560 27 2078 75 -0.46 0.05 1000 -1000 -0.057 -1000
Glypican 2 network 0.0539 26 106 4 0.028 0.058 1000 -1000 0.009 -1000
Coregulation of Androgen receptor activity 0.0519 25 1928 76 -0.33 0.095 1000 -1000 -0.025 -1000
FOXA2 and FOXA3 transcription factor networks 0.0519 25 1174 46 -0.7 0.11 1000 -1000 -0.11 -1000
LPA4-mediated signaling events 0.0498 24 288 12 -0.099 0 1000 -1000 -0.025 -1000
Syndecan-1-mediated signaling events 0.0498 24 818 34 -0.092 0.15 1000 -1000 -0.037 -1000
TCR signaling in naïve CD8+ T cells 0.0456 22 2119 93 -0.061 0.033 1000 -1000 -0.049 -1000
Plasma membrane estrogen receptor signaling 0.0456 22 1900 86 -0.11 0.038 1000 -1000 -0.052 -1000
FOXM1 transcription factor network 0.0456 22 1167 51 0.022 0.36 1000 -1000 -0.12 -1000
ErbB4 signaling events 0.0436 21 1473 69 -0.13 0.16 1000 -1000 -0.042 -1000
Glucocorticoid receptor regulatory network 0.0436 21 2434 114 -0.33 0.076 1000 -1000 -0.055 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0436 21 705 33 -0.17 0.096 1000 -1000 -0.037 -1000
Regulation of Androgen receptor activity 0.0436 21 1520 70 -0.36 0.14 1000 -1000 -0.051 -1000
IL12-mediated signaling events 0.0415 20 1823 87 -0.18 0.044 1000 -1000 -0.077 -1000
Wnt signaling 0.0415 20 145 7 0.007 0.056 1000 -1000 -0.018 -1000
Glypican 1 network 0.0394 19 933 48 -0.14 0.086 1000 -1000 -0.035 -1000
Nectin adhesion pathway 0.0394 19 1244 63 -0.032 0.12 1000 -1000 -0.04 -1000
TCGA08_p53 0.0394 19 138 7 -0.029 0.022 1000 -1000 -0.012 -1000
Syndecan-3-mediated signaling events 0.0394 19 679 35 -0.24 0.056 1000 -1000 -0.026 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0373 18 992 54 -0.07 0.073 1000 -1000 -0.046 -1000
HIF-1-alpha transcription factor network 0.0373 18 1439 76 -0.11 0.14 1000 -1000 -0.13 -1000
S1P1 pathway 0.0373 18 681 36 -0.1 0.022 1000 -1000 -0.042 -1000
Caspase cascade in apoptosis 0.0353 17 1284 74 -0.068 0.082 1000 -1000 -0.05 -1000
FAS signaling pathway (CD95) 0.0353 17 823 47 -0.2 0.061 1000 -1000 -0.047 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0353 17 2159 120 -0.14 0.061 1000 -1000 -0.046 -1000
Visual signal transduction: Rods 0.0332 16 849 52 -0.041 0.094 1000 -1000 -0.036 -1000
JNK signaling in the CD4+ TCR pathway 0.0290 14 243 17 -0.035 0.032 1000 -1000 -0.042 -1000
p75(NTR)-mediated signaling 0.0290 14 1792 125 -0.049 0.15 1000 -1000 -0.069 -1000
PDGFR-alpha signaling pathway 0.0290 14 616 44 -0.13 0.046 1000 -1000 -0.041 -1000
Ras signaling in the CD4+ TCR pathway 0.0290 14 239 17 -0.017 0.031 1000 -1000 -0.03 -1000
Signaling events mediated by PTP1B 0.0270 13 998 76 -0.048 0.057 1000 -1000 -0.034 -1000
BCR signaling pathway 0.0270 13 1381 99 -0.088 0.051 1000 -1000 -0.05 -1000
S1P4 pathway 0.0270 13 327 25 -0.029 0.033 1000 -1000 -0.026 -1000
Noncanonical Wnt signaling pathway 0.0249 12 333 26 -0.052 0.056 1000 -1000 -0.054 -1000
Aurora A signaling 0.0249 12 742 60 -0.038 0.21 1000 -1000 -0.028 -1000
Effects of Botulinum toxin 0.0249 12 331 26 -0.037 0.031 1000 -1000 -0.013 -1000
EGFR-dependent Endothelin signaling events 0.0249 12 264 21 -0.025 0.049 1000 -1000 -0.039 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0228 11 311 28 -0.11 0.043 1000 -1000 -0.028 -1000
Osteopontin-mediated events 0.0228 11 443 38 -0.046 0.13 1000 -1000 -0.051 -1000
Hedgehog signaling events mediated by Gli proteins 0.0228 11 750 65 -0.53 0.055 1000 -1000 -0.04 -1000
Ephrin B reverse signaling 0.0228 11 561 48 -0.058 0.063 1000 -1000 -0.033 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0228 11 862 74 -0.14 0.049 1000 -1000 -0.066 -1000
Regulation of nuclear SMAD2/3 signaling 0.0207 10 1494 136 -0.21 0.15 1000 -1000 -0.042 -1000
Syndecan-4-mediated signaling events 0.0207 10 715 67 -0.032 0.086 1000 -1000 -0.034 -1000
Syndecan-2-mediated signaling events 0.0187 9 664 69 -0.033 0.086 1000 -1000 -0.049 -1000
Cellular roles of Anthrax toxin 0.0187 9 353 39 -0.062 0.023 1000 -1000 -0.019 -1000
HIF-2-alpha transcription factor network 0.0187 9 401 43 -0.073 0.075 1000 -1000 -0.074 -1000
LPA receptor mediated events 0.0187 9 930 102 -0.061 0.041 1000 -1000 -0.051 -1000
ErbB2/ErbB3 signaling events 0.0166 8 533 65 -0.039 0.034 1000 -1000 -0.05 -1000
Retinoic acid receptors-mediated signaling 0.0166 8 494 58 -0.15 0.046 1000 -1000 -0.047 -1000
IL2 signaling events mediated by PI3K 0.0166 8 466 58 -0.018 0.12 1000 -1000 -0.036 -1000
IL27-mediated signaling events 0.0166 8 431 51 -0.068 0.029 1000 -1000 -0.048 -1000
IL2 signaling events mediated by STAT5 0.0166 8 184 22 0.007 0.076 1000 -1000 -0.029 -1000
E-cadherin signaling in keratinocytes 0.0166 8 353 43 -0.051 0.064 1000 -1000 -0.034 -1000
Ceramide signaling pathway 0.0145 7 595 76 -0.011 0.06 1000 -1000 -0.036 -1000
EPHB forward signaling 0.0145 7 675 85 -0.041 0.085 1000 -1000 -0.071 -1000
Regulation of p38-alpha and p38-beta 0.0145 7 403 54 -0.042 0.053 1000 -1000 -0.05 -1000
TCGA08_rtk_signaling 0.0145 7 183 26 -0.061 0.079 1000 -1000 -0.007 -1000
IGF1 pathway 0.0145 7 452 57 -0.056 0.059 1000 -1000 -0.041 -1000
Insulin Pathway 0.0145 7 535 74 -0.089 0.06 1000 -1000 -0.056 -1000
Signaling events mediated by PRL 0.0145 7 241 34 -0.036 0.065 1000 -1000 -0.039 -1000
mTOR signaling pathway 0.0124 6 368 53 -0.018 0.088 1000 -1000 -0.04 -1000
IFN-gamma pathway 0.0124 6 458 68 -0.026 0.067 1000 -1000 -0.057 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0124 6 537 83 -0.067 0.041 1000 -1000 -0.033 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0124 6 273 45 -0.019 0.051 1000 -1000 -0.051 -1000
S1P3 pathway 0.0124 6 268 42 -0.11 0.043 1000 -1000 -0.04 -1000
PDGFR-beta signaling pathway 0.0124 6 631 97 -0.048 0.065 1000 -1000 -0.06 -1000
EPO signaling pathway 0.0104 5 296 55 -0.001 0.061 1000 -1000 -0.038 -1000
TRAIL signaling pathway 0.0104 5 253 48 -0.035 0.06 1000 -1000 -0.035 -1000
Class I PI3K signaling events 0.0104 5 434 73 -0.031 0.042 1000 -1000 -0.042 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0083 4 165 34 -0.032 0.051 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class II 0.0083 4 302 75 -0.034 0.056 1000 -1000 -0.032 -1000
BARD1 signaling events 0.0083 4 237 57 -0.042 0.09 1000 -1000 -0.041 -1000
Ephrin A reverse signaling 0.0083 4 33 7 0 0.03 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class III 0.0083 4 187 40 -0.077 0.042 1000 -1000 -0.028 -1000
IL1-mediated signaling events 0.0083 4 284 62 -0.021 0.041 1000 -1000 -0.045 -1000
ceramide signaling pathway 0.0083 4 220 49 0 0.033 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class I 0.0083 4 491 104 -0.043 0.055 1000 -1000 -0.033 -1000
FoxO family signaling 0.0083 4 258 64 -0.022 0.071 1000 -1000 -0.059 -1000
E-cadherin signaling in the nascent adherens junction 0.0083 4 352 76 -0.013 0.06 1000 -1000 -0.056 -1000
Arf6 trafficking events 0.0083 4 315 71 -0.054 0.04 1000 -1000 -0.031 -1000
VEGFR1 specific signals 0.0083 4 275 56 -0.13 0.057 1000 -1000 -0.048 -1000
Arf6 downstream pathway 0.0062 3 130 43 -0.045 0.046 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 0.0062 3 100 32 -0.009 0.043 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 0.0062 3 208 68 -0.034 0.049 1000 -1000 -0.036 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0062 3 120 37 -0.012 0.052 1000 -1000 -0.033 -1000
Regulation of Telomerase 0.0062 3 397 102 -0.041 0.068 1000 -1000 -0.038 -1000
p38 MAPK signaling pathway 0.0062 3 137 44 -0.003 0.054 1000 -1000 -0.035 -1000
Canonical NF-kappaB pathway 0.0041 2 101 39 -0.006 0.046 1000 -1000 -0.032 -1000
a4b1 and a4b7 Integrin signaling 0.0041 2 14 5 0.018 0.029 1000 -1000 0.005 -1000
Paxillin-dependent events mediated by a4b1 0.0041 2 102 36 -0.041 0.043 1000 -1000 -0.037 -1000
Circadian rhythm pathway 0.0021 1 29 22 -0.006 0.048 1000 -1000 -0.039 -1000
S1P5 pathway 0.0021 1 31 17 -0.015 0.03 1000 -1000 -0.011 -1000
Signaling mediated by p38-gamma and p38-delta 0.0021 1 26 15 -0.011 0.022 1000 -1000 -0.034 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0021 1 50 27 -0.009 0.053 1000 -1000 -0.037 -1000
Rapid glucocorticoid signaling 0.0021 1 31 20 -0.011 0.024 1000 -1000 -0.016 -1000
Class IB PI3K non-lipid kinase events 0.0021 1 3 3 -0.021 0.021 1000 -1000 -0.014 -1000
Arf1 pathway 0.0021 1 59 54 -0.005 0.031 1000 -1000 -0.02 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 15 23 0.003 0.042 1000 -1000 -0.035 -1000
PLK2 and PLK4 events 0.0000 0 1 3 -0.009 0.022 1000 -1000 -0.027 -1000
Atypical NF-kappaB pathway 0.0000 0 14 31 -0.008 0.023 1000 -1000 -0.029 -1000
E-cadherin signaling events 0.0000 0 0 5 0.021 0.042 1000 -1000 0.009 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 0 0.061 1000 -1000 0 -1000
Total NA 2447 158960 7203 -14 9.6 131000 -131000 -5.4 -131000
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.53 0.5 -10000 0 -0.97 264 264
NCK1/PAK1/Dok-R -0.25 0.21 -10000 0 -0.44 264 264
NCK1/Dok-R -0.61 0.63 -10000 0 -1.1 261 261
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
mol:beta2-estradiol 0.063 0.098 0.24 111 -10000 0 111
RELA 0.023 0.001 -10000 0 -10000 0 0
SHC1 0.02 0.005 -10000 0 -10000 0 0
Rac/GDP 0.017 0.003 -10000 0 -10000 0 0
F2 0.075 0.12 0.27 114 -10000 0 114
TNIP2 0.021 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.56 0.57 -10000 0 -1.1 262 262
FN1 0.01 0.083 -10000 0 -0.56 10 10
PLD2 -0.64 0.65 -10000 0 -1.2 261 261
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GRB14 -0.013 0.14 0.24 1 -0.56 30 31
ELK1 -0.57 0.56 -10000 0 -1.1 262 262
GRB7 0.026 0.032 0.38 4 -10000 0 4
PAK1 0.023 0.017 0.38 1 -10000 0 1
Tie2/Ang1/alpha5/beta1 Integrin -0.59 0.62 -10000 0 -1.1 261 261
CDKN1A -0.37 0.33 -10000 0 -0.66 264 264
ITGA5 0.023 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.62 0.64 -10000 0 -1.2 262 262
CRK 0.022 0.006 -10000 0 -10000 0 0
mol:NO -0.38 0.35 -10000 0 -0.69 264 264
PLG -0.65 0.65 -10000 0 -1.2 261 261
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.5 0.46 -10000 0 -0.91 264 264
GRB2 0.023 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.006 -10000 0 -10000 0 0
ANGPT2 -0.31 0.33 -10000 0 -0.69 169 169
BMX -0.7 0.67 -10000 0 -1.3 262 262
ANGPT1 -0.36 0.56 -10000 0 -1.4 113 113
tube development -0.42 0.37 -10000 0 -0.75 263 263
ANGPT4 -0.24 0.28 -10000 0 -0.56 206 206
response to hypoxia -0.037 0.033 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.68 0.68 -10000 0 -1.2 262 262
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
FGF2 0.007 0.094 -10000 0 -0.56 13 13
STAT5A (dimer) -0.48 0.44 -10000 0 -0.87 263 263
mol:L-citrulline -0.38 0.35 -10000 0 -0.69 264 264
AGTR1 -0.14 0.25 -10000 0 -0.56 126 126
MAPK14 -0.7 0.67 -10000 0 -1.3 264 264
Tie2/SHP2 -0.57 0.6 -10000 0 -1.2 235 235
TEK -0.64 0.66 -10000 0 -1.3 235 235
RPS6KB1 -0.51 0.47 -10000 0 -0.93 264 264
Angiotensin II/AT1 -0.099 0.19 -10000 0 -0.41 126 126
Tie2/Ang1/GRB2 -0.66 0.68 -10000 0 -1.2 262 262
MAPK3 -0.58 0.57 -10000 0 -1.1 259 259
MAPK1 -0.58 0.57 -10000 0 -1.1 261 261
Tie2/Ang1/GRB7 -0.66 0.68 -10000 0 -1.2 262 262
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.65 0.65 -10000 0 -1.2 262 262
PI3K -0.63 0.59 -10000 0 -1.1 264 264
FES -0.69 0.66 -10000 0 -1.3 264 264
Crk/Dok-R -0.62 0.64 -10000 0 -1.2 262 262
Tie2/Ang1/ABIN2 -0.66 0.68 -10000 0 -1.2 262 262
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.47 0.43 -10000 0 -0.85 264 264
STAT5A 0.023 0.003 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.5 0.47 -10000 0 -0.92 264 264
Tie2/Ang2 -0.6 0.55 -10000 0 -1.1 263 263
Tie2/Ang1 -0.71 0.74 -10000 0 -1.3 262 262
FOXO1 -0.47 0.44 -10000 0 -0.86 264 264
ELF1 -0.037 0.067 -10000 0 -10000 0 0
ELF2 -0.65 0.65 -10000 0 -1.2 262 262
mol:Choline -0.6 0.6 -10000 0 -1.1 261 261
cell migration -0.14 0.12 -10000 0 -0.24 264 264
FYN -0.49 0.44 -10000 0 -0.87 263 263
DOK2 -0.021 0.15 -10000 0 -0.56 34 34
negative regulation of cell cycle -0.33 0.3 -10000 0 -0.6 264 264
ETS1 -0.067 0.14 -10000 0 -0.29 107 107
PXN -0.41 0.38 -10000 0 -0.75 264 264
ITGB1 0.022 0.004 -10000 0 -10000 0 0
NOS3 -0.44 0.4 -10000 0 -0.8 264 264
RAC1 0.022 0.004 -10000 0 -10000 0 0
TNF -0.068 0.14 0.25 1 -0.29 116 117
MAPKKK cascade -0.6 0.6 -10000 0 -1.1 261 261
RASA1 0.021 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.66 0.68 -10000 0 -1.2 261 261
NCK1 0.019 0.009 -10000 0 -10000 0 0
vasculogenesis -0.34 0.31 -10000 0 -0.61 264 264
mol:Phosphatidic acid -0.6 0.6 -10000 0 -1.1 261 261
mol:Angiotensin II 0 0.001 -10000 0 -10000 0 0
mol:NADP -0.38 0.35 -10000 0 -0.69 264 264
Rac1/GTP -0.47 0.44 -10000 0 -0.86 264 264
MMP2 -0.64 0.65 -10000 0 -1.2 261 261
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.16 0.23 -10000 0 -0.73 29 29
IHH -0.3 0.31 -10000 0 -0.59 259 259
SHH Np/Cholesterol/GAS1 -0.03 0.12 0.2 1 -0.33 68 69
LRPAP1 0.021 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.03 0.12 0.32 68 -0.2 1 69
SMO/beta Arrestin2 -0.2 0.23 -10000 0 -0.4 250 250
SMO -0.22 0.23 -10000 0 -0.41 257 257
AKT1 -0.11 0.16 -10000 0 -0.56 31 31
ARRB2 0.022 0.006 -10000 0 -10000 0 0
BOC 0.019 0.041 0.24 2 -0.56 2 4
ADRBK1 0.023 0.004 -10000 0 -10000 0 0
heart looping -0.22 0.22 -10000 0 -0.41 257 257
STIL -0.18 0.19 0.24 1 -0.46 76 77
DHH N/PTCH2 0 0.12 -10000 0 -0.42 34 34
DHH N/PTCH1 -0.18 0.21 -10000 0 -0.33 289 289
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
DHH -0.022 0.15 -10000 0 -0.56 34 34
PTHLH -0.2 0.26 -10000 0 -0.75 27 27
determination of left/right symmetry -0.22 0.22 -10000 0 -0.41 257 257
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
skeletal system development -0.2 0.26 -10000 0 -0.74 27 27
IHH N/Hhip -0.44 0.29 -10000 0 -0.57 369 369
DHH N/Hhip -0.28 0.23 -10000 0 -0.44 302 302
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.22 0.22 -10000 0 -0.41 257 257
pancreas development -0.34 0.28 -10000 0 -0.56 293 293
HHAT 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.014 0.07 -10000 0 -0.56 7 7
somite specification -0.22 0.22 -10000 0 -0.41 257 257
SHH Np/Cholesterol/PTCH1 -0.18 0.2 -10000 0 -0.32 281 281
SHH Np/Cholesterol/PTCH2 -0.027 0.12 0.2 1 -0.32 64 65
SHH Np/Cholesterol/Megalin -0.19 0.2 -10000 0 -0.36 261 261
SHH -0.062 0.14 0.3 1 -0.41 61 62
catabolic process -0.18 0.21 -10000 0 -0.35 271 271
SMO/Vitamin D3 -0.2 0.22 -10000 0 -0.38 257 257
SHH Np/Cholesterol/Hhip -0.23 0.19 -10000 0 -0.37 302 302
LRP2 -0.27 0.29 -10000 0 -0.56 241 241
receptor-mediated endocytosis -0.32 0.26 -10000 0 -0.58 203 203
SHH Np/Cholesterol/BOC -0.024 0.11 -10000 0 -0.33 54 54
SHH Np/Cholesterol/CDO -0.028 0.12 0.2 1 -0.32 66 67
mesenchymal cell differentiation 0.23 0.19 0.36 302 -10000 0 302
mol:Vitamin D3 -0.18 0.2 0.25 2 -0.33 279 281
IHH N/PTCH2 -0.18 0.2 -10000 0 -0.37 257 257
CDON 0.016 0.059 -10000 0 -0.56 5 5
IHH N/PTCH1 -0.17 0.22 -10000 0 -0.36 271 271
Megalin/LRPAP1 -0.19 0.22 -10000 0 -0.41 241 241
PTCH2 0.02 0.048 0.24 2 -0.56 3 5
SHH Np/Cholesterol -0.034 0.11 -10000 0 -0.32 61 61
PTCH1 -0.18 0.21 -10000 0 -0.36 271 271
HHIP -0.34 0.28 -10000 0 -0.56 293 293
Endothelins

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
AKT1 -0.099 0.15 -10000 0 -0.38 87 87
PTK2B 0.021 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.28 -10000 0 -0.77 57 57
EDN1 -0.093 0.17 -10000 0 -0.46 66 66
EDN3 -0.051 0.18 0.24 13 -0.56 49 62
EDN2 0.043 0.11 0.24 64 -0.56 7 71
HRAS/GDP -0.22 0.26 -10000 0 -0.55 144 144
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.1 0.19 -10000 0 -0.39 116 116
ADCY4 -0.098 0.16 -10000 0 -0.38 92 92
ADCY5 -0.1 0.17 -10000 0 -0.4 90 90
ADCY6 -0.084 0.14 -10000 0 -0.36 71 71
ADCY7 -0.081 0.14 -10000 0 -0.36 70 70
ADCY1 -0.083 0.14 -10000 0 -0.36 71 71
ADCY2 -0.07 0.15 0.26 9 -0.37 68 77
ADCY3 -0.082 0.14 -10000 0 -0.35 74 74
ADCY8 -0.15 0.18 -10000 0 -0.36 181 181
ADCY9 -0.084 0.14 -10000 0 -0.36 71 71
arachidonic acid secretion -0.19 0.24 -10000 0 -0.49 159 159
ETB receptor/Endothelin-1/Gq/GTP -0.27 0.27 -10000 0 -0.43 302 302
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.077 0.15 -10000 0 -0.35 86 86
ETA receptor/Endothelin-1/Gs/GTP -0.076 0.15 -10000 0 -0.35 83 83
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
COL3A1 -0.1 0.15 -10000 0 -0.38 90 90
EDNRB -0.3 0.29 -10000 0 -0.56 263 263
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.11 0.18 -10000 0 -0.46 77 77
CYSLTR1 -0.15 0.24 -10000 0 -0.58 96 96
SLC9A1 -0.056 0.096 -10000 0 -0.26 62 62
mol:GDP -0.24 0.28 -10000 0 -0.56 160 160
SLC9A3 -0.38 0.37 -10000 0 -0.66 255 255
RAF1 -0.23 0.27 -10000 0 -0.57 156 156
JUN -0.14 0.24 -10000 0 -0.67 52 52
JAK2 -0.099 0.15 -10000 0 -0.39 85 85
mol:IP3 -0.21 0.25 -10000 0 -0.54 147 147
ETA receptor/Endothelin-1 -0.11 0.18 -10000 0 -0.44 93 93
PLCB1 0.021 0.006 -10000 0 -10000 0 0
PLCB2 0.01 0.075 -10000 0 -0.56 8 8
ETA receptor/Endothelin-3 -0.07 0.14 -10000 0 -0.42 59 59
FOS -0.24 0.32 -10000 0 -0.74 106 106
Gai/GDP -0.091 0.29 -10000 0 -0.86 54 54
CRK 0.021 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.26 0.28 -10000 0 -0.61 154 154
BCAR1 0.022 0.006 -10000 0 -10000 0 0
PRKCB1 -0.2 0.24 -10000 0 -0.51 148 148
GNAQ 0.017 0.03 -10000 0 -0.56 1 1
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
GNAL 0.019 0.046 -10000 0 -0.56 3 3
Gs family/GDP -0.21 0.25 -10000 0 -0.54 141 141
ETA receptor/Endothelin-1/Gq/GTP -0.12 0.2 -10000 0 -0.4 136 136
MAPK14 -0.22 0.23 -10000 0 -0.48 168 168
TRPC6 -0.16 0.3 -10000 0 -0.84 56 56
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.24 -10000 0 -0.41 255 255
ETB receptor/Endothelin-2 -0.22 0.23 0.27 1 -0.42 270 271
ETB receptor/Endothelin-3 -0.26 0.24 -10000 0 -0.44 291 291
ETB receptor/Endothelin-1 -0.28 0.24 -10000 0 -0.46 288 288
MAPK3 -0.25 0.32 -10000 0 -0.67 143 143
MAPK1 -0.25 0.32 -10000 0 -0.67 147 147
Rac1/GDP -0.21 0.25 -10000 0 -0.55 141 141
cAMP biosynthetic process -0.092 0.16 0.25 6 -0.4 64 70
MAPK8 -0.17 0.3 -10000 0 -0.69 89 89
SRC 0.022 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.17 0.16 -10000 0 -0.28 270 270
p130Cas/CRK/Src/PYK2 -0.23 0.28 -10000 0 -0.6 138 138
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.21 0.25 -10000 0 -0.55 143 143
COL1A2 -0.26 0.22 -10000 0 -0.45 212 212
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.014 0.11 0.27 3 -0.36 21 24
mol:DAG -0.21 0.25 -10000 0 -0.54 147 147
MAP2K2 -0.24 0.28 -10000 0 -0.6 151 151
MAP2K1 -0.24 0.28 -10000 0 -0.6 150 150
EDNRA -0.051 0.097 -10000 0 -0.3 36 36
positive regulation of muscle contraction -0.084 0.13 0.2 1 -0.36 68 69
Gq family/GDP -0.19 0.27 -10000 0 -0.57 138 138
HRAS/GTP -0.23 0.27 -10000 0 -0.55 165 165
PRKCH -0.2 0.24 -10000 0 -0.52 142 142
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA -0.2 0.24 0.21 2 -0.53 141 143
PRKCB -0.22 0.26 -10000 0 -0.55 148 148
PRKCE -0.2 0.24 0.21 1 -0.52 140 141
PRKCD -0.2 0.24 -10000 0 -0.53 138 138
PRKCG -0.21 0.24 -10000 0 -0.52 146 146
regulation of vascular smooth muscle contraction -0.28 0.38 -10000 0 -0.89 104 104
PRKCQ -0.22 0.27 -10000 0 -0.56 154 154
PLA2G4A -0.21 0.26 -10000 0 -0.54 159 159
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.02 0.009 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.02 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.077 0.15 -10000 0 -0.37 77 77
MMP1 0.11 0.1 0.36 30 -10000 0 30
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.006 -10000 0 -10000 0 0
LAT2 -0.11 0.21 -10000 0 -0.46 97 97
AP1 -0.11 0.26 -10000 0 -0.55 97 97
mol:PIP3 -0.13 0.23 0.24 9 -0.5 103 112
IKBKB -0.061 0.14 0.18 25 -0.3 75 100
AKT1 -0.056 0.2 0.4 19 -0.38 81 100
IKBKG -0.07 0.13 0.18 8 -0.3 77 85
MS4A2 -0.11 0.24 -10000 0 -0.56 106 106
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.012 0.011 -10000 0 -10000 0 0
MAP3K1 -0.028 0.22 0.29 33 -0.47 57 90
mol:Ca2+ -0.096 0.17 0.22 10 -0.36 101 111
LYN 0.012 0.043 -10000 0 -0.58 2 2
CBLB -0.1 0.2 -10000 0 -0.44 93 93
SHC1 0.022 0.005 -10000 0 -10000 0 0
RasGAP/p62DOK -0.001 0.11 -10000 0 -0.32 49 49
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
PLD2 -0.14 0.21 0.3 14 -0.38 175 189
PTPN13 -0.1 0.21 -10000 0 -0.54 61 61
PTPN11 0.007 0.028 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.04 0.17 0.32 19 -0.35 54 73
SYK 0.016 0.019 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.23 -10000 0 -0.46 135 135
LAT -0.11 0.2 -10000 0 -0.43 98 98
PAK2 -0.036 0.24 0.25 94 -0.52 61 155
NFATC2 -0.13 0.26 -10000 0 -0.72 68 68
HRAS -0.11 0.25 0.23 9 -0.52 96 105
GAB2 0.008 0.091 -10000 0 -0.56 12 12
PLA2G1B -0.082 0.25 -10000 0 -0.92 38 38
Fc epsilon R1 -0.14 0.26 -10000 0 -0.46 177 177
Antigen/IgE/Fc epsilon R1 -0.13 0.24 -10000 0 -0.42 177 177
mol:GDP -0.12 0.26 0.27 1 -0.6 83 84
JUN 0.022 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
FOS -0.042 0.18 -10000 0 -0.56 53 53
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.11 0.21 -10000 0 -0.4 129 129
CHUK -0.072 0.13 0.18 8 -0.3 74 82
KLRG1 -0.1 0.19 -10000 0 -0.36 126 126
VAV1 -0.11 0.21 -10000 0 -0.45 97 97
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.11 0.2 -10000 0 -0.44 98 98
negative regulation of mast cell degranulation -0.088 0.19 -10000 0 -0.48 63 63
BTK -0.14 0.29 -10000 0 -0.66 86 86
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.14 0.25 -10000 0 -0.42 170 170
GAB2/PI3K/SHP2 -0.11 0.16 -10000 0 -0.37 112 112
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.11 0.2 -10000 0 -0.35 166 166
RAF1 -0.046 0.27 -10000 0 -0.96 38 38
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.25 -10000 0 -0.41 177 177
FCER1G 0.001 0.098 -10000 0 -0.57 13 13
FCER1A -0.15 0.26 -10000 0 -0.57 133 133
Antigen/IgE/Fc epsilon R1/Fyn -0.12 0.24 -10000 0 -0.4 176 176
MAPK3 -0.045 0.25 -10000 0 -0.9 38 38
MAPK1 -0.046 0.25 -10000 0 -0.9 38 38
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.052 0.25 -10000 0 -0.84 35 35
DUSP1 -0.042 0.18 -10000 0 -0.56 52 52
NF-kappa-B/RelA -0.038 0.083 -10000 0 -0.2 52 52
actin cytoskeleton reorganization -0.099 0.22 -10000 0 -0.56 60 60
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.09 0.2 -10000 0 -0.49 68 68
FER -0.11 0.2 -10000 0 -0.44 97 97
RELA 0.023 0.001 -10000 0 -10000 0 0
ITK -0.065 0.15 -10000 0 -0.43 58 58
SOS1 0.023 0.003 -10000 0 -10000 0 0
PLCG1 -0.12 0.26 0.27 2 -0.55 99 101
cytokine secretion -0.031 0.058 -10000 0 -0.17 7 7
SPHK1 -0.11 0.2 -10000 0 -0.44 96 96
PTK2 -0.1 0.23 -10000 0 -0.6 59 59
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.25 -10000 0 -0.48 134 134
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.13 0.23 0.25 8 -0.5 97 105
MAP2K2 -0.048 0.25 -10000 0 -0.9 38 38
MAP2K1 -0.048 0.25 -10000 0 -0.9 38 38
MAP2K7 0.022 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.085 0.18 0.22 2 -0.46 63 65
MAP2K4 -0.039 0.27 -10000 0 -0.98 34 34
Fc epsilon R1/FcgammaRIIB -0.12 0.26 -10000 0 -0.43 177 177
mol:Choline -0.14 0.21 0.3 14 -0.38 175 189
SHC/Grb2/SOS1 -0.078 0.2 -10000 0 -0.44 84 84
FYN 0.022 0.027 -10000 0 -0.56 1 1
DOK1 0.023 0.004 -10000 0 -10000 0 0
PXN -0.098 0.21 -10000 0 -0.55 59 59
HCLS1 -0.1 0.2 -10000 0 -0.44 92 92
PRKCB -0.1 0.18 0.21 8 -0.39 97 105
FCGR2B 0.015 0.065 -10000 0 -0.56 6 6
IGHE -0.003 0.009 -10000 0 -10000 0 0
KLRG1/SHIP -0.09 0.19 -10000 0 -0.49 63 63
LCP2 0.014 0.065 -10000 0 -0.56 6 6
PLA2G4A -0.11 0.2 -10000 0 -0.44 99 99
RASA1 0.021 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.14 0.21 0.3 14 -0.38 175 189
IKK complex -0.043 0.11 0.19 11 -0.23 58 69
WIPF1 0.023 0.003 -10000 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 -0.024 0.16 -10000 0 -0.56 37 37
GNB1/GNG2 -0.067 0.093 -10000 0 -0.19 155 155
AKT1 -0.061 0.12 0.19 1 -0.24 51 52
EGF 0.015 0.072 0.24 3 -0.56 7 10
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.026 0.1 0.25 2 -0.37 27 29
mol:Ca2+ -0.096 0.16 -10000 0 -0.31 166 166
LYN -0.014 0.07 0.25 2 -0.37 8 10
RhoA/GTP -0.038 0.07 -10000 0 -0.14 61 61
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.11 0.18 -10000 0 -0.35 161 161
GNG2 0.016 0.059 -10000 0 -0.56 5 5
ARRB2 0.022 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.041 0.14 -10000 0 -0.56 22 22
G beta5/gamma2 -0.085 0.13 -10000 0 -0.26 153 153
PRKCH -0.11 0.19 -10000 0 -0.37 161 161
DNM1 0.024 0.014 0.24 2 -10000 0 2
TXA2/TP beta/beta Arrestin3 0.011 0.07 -10000 0 -0.57 6 6
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.01 0.083 -10000 0 -0.56 10 10
G12 family/GTP -0.096 0.16 -10000 0 -0.31 158 158
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
ADRBK2 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.027 0.01 -10000 0 -10000 0 0
mol:GDP 0.055 0.12 0.39 27 -10000 0 27
mol:NADP 0.02 0.038 -10000 0 -0.56 2 2
RAB11A 0.023 0.002 -10000 0 -10000 0 0
PRKG1 -0.023 0.16 -10000 0 -0.56 37 37
mol:IP3 -0.12 0.2 -10000 0 -0.39 166 166
cell morphogenesis 0.027 0.01 -10000 0 -10000 0 0
PLCB2 -0.18 0.28 -10000 0 -0.54 166 166
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.015 0.083 0.25 2 -0.33 17 19
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.014 0.073 0.25 2 -0.4 9 11
RHOA 0.021 0.007 -10000 0 -10000 0 0
PTGIR 0.008 0.091 -10000 0 -0.56 12 12
PRKCB1 -0.12 0.2 -10000 0 -0.39 164 164
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
mol:L-citrulline 0.02 0.038 -10000 0 -0.56 2 2
TXA2/TXA2-R family -0.18 0.28 -10000 0 -0.55 163 163
LCK -0.013 0.071 0.25 2 -0.39 8 10
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.01 0.077 -10000 0 -0.34 17 17
TXA2-R family/G12 family/GDP/G beta/gamma -0.002 0.11 -10000 0 -0.44 23 23
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.013 0.076 -10000 0 -0.34 16 16
MAPK14 -0.072 0.12 -10000 0 -0.23 158 158
TGM2/GTP -0.14 0.24 -10000 0 -0.45 165 165
MAPK11 -0.072 0.12 -10000 0 -0.24 150 150
ARHGEF1 -0.055 0.095 -10000 0 -0.18 149 149
GNAI2 0.021 0.007 -10000 0 -10000 0 0
JNK cascade -0.12 0.2 -10000 0 -0.4 163 163
RAB11/GDP 0.023 0.003 -10000 0 -10000 0 0
ICAM1 -0.097 0.17 -10000 0 -0.32 162 162
cAMP biosynthetic process -0.12 0.19 -10000 0 -0.36 167 167
Gq family/GTP/EBP50 -0.035 0.098 0.24 3 -0.2 109 112
actin cytoskeleton reorganization 0.027 0.01 -10000 0 -10000 0 0
SRC -0.013 0.068 0.25 2 -0.38 7 9
GNB5 0.023 0.003 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
EGF/EGFR -0.008 0.093 0.21 11 -0.31 20 31
VCAM1 -0.091 0.15 -10000 0 -0.3 163 163
TP beta/Gq family/GDP/G beta5/gamma2 -0.041 0.14 -10000 0 -0.56 22 22
platelet activation -0.096 0.16 -10000 0 -0.31 158 158
PGI2/IP 0.006 0.067 -10000 0 -0.41 12 12
PRKACA -0.002 0.079 -10000 0 -0.37 18 18
Gq family/GDP/G beta5/gamma2 -0.04 0.14 -10000 0 -0.53 22 22
TXA2/TP beta/beta Arrestin2 0.009 0.045 -10000 0 -0.37 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.011 0.076 -10000 0 -0.36 18 18
mol:DAG -0.14 0.23 -10000 0 -0.44 164 164
EGFR 0.022 0.084 0.36 11 -0.56 6 17
TXA2/TP alpha -0.16 0.26 -10000 0 -0.5 167 167
Gq family/GTP -0.058 0.12 -10000 0 -0.25 122 122
YES1 -0.013 0.068 0.25 2 -0.38 7 9
GNAI2/GTP -0.006 0.07 -10000 0 -0.34 14 14
PGD2/DP 0.006 0.062 -10000 0 -0.37 12 12
SLC9A3R1 0.025 0.024 0.27 4 -10000 0 4
FYN -0.014 0.071 0.25 2 -0.44 6 8
mol:NO 0.02 0.038 -10000 0 -0.56 2 2
GNA15 0.022 0.004 -10000 0 -10000 0 0
PGK/cGMP -0.002 0.11 -10000 0 -0.36 39 39
RhoA/GDP 0.021 0.007 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.001 0.13 -10000 0 -0.38 38 38
NOS3 0.02 0.038 -10000 0 -0.56 2 2
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA -0.11 0.19 -10000 0 -0.37 160 160
PRKCB -0.12 0.2 -10000 0 -0.38 162 162
PRKCE -0.11 0.19 0.27 1 -0.37 155 156
PRKCD -0.12 0.2 -10000 0 -0.39 162 162
PRKCG -0.13 0.21 -10000 0 -0.4 162 162
muscle contraction -0.16 0.26 -10000 0 -0.5 163 163
PRKCZ -0.11 0.18 -10000 0 -0.35 163 163
ARR3 -0.011 0.016 -10000 0 -10000 0 0
TXA2/TP beta 0.01 0.08 -10000 0 -0.35 17 17
PRKCQ -0.13 0.2 -10000 0 -0.39 167 167
MAPKKK cascade -0.15 0.25 -10000 0 -0.48 164 164
SELE -0.12 0.2 -10000 0 -0.4 162 162
TP beta/GNAI2/GDP/G beta/gamma 0.021 0.09 -10000 0 -0.45 11 11
ROCK1 0.023 0.003 -10000 0 -10000 0 0
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
chemotaxis -0.2 0.31 -10000 0 -0.62 163 163
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
GNA11 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.003 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.42 0.53 -10000 0 -1.2 106 106
STAT6 (cleaved dimer) -0.44 0.54 -10000 0 -1.2 118 118
IGHG1 -0.13 0.18 -10000 0 -0.74 3 3
IGHG3 -0.42 0.51 -10000 0 -1.2 111 111
AKT1 -0.21 0.3 -10000 0 -0.92 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.27 -10000 0 -0.93 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.21 0.32 -10000 0 -0.97 39 39
THY1 -0.43 0.53 -10000 0 -1.2 106 106
MYB 0.027 0.053 0.24 15 -0.56 2 17
HMGA1 0.024 0.017 0.24 3 -10000 0 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.33 -10000 0 -0.74 79 79
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.32 -10000 0 -1 37 37
SP1 0.027 0.004 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
SOCS5 0.019 0.03 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.43 0.54 -10000 0 -1.2 113 113
SOCS1 -0.28 0.34 -10000 0 -0.75 103 103
SOCS3 -0.21 0.28 -10000 0 -0.91 22 22
FCER2 -0.4 0.51 -10000 0 -1.2 92 92
PARP14 0.021 0.009 -10000 0 -10000 0 0
CCL17 -0.5 0.61 -10000 0 -1.4 125 125
GRB2 0.023 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.26 -10000 0 -0.83 35 35
T cell proliferation -0.43 0.54 -10000 0 -1.2 110 110
IL4R/JAK1 -0.43 0.53 -10000 0 -1.2 107 107
EGR2 -0.45 0.55 -10000 0 -1.3 112 112
JAK2 -0.018 0.048 -10000 0 -10000 0 0
JAK3 0.027 0.009 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
JAK1 0.001 0.026 -10000 0 -10000 0 0
COL1A2 -0.11 0.17 -10000 0 -0.88 2 2
CCL26 -0.43 0.53 -10000 0 -1.2 106 106
IL4R -0.45 0.56 -10000 0 -1.3 107 107
PTPN6 0.026 0.022 -10000 0 -10000 0 0
IL13RA2 -0.45 0.56 -10000 0 -1.3 114 114
IL13RA1 -0.018 0.05 -10000 0 -10000 0 0
IRF4 -0.2 0.37 -10000 0 -0.89 91 91
ARG1 -0.12 0.22 -10000 0 -0.78 28 28
CBL -0.23 0.31 -10000 0 -0.7 77 77
GTF3A 0.028 0.012 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.017 0.067 -10000 0 -10000 0 0
IRF4/BCL6 -0.16 0.32 -10000 0 -0.77 85 85
CD40LG -0.074 0.22 -10000 0 -0.56 82 82
MAPK14 -0.23 0.31 -10000 0 -0.74 64 64
mitosis -0.2 0.28 -10000 0 -0.85 38 38
STAT6 -0.5 0.66 -10000 0 -1.5 108 108
SPI1 -0.014 0.15 -10000 0 -0.56 32 32
RPS6KB1 -0.19 0.27 -10000 0 -0.83 35 35
STAT6 (dimer) -0.5 0.66 -10000 0 -1.5 108 108
STAT6 (dimer)/PARP14 -0.45 0.58 -10000 0 -1.3 106 106
mast cell activation 0.009 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.23 0.34 -10000 0 -0.92 56 56
FRAP1 -0.21 0.3 -10000 0 -0.92 38 38
LTA -0.43 0.53 -10000 0 -1.2 106 106
FES 0.021 0.027 -10000 0 -0.56 1 1
T-helper 1 cell differentiation 0.48 0.61 1.4 108 -10000 0 108
CCL11 -0.42 0.52 -10000 0 -1.2 110 110
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.3 -10000 0 -0.98 32 32
IL2RG 0.019 0.07 -10000 0 -0.55 7 7
IL10 -0.44 0.53 -10000 0 -1.2 107 107
IRS1 0.023 0.004 -10000 0 -10000 0 0
IRS2 0.018 0.046 -10000 0 -0.56 3 3
IL4 -0.14 0.28 -10000 0 -1.1 30 30
IL5 -0.44 0.53 -10000 0 -1.2 107 107
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.46 -10000 0 -0.98 113 113
COL1A1 -0.15 0.26 -10000 0 -1 21 21
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.55 -10000 0 -1.3 104 104
IL2R gamma/JAK3 0.029 0.054 -10000 0 -0.41 7 7
TFF3 -0.48 0.6 -10000 0 -1.4 108 108
ALOX15 -0.64 0.73 -10000 0 -1.5 183 183
MYBL1 0.023 0.011 0.24 1 -10000 0 1
T-helper 2 cell differentiation -0.48 0.51 -10000 0 -1.1 150 150
SHC1 0.022 0.005 -10000 0 -10000 0 0
CEBPB 0.025 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.31 -10000 0 -0.96 36 36
mol:PI-3-4-5-P3 -0.21 0.3 -10000 0 -0.92 38 38
PI3K -0.22 0.33 -10000 0 -1 38 38
DOK2 -0.021 0.15 -10000 0 -0.56 34 34
ETS1 0.009 0.083 -10000 0 -0.52 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.23 -10000 0 -0.73 30 30
ITGB3 -0.44 0.54 -10000 0 -1.3 108 108
PIGR -0.8 0.78 -10000 0 -1.5 254 254
IGHE 0.046 0.053 0.2 12 -10000 0 12
MAPKKK cascade -0.15 0.22 -10000 0 -0.71 30 30
BCL6 0.013 0.011 -10000 0 -10000 0 0
OPRM1 -0.44 0.53 -10000 0 -1.2 107 107
RETNLB -0.42 0.53 -10000 0 -1.2 104 104
SELP -0.58 0.7 -10000 0 -1.5 147 147
AICDA -0.41 0.51 -10000 0 -1.2 105 105
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.058 0.089 0.27 16 -0.32 8 24
STMN1 0.013 0.06 -10000 0 -0.2 14 14
Aurora B/RasGAP/Survivin 0.22 0.14 0.32 285 -0.19 14 299
Chromosomal passenger complex/Cul3 protein complex 0.042 0.08 0.21 8 -0.31 12 20
BIRC5 0.21 0.085 0.25 406 -0.3 1 407
DES -0.3 0.31 -10000 0 -0.54 213 213
Aurora C/Aurora B/INCENP 0.12 0.09 0.3 1 -0.35 1 2
Aurora B/TACC1 0.094 0.093 -10000 0 -0.49 1 1
Aurora B/PP2A 0.12 0.099 0.2 6 -0.19 22 28
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.019 0.03 0.13 4 -0.11 18 22
mitotic metaphase/anaphase transition -0.003 0.005 -10000 0 -10000 0 0
NDC80 -0.014 0.11 0.35 19 -0.22 19 38
Cul3 protein complex 0.04 0.032 0.25 2 -10000 0 2
KIF2C 0.072 0.086 0.15 56 -0.37 11 67
PEBP1 0.021 0.005 -10000 0 -10000 0 0
KIF20A 0.12 0.13 0.24 232 -0.29 15 247
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.098 -10000 0 -0.18 13 13
SEPT1 0.023 0.01 0.24 1 -10000 0 1
SMC2 0.023 0.003 -10000 0 -10000 0 0
SMC4 0.016 0.011 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.074 0.18 0.28 2 -0.57 30 32
PSMA3 0.022 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.003 -10000 0 -10000 0 0
H3F3B 0.045 0.062 0.18 7 -0.22 19 26
AURKB 0.16 0.14 0.25 322 -0.29 22 344
AURKC 0.022 0.029 0.24 1 -0.56 1 2
CDCA8 0.084 0.1 0.25 129 -0.3 1 130
cytokinesis 0.05 0.12 0.24 5 -0.4 22 27
Aurora B/Septin1 0.13 0.14 0.31 15 -0.4 16 31
AURKA 0.029 0.05 0.25 21 -10000 0 21
INCENP 0.024 0.01 -10000 0 -10000 0 0
KLHL13 0.029 0.04 0.27 12 -10000 0 12
BUB1 0.043 0.068 0.25 45 -10000 0 45
hSgo1/Aurora B/Survivin 0.27 0.2 0.39 312 -0.24 27 339
EVI5 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.1 0.096 0.26 35 -0.29 3 38
SGOL1 0.11 0.14 0.24 228 -0.29 21 249
CENPA 0.083 0.081 0.21 22 -0.24 10 32
NCAPG 0.056 0.089 0.24 82 -0.29 4 86
Aurora B/HC8 Proteasome 0.12 0.099 -10000 0 -0.2 17 17
NCAPD2 0.022 0.017 0.38 1 -10000 0 1
Aurora B/PP1-gamma 0.13 0.099 -10000 0 -0.2 16 16
RHOA 0.021 0.007 -10000 0 -10000 0 0
NCAPH 0.14 0.11 0.24 243 -10000 0 243
NPM1 0.019 0.18 -10000 0 -0.64 29 29
RASA1 0.021 0.006 -10000 0 -10000 0 0
KLHL9 0.019 0.009 -10000 0 -10000 0 0
mitotic prometaphase -0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.099 -10000 0 -0.2 17 17
PPP1CC 0.023 0.002 -10000 0 -10000 0 0
Centraspindlin 0.11 0.11 0.27 67 -0.3 8 75
RhoA/GDP 0.016 0.005 -10000 0 -10000 0 0
NSUN2 0.064 0.12 -10000 0 -0.35 26 26
MYLK 0.052 0.071 0.17 45 -0.22 19 64
KIF23 0.068 0.088 0.24 94 -10000 0 94
VIM 0.005 0.091 0.28 3 -0.35 16 19
RACGAP1 0.026 0.008 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.037 0.14 -10000 0 -0.46 27 27
Chromosomal passenger complex 0.067 0.082 0.19 17 -0.28 13 30
Chromosomal passenger complex/EVI5 0.29 0.17 0.39 307 -0.29 1 308
TACC1 0.018 0.028 -10000 0 -0.56 1 1
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
CUL3 0.022 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.34 -10000 0 -1.1 49 49
MKNK1 0.023 0.004 -10000 0 -10000 0 0
MAPK14 -0.014 0.13 -10000 0 -0.32 67 67
ATF2/c-Jun -0.021 0.097 -10000 0 -0.4 5 5
MAPK11 -0.016 0.13 -10000 0 -0.32 66 66
MITF -0.039 0.15 -10000 0 -0.38 76 76
MAPKAPK5 -0.031 0.14 -10000 0 -0.37 72 72
KRT8 -0.03 0.14 -10000 0 -0.37 71 71
MAPKAPK3 0.021 0.007 -10000 0 -10000 0 0
MAPKAPK2 0.023 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.028 0.19 -10000 0 -0.47 70 70
CEBPB -0.03 0.14 -10000 0 -0.36 71 71
SLC9A1 -0.032 0.15 -10000 0 -0.38 70 70
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.026 0.14 -10000 0 -0.36 67 67
p38alpha-beta/MNK1 -0.008 0.16 -10000 0 -0.39 65 65
JUN -0.02 0.096 -10000 0 -0.4 5 5
PPARGC1A -0.11 0.24 -10000 0 -0.44 131 131
USF1 -0.029 0.14 -10000 0 -0.36 69 69
RAB5/GDP/GDI1 -0.016 0.11 -10000 0 -0.28 61 61
NOS2 -0.064 0.28 -10000 0 -1.1 28 28
DDIT3 -0.03 0.14 -10000 0 -0.36 71 71
RAB5A 0.021 0.006 -10000 0 -10000 0 0
HSPB1 -0.027 0.12 0.27 8 -0.31 63 71
p38alpha-beta/HBP1 -0.007 0.16 -10000 0 -0.39 63 63
CREB1 -0.032 0.15 -10000 0 -0.39 69 69
RAB5/GDP 0.016 0.005 -10000 0 -10000 0 0
EIF4E -0.032 0.13 -10000 0 -0.35 60 60
RPS6KA4 -0.031 0.14 -10000 0 -0.37 71 71
PLA2G4A -0.033 0.14 0.26 1 -0.35 66 67
GDI1 -0.027 0.14 -10000 0 -0.37 67 67
TP53 -0.051 0.18 -10000 0 -0.47 69 69
RPS6KA5 -0.031 0.14 -10000 0 -0.37 70 70
ESR1 -0.048 0.18 -10000 0 -0.41 84 84
HBP1 0.022 0.005 -10000 0 -10000 0 0
MEF2C -0.038 0.15 -10000 0 -0.38 74 74
MEF2A -0.03 0.14 -10000 0 -0.37 70 70
EIF4EBP1 -0.03 0.15 -10000 0 -0.39 66 66
KRT19 -0.036 0.16 -10000 0 -0.39 74 74
ELK4 -0.03 0.14 -10000 0 -0.37 70 70
ATF6 -0.029 0.14 -10000 0 -0.36 69 69
ATF1 -0.031 0.15 -10000 0 -0.38 69 69
p38alpha-beta/MAPKAPK2 -0.008 0.16 -10000 0 -0.39 66 66
p38alpha-beta/MAPKAPK3 -0.011 0.16 -10000 0 -0.39 66 66
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 -0.014 0.16 -10000 0 -0.52 39 39
alphaM/beta2 Integrin/GPIbA -0.014 0.16 -10000 0 -0.5 41 41
alphaM/beta2 Integrin/proMMP-9 -0.004 0.16 -10000 0 -0.5 38 38
PLAUR 0.022 0.004 -10000 0 -10000 0 0
HMGB1 0.014 0.021 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.011 0.15 -10000 0 -0.5 38 38
AGER -0.5 0.18 -10000 0 -0.57 429 429
RAP1A 0.022 0.005 -10000 0 -10000 0 0
SELPLG -0.013 0.14 -10000 0 -0.56 30 30
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.35 0.2 -10000 0 -0.39 428 428
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.033 0.047 0.24 24 -10000 0 24
CYR61 -0.004 0.12 -10000 0 -0.56 22 22
TLN1 0.021 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.15 0.26 -10000 0 -0.53 112 112
RHOA 0.021 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.24 -10000 0 -0.56 106 106
MYH2 -0.24 0.29 -10000 0 -0.61 147 147
MST1R -0.008 0.13 -10000 0 -0.56 24 24
leukocyte activation during inflammatory response -0.019 0.16 -10000 0 -0.41 58 58
APOB -0.014 0.14 0.24 4 -0.56 27 31
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.017 0.053 -10000 0 -0.56 4 4
JAM3 0.022 0.005 -10000 0 -10000 0 0
GP1BA 0.016 0.054 0.24 1 -0.56 4 5
alphaM/beta2 Integrin/CTGF -0.022 0.18 -10000 0 -0.53 46 46
alphaM/beta2 Integrin -0.2 0.31 -10000 0 -0.61 119 119
JAM3 homodimer 0.022 0.005 -10000 0 -10000 0 0
ICAM2 -0.013 0.14 -10000 0 -0.56 29 29
ICAM1 -0.023 0.16 -10000 0 -0.56 37 37
phagocytosis triggered by activation of immune response cell surface activating receptor -0.18 0.31 -10000 0 -0.6 119 119
cell adhesion -0.015 0.16 -10000 0 -0.5 41 41
NFKB1 -0.36 0.23 -10000 0 -0.71 108 108
THY1 0.023 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.005 -10000 0 -10000 0 0
Lipoprotein(a) 0.012 0.093 0.24 2 -0.35 27 29
alphaM/beta2 Integrin/LRP/tPA 0.001 0.15 -10000 0 -0.47 38 38
IL6 -0.39 0.32 -10000 0 -0.93 106 106
ITGB2 -0.007 0.11 -10000 0 -0.57 17 17
elevation of cytosolic calcium ion concentration 0.006 0.15 -10000 0 -0.47 38 38
alphaM/beta2 Integrin/JAM2/JAM3 -0.046 0.21 -10000 0 -0.47 81 81
JAM2 -0.058 0.2 -10000 0 -0.56 66 66
alphaM/beta2 Integrin/ICAM1 -0.026 0.21 -10000 0 -0.46 78 78
alphaM/beta2 Integrin/uPA/Plg 0.007 0.15 -10000 0 -0.47 38 38
RhoA/GTP -0.23 0.3 -10000 0 -0.65 125 125
positive regulation of phagocytosis -0.13 0.24 -10000 0 -0.57 77 77
Ron/MSP 0.007 0.099 -10000 0 -0.41 24 24
alphaM/beta2 Integrin/uPAR/uPA 0.008 0.16 -10000 0 -0.47 38 38
alphaM/beta2 Integrin/uPAR -0.012 0.16 -10000 0 -0.51 38 38
PLAU 0.036 0.054 0.24 30 -10000 0 30
PLAT 0.025 0.036 0.33 6 -10000 0 6
actin filament polymerization -0.23 0.27 -10000 0 -0.57 150 150
MST1 0.021 0.012 0.24 1 -10000 0 1
alphaM/beta2 Integrin/lipoprotein(a) -0.016 0.16 -10000 0 -0.42 58 58
TNF -0.34 0.23 -10000 0 -0.7 103 103
RAP1B 0.022 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.004 0.16 0.25 1 -0.51 38 39
fibrinolysis 0.005 0.15 -10000 0 -0.47 38 38
HCK 0.018 0.046 -10000 0 -0.56 3 3
dendritic cell antigen processing and presentation -0.18 0.31 -10000 0 -0.6 119 119
VTN -0.2 0.28 0.24 2 -0.56 184 186
alphaM/beta2 Integrin/CYR61 -0.027 0.19 -10000 0 -0.53 51 51
LPA 0.021 0.05 0.25 18 -10000 0 18
LRP1 0.023 0.002 -10000 0 -10000 0 0
cell migration -0.015 0.15 -10000 0 -0.48 38 38
FN1 0.01 0.083 -10000 0 -0.56 10 10
alphaM/beta2 Integrin/Thy1 -0.012 0.16 -10000 0 -0.51 38 38
MPO -0.001 0.11 -10000 0 -0.56 19 19
KNG1 0.007 0.052 0.31 12 -10000 0 12
RAP1/GDP 0.029 0.009 -10000 0 -10000 0 0
ROCK1 -0.2 0.28 -10000 0 -0.62 118 118
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.005 0.026 0.24 3 -10000 0 3
CTGF 0.005 0.1 -10000 0 -0.56 15 15
alphaM/beta2 Integrin/Hck -0.012 0.15 -10000 0 -0.48 38 38
ITGAM -0.032 0.16 -10000 0 -0.57 38 38
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.092 0.26 -10000 0 -0.48 120 120
HP -0.15 0.26 -10000 0 -0.56 138 138
leukocyte adhesion -0.34 0.23 -10000 0 -0.61 142 142
SELP -0.11 0.24 -10000 0 -0.56 106 106
TCGA08_retinoblastoma

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
CDKN2B 0.016 0.04 -10000 0 -0.44 3 3
CDKN2C 0.024 0.02 -10000 0 -10000 0 0
CDKN2A 0.096 0.14 0.24 200 -0.28 19 219
CCND2 -0.009 0.056 0.22 6 -0.38 7 13
RB1 -0.005 0.082 0.43 6 -0.24 34 40
CDK4 -0.003 0.072 0.25 20 -0.43 6 26
CDK6 -0.003 0.072 0.24 20 -0.44 6 26
G1/S progression 0.032 0.11 0.21 101 -0.43 6 107
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.059 0.36 8 -10000 0 8
VDR 0.022 0.027 -10000 0 -0.56 1 1
FAM120B 0.022 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.12 0.15 -10000 0 -0.42 20 20
RXRs/LXRs/DNA/Oxysterols -0.099 0.14 -10000 0 -0.48 18 18
MED1 0.023 0.003 -10000 0 -10000 0 0
mol:9cRA 0.001 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.001 0.072 -10000 0 -0.27 18 18
RXRs/NUR77 -0.17 0.22 -10000 0 -0.37 255 255
RXRs/PPAR -0.15 0.17 -10000 0 -0.3 250 250
NCOR2 0.022 0.027 -10000 0 -0.56 1 1
VDR/VDR/Vit D3 0.016 0.02 -10000 0 -0.41 1 1
RARs/VDR/DNA/Vit D3 0.047 0.029 -10000 0 -0.3 2 2
RARA 0.023 0.004 -10000 0 -10000 0 0
NCOA1 0.023 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.022 0.027 -10000 0 -0.56 1 1
RARs/RARs/DNA/9cRA 0.037 0.022 -10000 0 -0.29 1 1
RARG 0.023 0.002 -10000 0 -10000 0 0
RPS6KB1 0.038 0.08 0.67 6 -10000 0 6
RARs/THRs/DNA/SMRT 0 0.074 -10000 0 -0.28 19 19
THRA 0.023 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.02 -10000 0 -0.41 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.13 0.18 -10000 0 -0.32 231 231
NR1H4 -0.001 0.029 0.24 4 -10000 0 4
RXRs/LXRs/DNA -0.12 0.19 -10000 0 -0.31 230 230
NR1H2 0.024 0.012 -10000 0 -10000 0 0
NR1H3 0.024 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.12 0.18 -10000 0 -0.31 228 228
NR4A1 -0.056 0.2 -10000 0 -0.56 65 65
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.1 0.12 -10000 0 -0.23 228 228
RXRG -0.26 0.29 -10000 0 -0.56 233 233
RXR alpha/CCPG 0.033 0.012 -10000 0 -10000 0 0
RXRA 0.024 0.011 -10000 0 -10000 0 0
RXRB 0.023 0.012 -10000 0 -10000 0 0
THRB 0.002 0.1 -10000 0 -0.56 16 16
PPARG -0.041 0.18 -10000 0 -0.56 51 51
PPARD 0.023 0.003 -10000 0 -10000 0 0
TNF -0.1 0.2 -10000 0 -1.1 12 12
mol:Oxysterols 0.002 0.007 -10000 0 -10000 0 0
cholesterol transport -0.098 0.14 -10000 0 -0.47 18 18
PPARA 0.022 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.02 0.027 -10000 0 -0.56 1 1
RXRs/NUR77/BCL2 -0.16 0.18 -10000 0 -0.31 255 255
SREBF1 -0.09 0.13 -10000 0 -0.55 9 9
RXRs/RXRs/DNA/9cRA -0.13 0.18 -10000 0 -0.32 231 231
ABCA1 -0.09 0.13 -10000 0 -0.56 9 9
RARs/THRs 0.049 0.071 -10000 0 -0.31 16 16
RXRs/FXR -0.13 0.19 -10000 0 -0.33 231 231
BCL2 0.023 0.011 0.24 1 -10000 0 1
Aurora C signaling

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
INCENP 0.023 0.002 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.12 0.087 0.3 1 -0.36 1 2
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.004 0.022 -10000 0 -0.41 1 1
AURKB 0.15 0.14 0.24 322 -0.29 22 344
AURKC 0.022 0.029 0.24 1 -0.56 1 2
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.022 0.092 -10000 0 -0.39 23 23
Crk/p130 Cas/Paxillin -0.052 0.12 -10000 0 -0.29 75 75
JUN -0.018 0.12 0.27 7 -0.35 6 13
HRAS 0.022 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.005 0.16 0.28 22 -0.33 75 97
RAP1A 0.022 0.005 -10000 0 -10000 0 0
FRS2 0.022 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.016 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.007 0.17 0.27 22 -0.33 79 101
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.023 0.16 0.24 19 -0.33 86 105
RHOA 0.021 0.007 -10000 0 -10000 0 0
RAP1A/GTP -0.01 0.15 0.32 3 -0.3 80 83
GRB7 0.026 0.032 0.38 4 -10000 0 4
RET51/GFRalpha1/GDNF -0.008 0.17 0.27 21 -0.33 78 99
MAPKKK cascade -0.028 0.14 0.25 3 -0.31 68 71
BCAR1 0.022 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.022 0.16 0.24 20 -0.33 86 106
lamellipodium assembly -0.039 0.12 -10000 0 -0.26 76 76
RET51/GFRalpha1/GDNF/SHC -0.009 0.16 0.27 20 -0.33 77 97
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.022 0.16 0.24 18 -0.33 81 99
RET9/GFRalpha1/GDNF/Shank3 -0.024 0.16 0.24 18 -0.33 85 103
MAPK3 -0.042 0.14 0.33 1 -0.29 80 81
DOK1 0.023 0.004 -10000 0 -10000 0 0
DOK6 -0.025 0.16 -10000 0 -0.56 39 39
PXN 0.023 0.002 -10000 0 -10000 0 0
neurite development -0.048 0.13 0.32 1 -0.35 24 25
DOK5 0.02 0.048 0.24 2 -0.56 3 5
GFRA1 -0.11 0.24 -10000 0 -0.56 109 109
MAPK8 -0.033 0.12 0.28 7 -0.26 64 71
HRAS/GTP -0.019 0.16 0.32 3 -0.33 70 73
tube development -0.021 0.16 0.24 18 -0.32 85 103
MAPK1 -0.041 0.13 0.27 2 -0.29 74 76
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.033 0.12 -10000 0 -0.26 82 82
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
PDLIM7 0.021 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.024 0.2 0.36 4 -0.36 101 105
SHC1 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.009 0.17 0.27 21 -0.33 80 101
RET51/GFRalpha1/GDNF/Dok5 -0.01 0.17 0.28 20 -0.34 80 100
PRKCA 0.02 0.038 -10000 0 -0.56 2 2
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
CREB1 -0.038 0.13 0.27 4 -0.29 79 83
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.036 0.12 0.18 15 -0.27 83 98
RET51/GFRalpha1/GDNF/Grb7 -0.006 0.17 0.28 25 -0.33 80 105
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.03 0.041 0.25 16 -10000 0 16
DOK4 0.022 0.005 -10000 0 -10000 0 0
JNK cascade -0.018 0.12 0.26 7 -0.34 6 13
RET9/GFRalpha1/GDNF/FRS2 -0.02 0.16 0.24 19 -0.33 81 100
SHANK3 0.021 0.027 -10000 0 -0.56 1 1
RASA1 0.021 0.006 -10000 0 -10000 0 0
NCK1 0.019 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.034 0.12 -10000 0 -0.26 79 79
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.029 0.12 0.27 2 -0.26 82 84
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.031 0.12 0.28 2 -0.27 76 78
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.027 0.12 0.28 2 -0.26 75 77
PI3K -0.038 0.18 0.28 10 -0.38 80 90
SOS1 0.023 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.016 0.16 0.24 17 -0.32 85 102
GRB10 0.022 0.005 -10000 0 -10000 0 0
activation of MAPKK activity -0.026 0.11 0.21 19 -0.25 70 89
RET51/GFRalpha1/GDNF/FRS2 -0.006 0.17 0.28 21 -0.33 78 99
GAB1 0.022 0.006 -10000 0 -10000 0 0
IRS1 0.023 0.004 -10000 0 -10000 0 0
IRS2 0.018 0.046 -10000 0 -0.56 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.031 0.12 -10000 0 -0.27 80 80
RET51/GFRalpha1/GDNF/PKC alpha -0.01 0.17 0.28 21 -0.33 83 104
GRB2 0.023 0.004 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GDNF 0.055 0.1 0.28 77 -10000 0 77
RAC1 0.022 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.008 0.17 0.37 4 -0.33 82 86
Rac1/GTP -0.034 0.14 0.21 6 -0.31 76 82
RET9/GFRalpha1/GDNF -0.035 0.17 0.24 20 -0.35 91 111
GFRalpha1/GDNF -0.044 0.2 0.26 20 -0.37 110 130
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.07 0.15 0.31 24 -0.32 42 66
SMAD6-7/SMURF1 0.003 0.12 -10000 0 -0.35 43 43
NOG 0.001 0.11 0.24 1 -0.56 17 18
SMAD9 -0.09 0.23 -10000 0 -0.52 93 93
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD5 -0.04 0.14 -10000 0 -0.39 50 50
BMP7/USAG1 -0.015 0.22 0.26 3 -0.43 94 97
SMAD5/SKI -0.039 0.16 -10000 0 -0.45 44 44
SMAD1 0.007 0.063 -10000 0 -0.62 2 2
BMP2 -0.05 0.19 -10000 0 -0.56 59 59
SMAD1/SMAD1/SMAD4 -0.016 0.11 -10000 0 -0.48 6 6
BMPR1A 0.022 0.005 -10000 0 -10000 0 0
BMPR1B -0.022 0.15 -10000 0 -0.56 36 36
BMPR1A-1B/BAMBI 0.012 0.11 0.25 1 -0.36 38 39
AHSG 0.018 0.062 0.35 15 -10000 0 15
CER1 -0.008 0.024 0.24 1 -0.29 1 2
BMP2-4/CER1 -0.017 0.14 -10000 0 -0.37 62 62
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.039 0.15 -10000 0 -0.46 38 38
BMP2-4 (homodimer) -0.031 0.16 -10000 0 -0.43 64 64
RGMB 0.021 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.015 0.12 -10000 0 -0.34 45 45
RGMA 0.047 0.073 0.25 51 -10000 0 51
SMURF1 0.022 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.031 0.13 -10000 0 -0.42 29 29
BMP2-4/USAG1 -0.084 0.21 -10000 0 -0.4 132 132
SMAD6/SMURF1/SMAD5 -0.036 0.16 0.35 1 -0.45 43 44
SOSTDC1 -0.087 0.23 0.24 1 -0.56 90 91
BMP7/BMPR2/BMPR1A-1B 0.052 0.14 0.25 2 -0.34 41 43
SKI 0.022 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.009 0.087 -10000 0 -0.56 11 11
HFE2 -0.003 0.025 0.24 2 -10000 0 2
ZFYVE16 0.021 0.006 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD -0.018 0.12 0.25 1 -0.38 40 41
SMAD5/SMAD5/SMAD4 -0.039 0.16 0.35 1 -0.46 42 43
MAPK1 0.022 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.017 0.12 -10000 0 -0.39 25 25
BMP7 (homodimer) 0.087 0.13 0.24 160 -0.49 8 168
NUP214 0.023 0.003 -10000 0 -10000 0 0
BMP6/FETUA 0.018 0.069 0.26 10 -0.33 11 21
SMAD1/SKI 0.006 0.088 -10000 0 -0.53 4 4
SMAD6 -0.039 0.18 -10000 0 -0.56 51 51
CTDSP2 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.01 0.13 0.25 12 -0.37 41 53
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.15 0.11 0.24 283 -0.29 2 285
BMPR2 (homodimer) 0.022 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.042 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.002 0.12 -10000 0 -0.41 36 36
CHRDL1 -0.27 0.29 -10000 0 -0.56 243 243
ENDOFIN/SMAD1 0.008 0.086 -10000 0 -0.52 4 4
SMAD6-7/SMURF1/SMAD1 -0.007 0.12 -10000 0 -0.5 7 7
SMAD6/SMURF1 0.022 0.006 -10000 0 -10000 0 0
BAMBI 0.021 0.042 0.31 2 -0.56 2 4
SMURF2 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.2 0.23 -10000 0 -0.4 252 252
BMP2-4/GREM1 0.051 0.19 0.25 1 -0.39 63 64
SMAD7 0.021 0.027 -10000 0 -0.56 1 1
SMAD8A/SMAD8A/SMAD4 -0.09 0.23 -10000 0 -0.5 101 101
SMAD1/SMAD6 0.006 0.087 -10000 0 -0.49 5 5
TAK1/SMAD6 0.032 0.009 -10000 0 -10000 0 0
BMP7 0.087 0.13 0.24 160 -0.49 8 168
BMP6 0.009 0.087 -10000 0 -0.56 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.025 0.13 -10000 0 -0.39 32 32
PPM1A 0.022 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.006 0.087 -10000 0 -0.5 4 4
SMAD7/SMURF1 0.03 0.023 -10000 0 -0.41 1 1
CTDSPL 0.021 0.007 -10000 0 -10000 0 0
PPP1CA 0.023 0.004 -10000 0 -10000 0 0
XIAP 0.023 0.003 -10000 0 -10000 0 0
CTDSP1 0.022 0.004 -10000 0 -10000 0 0
PPP1R15A 0.023 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.037 0.15 -10000 0 -0.44 38 38
CHRD 0.011 0.042 0.38 1 -0.56 2 3
BMPR2 0.022 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.038 0.13 0.2 1 -0.45 27 28
BMP4 0.012 0.08 0.24 1 -0.56 9 10
FST 0.049 0.091 0.24 70 -0.33 7 77
BMP2-4/NOG -0.025 0.16 -10000 0 -0.39 73 73
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.059 0.13 -10000 0 -0.32 35 35
Nongenotropic Androgen signaling

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
PTK2 -0.005 0.002 -10000 0 -10000 0 0
GNB1/GNG2 -0.038 0.15 -10000 0 -0.32 100 100
regulation of S phase of mitotic cell cycle -0.035 0.093 -10000 0 -0.27 48 48
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
SHBG/T-DHT 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.022 0.006 -10000 0 -10000 0 0
AKT1 -0.004 0.003 -10000 0 -10000 0 0
MAP2K1 -0.073 0.12 -10000 0 -0.29 93 93
T-DHT/AR -0.072 0.17 -10000 0 -0.4 101 101
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 54 54
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
mol:GDP -0.08 0.16 -10000 0 -0.38 100 100
cell proliferation -0.097 0.17 -10000 0 -0.43 70 70
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
FOS -0.11 0.26 -10000 0 -0.8 57 57
mol:Ca2+ -0.01 0.024 -10000 0 -0.073 38 38
MAPK3 -0.089 0.14 -10000 0 -0.35 71 71
MAPK1 -0.043 0.097 -10000 0 -0.32 27 27
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 54 54
cAMP biosynthetic process 0.003 0.017 -10000 0 -10000 0 0
GNG2 0.016 0.059 -10000 0 -0.56 5 5
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 54 54
HRAS/GTP -0.036 0.14 -10000 0 -0.3 95 95
actin cytoskeleton reorganization 0.017 0.018 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 54 54
PI3K 0.016 0.016 -10000 0 -10000 0 0
apoptosis 0.076 0.16 0.44 62 -10000 0 62
T-DHT/AR/PELP1 -0.051 0.15 -10000 0 -0.35 98 98
HRAS/GDP -0.068 0.16 -10000 0 -0.37 99 99
CREB1 -0.082 0.17 -10000 0 -0.47 62 62
RAC1-CDC42/GTP 0.022 0.023 -10000 0 -10000 0 0
AR -0.098 0.23 -10000 0 -0.56 98 98
GNB1 0.021 0.027 -10000 0 -0.56 1 1
RAF1 -0.071 0.12 0.2 1 -0.29 95 96
RAC1-CDC42/GDP -0.027 0.17 -10000 0 -0.35 96 96
T-DHT/AR/PELP1/Src -0.039 0.14 -10000 0 -0.32 96 96
MAP2K2 -0.073 0.12 -10000 0 -0.29 92 92
T-DHT/AR/PELP1/Src/PI3K -0.035 0.094 -10000 0 -0.27 48 48
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
SHBG 0.02 0.01 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.035 0.17 -10000 0 -0.6 29 29
mol:T-DHT 0 0.001 0.002 2 -0.002 35 37
RAC1 0.022 0.004 -10000 0 -10000 0 0
GNRH1 -0.006 0.026 -10000 0 -0.41 2 2
Gi family/GTP -0.033 0.092 -10000 0 -0.33 25 25
CDC42 0.022 0.004 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.025 0.14 0.32 2 -0.39 50 52
CRKL -0.038 0.14 -10000 0 -0.41 53 53
HRAS -0.031 0.15 -10000 0 -0.4 48 48
mol:PIP3 -0.007 0.14 -10000 0 -0.35 52 52
SPRED1 0.023 0.003 -10000 0 -10000 0 0
SPRED2 0.022 0.006 -10000 0 -10000 0 0
GAB1 -0.039 0.15 -10000 0 -0.42 60 60
FOXO3 -0.026 0.14 0.28 1 -0.38 55 56
AKT1 -0.027 0.16 0.3 1 -0.39 63 64
BAD -0.026 0.14 0.28 1 -0.38 56 57
megakaryocyte differentiation -0.055 0.17 -10000 0 -0.44 71 71
GSK3B -0.006 0.16 0.3 8 -0.38 46 54
RAF1 -0.021 0.12 0.26 1 -0.32 44 45
SHC1 0.022 0.005 -10000 0 -10000 0 0
STAT3 -0.041 0.15 -10000 0 -0.42 59 59
STAT1 -0.11 0.36 -10000 0 -1 60 60
HRAS/SPRED1 -0.012 0.13 -10000 0 -0.39 18 18
cell proliferation -0.039 0.15 -10000 0 -0.41 61 61
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
TEC 0.018 0.046 -10000 0 -0.56 3 3
RPS6KB1 -0.032 0.15 -10000 0 -0.41 60 60
HRAS/SPRED2 -0.013 0.12 -10000 0 -0.35 31 31
LYN/TEC/p62DOK -0.011 0.16 -10000 0 -0.42 52 52
MAPK3 -0.016 0.095 0.22 2 -0.29 17 19
STAP1 -0.053 0.17 -10000 0 -0.44 70 70
GRAP2 -0.006 0.12 -10000 0 -0.56 23 23
JAK2 -0.094 0.32 -10000 0 -0.91 60 60
STAT1 (dimer) -0.11 0.35 -10000 0 -1 60 60
mol:Gleevec 0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.012 0.16 -10000 0 -0.41 57 57
actin filament polymerization -0.04 0.14 -10000 0 -0.42 54 54
LYN 0.02 0.038 -10000 0 -0.56 2 2
STAP1/STAT5A (dimer) -0.078 0.24 -10000 0 -0.65 63 63
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.014 0.14 -10000 0 -0.38 51 51
PI3K -0.02 0.12 -10000 0 -0.4 29 29
PTEN 0.021 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.11 0.42 -10000 0 -1.2 60 60
MAPK8 -0.04 0.15 -10000 0 -0.42 61 61
STAT3 (dimer) -0.04 0.14 -10000 0 -0.41 59 59
positive regulation of transcription -0.012 0.08 0.2 2 -0.24 16 18
mol:GDP -0.029 0.15 -10000 0 -0.4 50 50
PIK3C2B -0.04 0.15 -10000 0 -0.42 58 58
CBL/CRKL -0.024 0.14 -10000 0 -0.39 53 53
FER -0.039 0.15 -10000 0 -0.42 60 60
SH2B3 -0.042 0.15 -10000 0 -0.42 61 61
PDPK1 -0.003 0.13 -10000 0 -0.33 47 47
SNAI2 -0.04 0.15 -10000 0 -0.42 59 59
positive regulation of cell proliferation -0.082 0.27 -10000 0 -0.76 61 61
KITLG 0.017 0.023 -10000 0 -10000 0 0
cell motility -0.082 0.27 -10000 0 -0.76 61 61
PTPN6 0.022 0.011 -10000 0 -10000 0 0
EPOR -0.033 0.2 -10000 0 -1 9 9
STAT5A (dimer) -0.064 0.22 -10000 0 -0.62 61 61
SOCS1 0.021 0.027 -10000 0 -0.56 1 1
cell migration 0.051 0.16 0.42 70 -10000 0 70
SOS1 0.023 0.003 -10000 0 -10000 0 0
EPO 0.019 0.03 0.24 6 -10000 0 6
VAV1 0.019 0.046 -10000 0 -0.56 3 3
GRB10 -0.039 0.14 -10000 0 -0.41 58 58
PTPN11 0.023 0.007 -10000 0 -10000 0 0
SCF/KIT -0.04 0.16 -10000 0 -0.44 61 61
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.018 0.097 0.23 2 -0.31 15 17
CBL 0.023 0.004 -10000 0 -10000 0 0
KIT -0.16 0.46 -10000 0 -1.3 66 66
MAP2K2 -0.018 0.097 0.23 2 -0.31 16 18
SHC/Grb2/SOS1 -0.008 0.15 -10000 0 -0.4 51 51
STAT5A -0.064 0.23 -10000 0 -0.65 60 60
GRB2 0.023 0.004 -10000 0 -10000 0 0
response to radiation -0.039 0.14 -10000 0 -0.41 59 59
SHC/GRAP2 0.01 0.096 -10000 0 -0.41 23 23
PTPRO -0.057 0.18 -10000 0 -0.44 71 71
SH2B2 -0.041 0.14 -10000 0 -0.43 54 54
DOK1 0.023 0.004 -10000 0 -10000 0 0
MATK -0.052 0.16 -10000 0 -0.43 70 70
CREBBP 0.017 0.045 -10000 0 -10000 0 0
BCL2 -0.041 0.22 -10000 0 -0.98 17 17
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.009 0.095 -10000 0 -0.41 23 23
alphaV beta3 Integrin 0.026 0.084 -10000 0 -0.37 19 19
PTK2 -0.17 0.19 0.36 1 -0.53 59 60
IGF1R 0.022 0.004 -10000 0 -10000 0 0
PI4KB 0.022 0.006 -10000 0 -10000 0 0
MFGE8 0.023 0.003 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
CDKN1B -0.18 0.25 -10000 0 -0.49 182 182
VEGFA 0.023 0.004 -10000 0 -10000 0 0
ILK -0.18 0.26 -10000 0 -0.5 184 184
ROCK1 0.023 0.003 -10000 0 -10000 0 0
AKT1 -0.17 0.23 -10000 0 -0.46 179 179
PTK2B -0.018 0.097 0.35 2 -0.35 25 27
alphaV/beta3 Integrin/JAM-A -0.097 0.18 -10000 0 -0.33 173 173
CBL 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.037 0.054 -10000 0 -0.36 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.045 0.065 -10000 0 -0.32 13 13
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.097 0.16 -10000 0 -0.44 51 51
alphaV/beta3 Integrin/Syndecan-1 0.036 0.056 -10000 0 -0.36 9 9
PI4KA 0.022 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.017 0.11 -10000 0 -0.36 35 35
PI4 Kinase 0.031 0.011 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.1 0.097 0.25 1 -0.37 8 9
RPS6KB1 -0.037 0.098 0.32 1 -0.49 10 11
TLN1 0.021 0.007 -10000 0 -10000 0 0
MAPK3 -0.085 0.17 -10000 0 -0.57 37 37
GPR124 0.019 0.009 -10000 0 -10000 0 0
MAPK1 -0.083 0.17 -10000 0 -0.58 36 36
PXN 0.023 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.2 0.2 -10000 0 -0.36 286 286
cell adhesion 0.026 0.051 -10000 0 -0.34 7 7
ANGPTL3 0.007 0.029 0.24 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.023 0.082 -10000 0 -0.35 20 20
IGF-1R heterotetramer 0.022 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
TGFBR2 -0.01 0.13 -10000 0 -0.56 26 26
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
IGF1 0.005 0.1 0.24 1 -0.56 15 16
RAC1 0.022 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.032 0.049 -10000 0 -0.36 6 6
apoptosis 0.023 0.003 -10000 0 -10000 0 0
CD47 0.019 0.028 -10000 0 -0.56 1 1
alphaV/beta3 Integrin/CD47 0.033 0.053 -10000 0 -0.36 7 7
VCL 0.022 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.017 0.1 -10000 0 -0.38 28 28
CSF1 0.017 0.053 -10000 0 -0.56 4 4
PIK3C2A -0.18 0.25 -10000 0 -0.5 184 184
PI4 Kinase/Pyk2 -0.098 0.17 -10000 0 -0.33 128 128
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.029 0.1 -10000 0 -0.37 25 25
FAK1/Vinculin -0.13 0.16 0.34 1 -0.42 57 58
alphaV beta3/Integrin/ppsTEM5 0.032 0.049 -10000 0 -0.36 6 6
RHOA 0.021 0.007 -10000 0 -10000 0 0
VTN -0.2 0.28 0.24 2 -0.56 184 186
BCAR1 0.022 0.006 -10000 0 -10000 0 0
FGF2 0.006 0.095 -10000 0 -0.56 13 13
F11R -0.019 0.063 -10000 0 -0.41 12 12
alphaV/beta3 Integrin/Lactadherin 0.038 0.052 -10000 0 -0.36 8 8
alphaV/beta3 Integrin/TGFBR2 0.012 0.12 -10000 0 -0.41 29 29
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.037 -10000 0 -0.33 3 3
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.047 -10000 0 -0.32 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.083 -10000 0 -0.56 10 10
alphaV/beta3 Integrin/Pyk2 0.02 0.097 -10000 0 -0.35 25 25
SDC1 0.021 0.027 -10000 0 -0.56 1 1
VAV3 -0.012 0.043 -10000 0 -0.31 4 4
PTPN11 0.023 0.002 -10000 0 -10000 0 0
IRS1 0.023 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.14 0.16 0.34 1 -0.42 55 56
cell migration -0.12 0.14 0.26 3 -0.39 52 55
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PI3K -0.059 0.14 -10000 0 -0.32 83 83
SPP1 0.13 0.12 0.24 246 -0.29 6 252
KDR -0.008 0.13 -10000 0 -0.56 24 24
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.023 0.003 -10000 0 -10000 0 0
COL4A3 -0.33 0.28 -10000 0 -0.56 293 293
angiogenesis -0.11 0.19 -10000 0 -0.56 42 42
Rac1/GTP 0.019 0.038 -10000 0 -0.29 4 4
EDIL3 -0.006 0.12 -10000 0 -0.56 22 22
cell proliferation 0.012 0.11 -10000 0 -0.41 29 29
Calcium signaling in the CD4+ TCR pathway

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.004 0.036 -10000 0 -0.43 1 1
NFATC2 -0.05 0.13 -10000 0 -0.38 61 61
NFATC3 -0.003 0.03 -10000 0 -10000 0 0
CD40LG -0.17 0.29 0.34 2 -0.64 112 114
PTGS2 -0.15 0.27 0.34 2 -0.6 98 100
JUNB 0.021 0.027 -10000 0 -0.56 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.024 -10000 0 -10000 0 0
CaM/Ca2+ 0.003 0.024 -10000 0 -10000 0 0
CALM1 0.011 0.022 -10000 0 -10000 0 0
JUN 0.011 0.023 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.013 -10000 0 -10000 0 0
FOSL1 0.024 0.014 0.24 2 -10000 0 2
CREM 0.022 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.055 0.17 -10000 0 -0.43 52 52
FOS -0.054 0.18 -10000 0 -0.56 53 53
IFNG -0.13 0.23 0.34 1 -0.53 85 86
AP-1/NFAT1-c-4 -0.14 0.28 -10000 0 -0.62 86 86
FASLG -0.13 0.25 0.34 2 -0.58 82 84
NFAT1-c-4/ICER1 -0.048 0.14 -10000 0 -0.36 60 60
IL2RA -0.13 0.23 0.34 1 -0.54 85 86
FKBP12/FK506 0.016 0.004 -10000 0 -10000 0 0
CSF2 -0.15 0.26 0.34 2 -0.58 106 108
JunB/Fra1/NFAT1-c-4 -0.04 0.14 -10000 0 -0.36 57 57
IL4 -0.13 0.23 0.33 2 -0.54 83 85
IL2 -0.033 0.21 -10000 0 -0.93 25 25
IL3 -0.048 0.2 -10000 0 -0.71 37 37
FKBP1A 0.022 0.005 -10000 0 -10000 0 0
BATF3 0.023 0.004 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.022 0.006 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.017 0.063 -10000 0 -0.36 12 12
ARNO/beta Arrestin1-2 -0.1 0.22 -10000 0 -0.59 50 50
EGFR 0.022 0.084 0.36 11 -0.56 6 17
EPHA2 0.018 0.046 -10000 0 -0.56 3 3
USP6 0.022 0.006 -10000 0 -10000 0 0
IQSEC1 0.021 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.023 0.083 0.26 8 -0.44 12 20
ARRB2 0.007 0.004 -10000 0 -10000 0 0
mol:GTP 0.037 0.062 0.15 26 -0.18 8 34
ARRB1 -0.084 0.22 -10000 0 -0.56 88 88
FBXO8 0.021 0.006 -10000 0 -10000 0 0
TSHR 0.027 0.04 0.24 16 -10000 0 16
EGF 0.015 0.072 0.24 3 -0.56 7 10
somatostatin receptor activity 0 0 0.001 5 -0.001 110 115
ARAP2 0.02 0.027 -10000 0 -0.56 1 1
mol:GDP -0.091 0.16 0.2 1 -0.33 111 112
mol:PI-3-4-5-P3 0 0 0.001 3 -0.001 64 67
ITGA2B 0.005 0.098 -10000 0 -0.56 14 14
ARF6 0.022 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.039 -10000 0 -0.33 3 3
ADAP1 0.014 0.07 -10000 0 -0.56 7 7
KIF13B 0.015 0.059 -10000 0 -0.56 5 5
HGF/MET -0.056 0.18 0.26 1 -0.41 96 97
PXN 0.023 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.084 0.14 0.23 4 -0.29 112 116
EGFR/EGFR/EGF/EGF/ARFGEP100 0.034 0.076 0.25 8 -0.38 12 20
ADRB2 -0.12 0.25 -10000 0 -0.56 117 117
receptor agonist activity 0 0 0 7 0 99 106
actin filament binding 0 0 0 5 -0.001 113 118
SRC 0.022 0.004 -10000 0 -10000 0 0
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 12 -0.001 82 94
ARF6/GDP -0.017 0.17 0.25 9 -0.5 35 44
ARF6/GDP/GULP/ACAP1 -0.072 0.16 -10000 0 -0.37 74 74
alphaIIb/beta3 Integrin/paxillin/GIT1 0.039 0.081 -10000 0 -0.33 22 22
ACAP1 0.021 0.029 0.24 1 -0.56 1 2
ACAP2 0.014 0.011 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.018 0.2 1 -10000 0 1
EFNA1 0.022 0.005 -10000 0 -10000 0 0
HGF -0.092 0.23 -10000 0 -0.56 94 94
CYTH3 -0.004 0.003 -10000 0 -10000 0 0
CYTH2 -0.01 0.16 -10000 0 -1 12 12
NCK1 0.019 0.009 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 7 0 92 99
endosomal lumen acidification 0 0 0 25 0 78 103
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.014 0.07 -10000 0 -0.56 7 7
GNAQ/ARNO 0.002 0.15 -10000 0 -0.95 12 12
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0 3 0 18 21
MET 0.02 0.041 0.38 1 -0.56 2 3
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.022 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 10 -0.001 97 107
GNA11 0.022 0.004 -10000 0 -10000 0 0
LHCGR -0.005 0.021 0.24 1 -10000 0 1
AGTR1 -0.14 0.25 -10000 0 -0.56 126 126
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.018 0.2 1 -10000 0 1
IPCEF1/ARNO 0.008 0.15 -10000 0 -0.84 13 13
alphaIIb/beta3 Integrin 0.013 0.094 -10000 0 -0.41 22 22
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.028 0.063 0.22 2 -0.3 14 16
RGS9BP 0.009 0.083 -10000 0 -0.56 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.004 0.031 0.38 2 -10000 0 2
mol:Na + 0.092 0.072 0.17 158 -0.16 2 160
mol:ADP -0.005 0.053 0.32 11 -10000 0 11
GNAT2 0.018 0.013 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.008 0.14 -10000 0 -0.36 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.009 -10000 0 -10000 0 0
GRK7 0.028 0.06 0.3 21 -10000 0 21
CNGB3 0.13 0.12 0.24 236 -0.29 2 238
Cone Metarhodopsin II/X-Arrestin 0.014 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.078 0.21 34 -0.18 2 36
Cone PDE6 0.006 0.12 -10000 0 -0.32 54 54
Cone Metarhodopsin II 0.027 0.036 0.22 10 -10000 0 10
Na + (4 Units) 0.11 0.095 0.29 49 -0.17 4 53
GNAT2/GDP 0.003 0.12 -10000 0 -0.32 58 58
GNB5 0.023 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.005 0.045 0.18 27 -10000 0 27
Cone Transducin 0.03 0.067 0.24 2 -0.32 14 16
SLC24A2 0.056 0.097 0.25 87 -0.29 4 91
GNB3/GNGT2 0.021 0.08 0.26 2 -0.38 16 18
GNB3 0.026 0.034 0.27 8 -10000 0 8
GNAT2/GTP 0.016 0.004 -10000 0 -10000 0 0
CNGA3 0.011 0.027 0.31 2 -10000 0 2
ARR3 -0.011 0.016 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.093 0.072 0.17 158 -0.16 2 160
mol:Pi -0.008 0.13 -10000 0 -0.36 58 58
Cone CNG Channel 0.08 0.064 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.056 0.097 0.25 87 -0.29 4 91
RGS9 -0.041 0.18 -10000 0 -0.56 52 52
PDE6C -0.008 0.017 -10000 0 -10000 0 0
GNGT2 0.003 0.1 -10000 0 -0.56 16 16
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.011 0.015 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.01 0.054 0.16 37 -10000 0 37
BUB1B 0.025 0.028 0.11 2 -0.21 2 4
PLK1 0.011 0.018 0.079 7 -10000 0 7
PLK1S1 0.01 0.021 0.091 1 -0.18 4 5
KIF2A 0.007 0.019 0.22 2 -10000 0 2
regulation of mitotic centrosome separation 0.011 0.018 0.079 7 -10000 0 7
GOLGA2 0.023 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.12 0.11 0.23 221 -0.23 1 222
WEE1 0.009 0.06 -10000 0 -0.33 12 12
cytokinesis 0.021 0.076 0.2 4 -0.3 14 18
PP2A-alpha B56 0.057 0.05 -10000 0 -0.49 2 2
AURKA 0.013 0.025 0.13 5 -0.19 3 8
PICH/PLK1 0.036 0.053 0.23 10 -0.22 1 11
CENPE 0.002 0.024 0.27 1 -0.19 1 2
RhoA/GTP 0.016 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.02 0.22 2 -10000 0 2
PPP2CA 0.021 0.006 -10000 0 -10000 0 0
FZR1 0.022 0.004 -10000 0 -10000 0 0
TPX2 0.057 0.043 0.17 36 -10000 0 36
PAK1 0.023 0.016 0.36 1 -10000 0 1
SPC24 0.088 0.1 0.24 143 -0.29 1 144
FBXW11 0.021 0.006 -10000 0 -10000 0 0
CLSPN 0.014 0.045 -10000 0 -0.22 13 13
GORASP1 0.021 0.007 -10000 0 -10000 0 0
metaphase 0 0.002 0.014 6 -0.012 3 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.01 0.044 6 -10000 0 6
G2 phase of mitotic cell cycle -0.001 0.002 0.014 4 -10000 0 4
STAG2 0.023 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.028 0.16 -10000 0 -0.52 42 42
spindle elongation 0.011 0.018 0.079 7 -10000 0 7
ODF2 0.023 0.004 -10000 0 -10000 0 0
BUB1 0.036 0.055 -10000 0 -0.53 2 2
TPT1 -0.004 0.053 -10000 0 -0.18 37 37
CDC25C 0.045 0.1 0.2 2 -0.29 34 36
CDC25B 0.021 0.011 -10000 0 -10000 0 0
SGOL1 0.01 0.054 -10000 0 -0.16 37 37
RHOA 0.021 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.041 0.055 -10000 0 -0.22 2 2
CDC14B -0.005 0.003 -10000 0 -10000 0 0
CDC20 0.16 0.11 0.24 303 -0.29 4 307
PLK1/PBIP1 0.004 0.011 -10000 0 -10000 0 0
mitosis -0.002 0.004 0.024 3 -0.018 15 18
FBXO5 0.007 0.021 0.14 3 -10000 0 3
CDC2 0.001 0.003 -10000 0 -0.012 5 5
NDC80 0.1 0.11 0.25 165 -0.29 1 166
metaphase plate congression 0.004 0.05 -10000 0 -0.23 20 20
ERCC6L 0.032 0.055 0.2 9 -0.26 1 10
NLP/gamma Tubulin 0.006 0.014 -10000 0 -0.099 2 2
microtubule cytoskeleton organization -0.004 0.053 -10000 0 -0.18 37 37
G2/M transition DNA damage checkpoint -0.001 0.002 0.011 2 -10000 0 2
PPP1R12A 0.023 0.003 -10000 0 -10000 0 0
interphase -0.001 0.002 0.011 2 -10000 0 2
PLK1/PRC1-2 0.11 0.1 0.27 63 -0.2 3 66
GRASP65/GM130/RAB1/GTP/PLK1 0.039 0.021 -10000 0 -10000 0 0
RAB1A 0.022 0.006 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.015 0.072 7 -10000 0 7
mitotic prometaphase 0 0.004 0.018 20 -10000 0 20
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.1 -10000 0 -0.46 17 17
microtubule-based process 0.089 0.086 0.17 229 -0.17 10 239
Golgi organization 0.011 0.018 0.079 7 -10000 0 7
Cohesin/SA2 0.023 0.015 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.034 0.006 -10000 0 -10000 0 0
KIF20A 0.12 0.13 0.24 232 -0.29 15 247
APC/C/CDC20 0.11 0.08 0.17 294 -0.16 4 298
PPP2R1A 0.022 0.004 -10000 0 -10000 0 0
chromosome segregation 0.004 0.011 -10000 0 -10000 0 0
PRC1 0.046 0.071 0.26 48 -10000 0 48
ECT2 0.1 0.11 0.22 214 -10000 0 214
C13orf34 0.008 0.015 0.068 7 -10000 0 7
NUDC 0.004 0.05 -10000 0 -0.23 20 20
regulation of attachment of spindle microtubules to kinetochore 0.025 0.028 0.11 2 -0.21 2 4
spindle assembly 0.008 0.015 0.075 4 -10000 0 4
spindle stabilization 0.01 0.021 0.091 1 -0.18 4 5
APC/C/HCDH1 0.019 0.005 -10000 0 -10000 0 0
MKLP2/PLK1 0.089 0.086 0.17 229 -0.17 10 239
CCNB1 0.045 0.073 0.24 54 -0.3 2 56
PPP1CB 0.023 0.004 -10000 0 -10000 0 0
BTRC 0.022 0.005 -10000 0 -10000 0 0
ROCK2 0.006 0.047 -10000 0 -0.28 3 3
TUBG1 0.008 0.024 -10000 0 -0.18 6 6
G2/M transition of mitotic cell cycle 0.006 0.028 -10000 0 -0.22 2 2
MLF1IP -0.006 0.011 -10000 0 -10000 0 0
INCENP 0.023 0.002 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.031 0.035 0.24 12 -10000 0 12
NFATC2 -0.044 0.23 -10000 0 -0.58 64 64
NFATC3 0.012 0.064 -10000 0 -0.27 9 9
CD40LG -0.18 0.36 -10000 0 -0.91 67 67
ITCH -0.019 0.097 -10000 0 -0.26 67 67
CBLB -0.018 0.094 -10000 0 -0.26 63 63
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.1 0.28 -10000 0 -0.79 48 48
JUNB 0.021 0.027 -10000 0 -0.56 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.023 0.12 -10000 0 -0.3 75 75
T cell anergy -0.051 0.16 0.25 2 -0.4 75 77
TLE4 -0.033 0.17 -10000 0 -0.49 39 39
Jun/NFAT1-c-4/p21SNFT -0.05 0.27 -10000 0 -0.89 26 26
AP-1/NFAT1-c-4 -0.13 0.37 -10000 0 -1 42 42
IKZF1 -0.037 0.2 -10000 0 -0.58 38 38
T-helper 2 cell differentiation -0.076 0.26 -10000 0 -0.76 41 41
AP-1/NFAT1 -0.069 0.21 -10000 0 -0.43 90 90
CALM1 -0.003 0.076 -10000 0 -0.18 58 58
EGR2 -0.063 0.27 -10000 0 -0.99 26 26
EGR3 -0.066 0.28 -10000 0 -1 26 26
NFAT1/FOXP3 -0.009 0.18 -10000 0 -0.47 39 39
EGR1 0.012 0.07 -10000 0 -0.56 7 7
JUN 0.004 0.034 -10000 0 -10000 0 0
EGR4 0.027 0.039 0.26 11 -10000 0 11
mol:Ca2+ -0.023 0.067 -10000 0 -0.27 2 2
GBP3 -0.048 0.21 -10000 0 -0.68 33 33
FOSL1 0.024 0.014 0.24 2 -10000 0 2
NFAT1-c-4/MAF/IRF4 -0.036 0.25 -10000 0 -0.87 26 26
DGKA -0.031 0.16 -10000 0 -0.56 22 22
CREM 0.022 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.079 0.27 -10000 0 -0.85 32 32
CTLA4 -0.023 0.15 -10000 0 -0.51 19 19
NFAT1-c-4 (dimer)/EGR1 -0.046 0.26 -10000 0 -0.91 25 25
NFAT1-c-4 (dimer)/EGR4 -0.039 0.25 -10000 0 -0.87 25 25
FOS -0.06 0.18 -10000 0 -0.57 53 53
IFNG -0.12 0.32 -10000 0 -0.92 49 49
T cell activation -0.067 0.19 -10000 0 -0.63 24 24
MAF 0.022 0.006 -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 0.032 0.16 0.71 15 -10000 0 15
TNF -0.064 0.25 -10000 0 -0.85 29 29
FASLG -0.13 0.42 -10000 0 -1.4 37 37
TBX21 -0.034 0.18 -10000 0 -0.56 48 48
BATF3 0.023 0.004 -10000 0 -10000 0 0
PRKCQ -0.028 0.16 -10000 0 -0.56 40 40
PTPN1 -0.031 0.16 -10000 0 -0.55 23 23
NFAT1-c-4/ICER1 -0.043 0.24 -10000 0 -0.86 25 25
GATA3 0.008 0.096 0.24 3 -0.56 13 16
T-helper 1 cell differentiation -0.11 0.31 -10000 0 -0.88 50 50
IL2RA -0.097 0.28 -10000 0 -0.76 54 54
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.029 0.16 -10000 0 -0.54 24 24
E2F1 0.025 0.006 -10000 0 -10000 0 0
PPARG -0.041 0.18 -10000 0 -0.56 51 51
SLC3A2 -0.032 0.16 -10000 0 -0.52 27 27
IRF4 0.015 0.065 -10000 0 -0.56 6 6
PTGS2 -0.16 0.33 -10000 0 -0.86 62 62
CSF2 -0.16 0.33 -10000 0 -0.89 54 54
JunB/Fra1/NFAT1-c-4 -0.032 0.24 -10000 0 -0.83 25 25
IL4 -0.079 0.27 -10000 0 -0.84 36 36
IL5 -0.14 0.3 -10000 0 -0.87 42 42
IL2 -0.068 0.19 -10000 0 -0.64 24 24
IL3 -0.046 0.17 -10000 0 -0.77 20 20
RNF128 -0.084 0.24 -10000 0 -0.64 77 77
NFATC1 -0.031 0.16 -10000 0 -0.71 15 15
CDK4 0.04 0.14 0.6 9 -10000 0 9
PTPRK -0.031 0.16 -10000 0 -0.55 22 22
IL8 -0.14 0.3 -10000 0 -0.89 41 41
POU2F1 0.022 0.006 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.023 0.016 -10000 0 -10000 0 0
AES 0.023 0.012 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.012 -10000 0 -10000 0 0
SMAD4 0.022 0.005 -10000 0 -10000 0 0
DKK2 -0.074 0.22 -10000 0 -0.56 79 79
TLE1 0.023 0.012 -10000 0 -10000 0 0
MACF1 0.021 0.038 -10000 0 -0.56 2 2
CTNNB1 0.088 0.13 0.29 37 -0.4 6 43
WIF1 -0.34 0.28 0.23 1 -0.56 295 296
beta catenin/RanBP3 0.007 0.1 0.42 16 -0.43 2 18
KREMEN2 0.16 0.12 0.24 305 -0.29 7 312
DKK1 0.02 0.094 0.25 20 -0.53 10 30
beta catenin/beta TrCP1 0.096 0.12 0.28 36 -0.37 5 41
FZD1 0.022 0.006 -10000 0 -10000 0 0
AXIN2 -0.039 0.27 0.57 7 -1.4 17 24
AXIN1 0.023 0.005 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.024 0.12 -10000 0 -0.6 13 13
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.055 0.13 -10000 0 -0.53 13 13
Axin1/APC/GSK3 0.055 0.077 0.23 18 -0.32 4 22
Axin1/APC/GSK3/beta catenin/Macf1 0.049 0.1 0.3 8 -0.46 3 11
HNF1A 0.027 0.03 0.24 8 -10000 0 8
CTBP1 0.021 0.014 -10000 0 -10000 0 0
MYC 0.058 0.18 0.58 48 -10000 0 48
RANBP3 0.022 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.029 0.2 -10000 0 -0.39 74 74
NKD1 -0.023 0.16 0.24 4 -0.56 38 42
TCF4 0.021 0.03 -10000 0 -0.56 1 1
TCF3 0.022 0.013 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.052 0.024 -10000 0 -10000 0 0
Ran/GTP 0.017 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.006 0.11 0.39 15 -0.4 14 29
LEF1 0.023 0.017 0.24 1 -10000 0 1
DVL1 0.054 0.08 -10000 0 -0.52 4 4
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.052 0.16 -10000 0 -0.61 14 14
DKK1/LRP6/Kremen 2 0.11 0.11 0.32 14 -0.39 9 23
LRP6 0.022 0.006 -10000 0 -10000 0 0
CSNK1A1 0.022 0.015 -10000 0 -10000 0 0
NLK 0.021 0.009 -10000 0 -10000 0 0
CCND1 0.064 0.26 0.57 67 -1.4 6 73
WNT1 0.022 0.017 0.24 2 -10000 0 2
GSK3A 0.023 0.005 -10000 0 -10000 0 0
GSK3B 0.02 0.008 -10000 0 -10000 0 0
FRAT1 0.021 0.027 -10000 0 -0.56 1 1
PPP2R5D 0.067 0.088 0.32 38 -0.32 2 40
APC 0.02 0.064 0.35 5 -10000 0 5
WNT1/LRP6/FZD1 0.14 0.12 0.23 269 -10000 0 269
CREBBP 0.022 0.013 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.036 0.021 -10000 0 -10000 0 0
VLDLR 0.019 0.027 -10000 0 -0.56 1 1
CRKL 0.022 0.005 -10000 0 -10000 0 0
LRPAP1 0.021 0.006 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
ITGA3 0.017 0.059 -10000 0 -0.56 5 5
RELN/VLDLR/Fyn -0.023 0.15 -10000 0 -0.36 75 75
MAPK8IP1/MKK7/MAP3K11/JNK1 0.059 0.03 -10000 0 -0.31 1 1
AKT1 -0.023 0.08 0.21 1 -0.26 35 36
MAP2K7 0.022 0.005 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
DAB1 0.028 0.06 0.25 30 -10000 0 30
RELN/LRP8/DAB1 -0.011 0.14 0.3 1 -0.32 76 77
LRPAP1/LRP8 0.032 0.014 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.002 0.14 0.29 1 -0.31 76 77
DAB1/alpha3/beta1 Integrin -0.009 0.12 -10000 0 -0.3 66 66
long-term memory -0.012 0.16 0.31 2 -0.33 85 87
DAB1/LIS1 0.003 0.13 0.28 1 -0.3 72 73
DAB1/CRLK/C3G -0.005 0.12 -10000 0 -0.29 61 61
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
DAB1/NCK2 0.004 0.13 0.28 1 -0.3 71 72
ARHGEF2 0.022 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.004 0.13 0.24 23 -0.56 22 45
CDK5R1 0.027 0.029 0.24 9 -10000 0 9
RELN -0.07 0.21 0.24 3 -0.56 76 79
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.02 0.15 -10000 0 -0.36 76 76
GRIN2A/RELN/LRP8/DAB1/Fyn -0.002 0.17 0.31 2 -0.33 89 91
MAPK8 0.022 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.014 0.14 0.33 2 -0.32 75 77
ITGB1 0.022 0.004 -10000 0 -10000 0 0
MAP1B -0.049 0.12 0.28 2 -0.31 74 76
RELN/LRP8 -0.021 0.14 -10000 0 -0.35 76 76
GRIN2B/RELN/LRP8/DAB1/Fyn 0.008 0.14 0.31 2 -0.32 71 73
PI3K 0.017 0.017 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.029 0.042 -10000 0 -0.37 5 5
RAP1A -0.04 0.11 0.33 7 -0.31 1 8
PAFAH1B1 0.022 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.029 0.24 1 -0.56 1 2
CRLK/C3G 0.032 0.009 -10000 0 -10000 0 0
GRIN2B 0 0.029 0.24 4 -10000 0 4
NCK2 0.023 0.002 -10000 0 -10000 0 0
neuron differentiation -0.012 0.093 -10000 0 -0.37 10 10
neuron adhesion -0.042 0.11 0.32 9 -0.33 1 10
LRP8 0.024 0.017 0.24 3 -10000 0 3
GSK3B -0.021 0.072 0.2 1 -0.26 26 27
RELN/VLDLR/DAB1/Fyn -0.005 0.14 0.33 2 -0.31 74 76
MAP3K11 0.023 0.001 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.022 0.089 -10000 0 -0.28 37 37
CDK5 0.022 0.004 -10000 0 -10000 0 0
MAPT -0.002 0.09 0.75 4 -0.51 6 10
neuron migration -0.015 0.13 0.4 1 -0.34 30 31
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.012 0.094 -10000 0 -0.38 10 10
RELN/VLDLR -0.01 0.14 -10000 0 -0.32 74 74
IL23-mediated signaling events

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
CCL2 -0.1 0.42 -10000 0 -1.2 45 45
IL23A -0.081 0.39 -10000 0 -1.1 36 36
NF kappa B1 p50/RelA/I kappa B alpha -0.071 0.4 -10000 0 -1.1 44 44
positive regulation of T cell mediated cytotoxicity -0.1 0.45 -10000 0 -1.2 52 52
ITGA3 -0.093 0.4 -10000 0 -1.1 43 43
IL17F -0.001 0.28 -10000 0 -0.7 34 34
IL12B 0.02 0.04 -10000 0 -10000 0 0
STAT1 (dimer) -0.098 0.43 -10000 0 -1.1 50 50
CD4 -0.089 0.42 -10000 0 -1.2 40 40
IL23 -0.073 0.38 -10000 0 -1.1 35 35
IL23R -0.004 0.18 -10000 0 -0.91 13 13
IL1B -0.091 0.41 -10000 0 -1.2 36 36
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.084 0.38 -10000 0 -1.1 39 39
TYK2 0.016 0.034 -10000 0 -10000 0 0
STAT4 0.013 0.075 -10000 0 -0.56 8 8
STAT3 0.023 0.003 -10000 0 -10000 0 0
IL18RAP -0.004 0.12 -10000 0 -0.56 22 22
IL12RB1 -0.017 0.14 -10000 0 -0.58 28 28
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.002 0.12 -10000 0 -0.44 28 28
IL23R/JAK2 0.012 0.17 -10000 0 -0.88 10 10
positive regulation of chronic inflammatory response -0.1 0.45 -10000 0 -1.2 52 52
natural killer cell activation 0 0.006 -10000 0 -10000 0 0
JAK2 0.02 0.04 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
NFKB1 0.021 0.011 -10000 0 -10000 0 0
RELA 0.022 0.011 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.067 0.36 -10000 0 -1 36 36
ALOX12B -0.081 0.38 -10000 0 -1 41 41
CXCL1 -0.11 0.44 -10000 0 -1.2 51 51
T cell proliferation -0.1 0.45 -10000 0 -1.2 52 52
NFKBIA 0.021 0.011 -10000 0 -10000 0 0
IL17A 0.008 0.23 -10000 0 -0.56 25 25
PI3K -0.097 0.38 -10000 0 -1.1 42 42
IFNG -0.002 0.036 0.1 3 -0.12 22 25
STAT3 (dimer) -0.088 0.36 -10000 0 -1.1 37 37
IL18R1 0.017 0.059 -10000 0 -0.56 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 -0.061 0.31 -10000 0 -0.86 41 41
IL18/IL18R 0.023 0.11 -10000 0 -0.41 24 24
macrophage activation -0.004 0.018 0.033 1 -0.044 25 26
TNF -0.096 0.42 -10000 0 -1.2 40 40
STAT3/STAT4 -0.089 0.42 -10000 0 -1.1 51 51
STAT4 (dimer) -0.1 0.43 -10000 0 -1.1 52 52
IL18 0.019 0.046 -10000 0 -0.56 3 3
IL19 -0.085 0.38 -10000 0 -1.1 39 39
STAT5A (dimer) -0.098 0.43 -10000 0 -1.1 52 52
STAT1 0.022 0.004 -10000 0 -10000 0 0
SOCS3 0.02 0.038 -10000 0 -0.56 2 2
CXCL9 -0.1 0.42 -10000 0 -1.1 46 46
MPO -0.11 0.44 -10000 0 -1.1 54 54
positive regulation of humoral immune response -0.1 0.45 -10000 0 -1.2 52 52
IL23/IL23R/JAK2/TYK2 -0.12 0.51 -10000 0 -1.3 52 52
IL6 -0.2 0.56 -10000 0 -1.3 93 93
STAT5A 0.023 0.003 -10000 0 -10000 0 0
IL2 0.008 0.022 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.006 -10000 0 -10000 0 0
CD3E -0.095 0.4 -10000 0 -1.1 39 39
keratinocyte proliferation -0.1 0.45 -10000 0 -1.2 52 52
NOS2 -0.12 0.46 -10000 0 -1.2 57 57
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.031 0.032 0.26 1 -0.41 2 3
CRKL -0.052 0.18 0.25 4 -0.61 33 37
mol:PIP3 0.011 0.014 -10000 0 -10000 0 0
AKT1 0.012 0.042 -10000 0 -10000 0 0
PTK2B 0.021 0.007 -10000 0 -10000 0 0
RAPGEF1 -0.05 0.17 0.25 3 -0.58 33 36
RANBP10 0.022 0.005 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.034 0.16 0.25 1 -0.36 89 90
MAP3K5 -0.045 0.17 0.28 1 -0.55 35 36
HGF/MET/CIN85/CBL/ENDOPHILINS -0.023 0.16 0.25 1 -0.33 92 93
AP1 -0.025 0.12 -10000 0 -0.36 53 53
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
apoptosis -0.1 0.3 -10000 0 -0.78 76 76
STAT3 (dimer) -0.041 0.12 -10000 0 -0.28 83 83
GAB1/CRKL/SHP2/PI3K -0.022 0.14 -10000 0 -0.53 24 24
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
CBL/CRK -0.046 0.17 -10000 0 -0.58 33 33
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.022 0.004 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
ELK1 -0.003 0.076 0.28 24 -0.21 2 26
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.028 0.091 0.15 1 -0.3 26 27
PAK1 0.013 0.048 0.39 1 -10000 0 1
HGF/MET/RANBP10 -0.035 0.16 0.25 1 -0.35 92 93
HRAS -0.058 0.17 -10000 0 -0.58 20 20
DOCK1 -0.05 0.17 0.24 3 -0.57 33 36
GAB1 -0.059 0.19 -10000 0 -0.64 33 33
CRK -0.059 0.18 -10000 0 -0.62 32 32
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.088 0.22 -10000 0 -0.5 97 97
JUN 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.036 0.092 0.18 1 -0.22 93 94
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
cell morphogenesis 0.018 0.16 0.29 27 -0.41 23 50
GRB2/SHC -0.008 0.092 -10000 0 -0.29 9 9
FOS -0.042 0.18 -10000 0 -0.56 53 53
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.003 0.075 0.28 24 -0.21 2 26
HGF/MET/MUC20 -0.046 0.15 0.24 1 -0.35 96 97
cell migration -0.008 0.09 -10000 0 -0.28 9 9
GRB2 0.023 0.004 -10000 0 -10000 0 0
CBL 0.023 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.03 0.032 0.26 1 -0.41 2 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.036 0.12 -10000 0 -0.28 83 83
MET/MUC20 0.015 0.03 0.25 1 -0.41 2 3
RAP1B -0.042 0.16 0.29 4 -0.54 33 37
RAP1A -0.049 0.16 0.25 2 -0.54 33 35
HGF/MET/RANBP9 -0.034 0.16 0.25 1 -0.36 91 92
RAF1 -0.053 0.16 -10000 0 -0.58 16 16
STAT3 -0.042 0.12 -10000 0 -0.28 83 83
cell proliferation -0.055 0.16 0.25 4 -0.38 78 82
RPS6KB1 -0.005 0.041 -10000 0 -0.3 2 2
MAPK3 -0.004 0.1 0.74 7 -10000 0 7
MAPK1 -0.001 0.11 0.58 12 -10000 0 12
RANBP9 0.022 0.004 -10000 0 -10000 0 0
MAPK8 -0.025 0.16 0.28 2 -0.51 32 34
SRC -0.043 0.11 -10000 0 -0.27 80 80
PI3K 0 0.064 -10000 0 -0.2 30 30
MET/Glomulin 0.014 0.035 0.27 1 -0.36 2 3
SOS1 0.023 0.003 -10000 0 -10000 0 0
MAP2K1 -0.051 0.15 -10000 0 -0.55 15 15
MET 0.021 0.041 0.38 1 -0.56 2 3
MAP4K1 -0.048 0.18 0.28 2 -0.59 36 38
PTK2 0.021 0.006 -10000 0 -10000 0 0
MAP2K2 -0.051 0.15 -10000 0 -0.55 15 15
BAD 0.01 0.041 -10000 0 -10000 0 0
MAP2K4 -0.042 0.15 0.27 1 -0.5 33 34
SHP2/GRB2/SOS1/GAB1 -0.033 0.16 -10000 0 -0.54 32 32
INPPL1 0.022 0.005 -10000 0 -10000 0 0
PXN 0.023 0.002 -10000 0 -10000 0 0
SH3KBP1 0.02 0.038 -10000 0 -0.56 2 2
HGS -0.036 0.085 0.16 1 -0.2 91 92
PLCgamma1/PKC 0.017 0.003 -10000 0 -10000 0 0
HGF -0.092 0.23 -10000 0 -0.56 94 94
RASA1 0.021 0.006 -10000 0 -10000 0 0
NCK1 0.019 0.009 -10000 0 -10000 0 0
PTPRJ 0.021 0.027 -10000 0 -0.56 1 1
NCK/PLCgamma1 -0.01 0.092 -10000 0 -0.22 71 71
PDPK1 0.009 0.021 0.26 1 -10000 0 1
HGF/MET/SHIP -0.035 0.16 0.25 1 -0.36 93 94
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.032 0.061 -10000 0 -0.38 10 10
HDAC1 0.021 0.005 -10000 0 -10000 0 0
AES 0.022 0.004 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.014 0.24 2 -10000 0 2
LRP6/FZD1 0.03 0.011 -10000 0 -10000 0 0
TLE1 0.022 0.004 -10000 0 -10000 0 0
AP1 -0.052 0.15 -10000 0 -0.34 83 83
NCSTN 0.022 0.005 -10000 0 -10000 0 0
ADAM10 0.023 0.003 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.01 0.17 -10000 0 -0.77 22 22
NICD/RBPSUH 0.028 0.06 -10000 0 -0.37 10 10
WIF1 -0.34 0.28 0.24 1 -0.56 295 296
NOTCH1 0.012 0.057 -10000 0 -0.39 9 9
PSENEN 0.021 0.007 -10000 0 -10000 0 0
KREMEN2 0.16 0.12 0.24 305 -0.29 7 312
DKK1 0.02 0.094 0.25 20 -0.53 10 30
beta catenin/beta TrCP1 -0.003 0.11 0.27 1 -0.38 16 17
APH1B 0.023 0.002 -10000 0 -10000 0 0
APH1A 0.022 0.006 -10000 0 -10000 0 0
AXIN1 -0.001 0.08 0.27 1 -0.5 8 9
CtBP/CBP/TCF1/TLE1/AES 0.011 0.034 -10000 0 -10000 0 0
PSEN1 0.022 0.005 -10000 0 -10000 0 0
FOS -0.042 0.18 -10000 0 -0.56 53 53
JUN 0.022 0.004 -10000 0 -10000 0 0
MAP3K7 0.022 0.003 -10000 0 -10000 0 0
CTNNB1 -0.01 0.11 0.24 5 -0.39 19 24
MAPK3 0.023 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.029 0.2 -10000 0 -0.39 74 74
HNF1A 0.026 0.028 0.24 8 -10000 0 8
CTBP1 0.021 0.007 -10000 0 -10000 0 0
MYC 0.02 0.02 -10000 0 -10000 0 0
NKD1 -0.023 0.16 0.24 4 -0.56 38 42
FZD1 0.022 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.031 0.062 -10000 0 -0.38 10 10
apoptosis -0.052 0.15 -10000 0 -0.34 84 84
Delta 1/NOTCHprecursor 0.03 0.061 -10000 0 -0.38 10 10
DLL1 0.022 0.004 -10000 0 -10000 0 0
PPARD 0.006 0.14 -10000 0 -0.95 9 9
Gamma Secretase 0.056 0.028 -10000 0 -10000 0 0
APC -0.017 0.11 0.27 1 -0.42 24 25
DVL1 -0.044 0.092 -10000 0 -0.35 28 28
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.11 0.11 0.32 14 -0.39 9 23
LRP6 0.022 0.006 -10000 0 -10000 0 0
CSNK1A1 0.022 0.006 -10000 0 -10000 0 0
NLK 0.009 0.004 -10000 0 -10000 0 0
CCND1 0.003 0.15 -10000 0 -1.4 6 6
WNT1 0.018 0.02 0.24 2 -10000 0 2
Axin1/APC/beta catenin -0.015 0.13 0.28 3 -0.45 27 30
DKK2 -0.074 0.22 -10000 0 -0.56 79 79
NOTCH1 precursor/DVL1 -0.027 0.11 -10000 0 -0.5 17 17
GSK3B 0.02 0.008 -10000 0 -10000 0 0
FRAT1 0.021 0.027 -10000 0 -0.56 1 1
NOTCH/Deltex homolog 1 0.033 0.062 -10000 0 -0.38 10 10
PPP2R5D 0.013 0.097 0.28 37 -0.42 7 44
MAPK1 0.022 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.18 0.18 -10000 0 -0.33 269 269
RBPJ 0.021 0.007 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.026 0.058 -10000 0 -0.41 8 8
AKT1 -0.005 0.18 0.37 9 -0.55 30 39
PTK2B -0.06 0.19 0.37 6 -0.68 25 31
VEGFR2 homodimer/Frs2 -0.059 0.2 -10000 0 -0.46 79 79
CAV1 -0.13 0.26 -10000 0 -0.56 125 125
CALM1 0.022 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.043 0.19 -10000 0 -0.43 76 76
endothelial cell proliferation -0.011 0.18 0.35 15 -0.54 29 44
mol:Ca2+ -0.042 0.18 0.36 4 -0.66 22 26
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.03 0.19 -10000 0 -0.7 22 22
RP11-342D11.1 -0.059 0.17 -10000 0 -0.67 22 22
CDH5 -0.085 0.22 -10000 0 -0.56 88 88
VEGFA homodimer 0.051 0.022 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
SHC2 0.02 0.038 -10000 0 -0.56 2 2
HRAS/GDP -0.027 0.15 -10000 0 -0.57 22 22
SH2D2A 0.021 0.027 -10000 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.024 0.17 -10000 0 -0.56 29 29
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.041 0.19 -10000 0 -0.44 69 69
VEGFR1 homodimer 0.022 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.015 0.17 -10000 0 -0.62 22 22
GRB10 -0.042 0.18 0.35 3 -0.67 22 25
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.004 -10000 0 -10000 0 0
PAK1 0.023 0.017 0.38 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.077 0.25 -10000 0 -0.68 50 50
HRAS 0.022 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.037 0.13 -10000 0 -0.42 33 33
HIF1A 0.022 0.004 -10000 0 -10000 0 0
FRS2 0.022 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.03 0.18 -10000 0 -0.68 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.004 0.12 -10000 0 -0.56 21 21
Nck/Pak 0.028 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.043 0.19 -10000 0 -0.44 78 78
mol:GDP -0.022 0.16 -10000 0 -0.6 22 22
mol:NADP -0.015 0.17 0.35 8 -0.49 31 39
eNOS/Hsp90 -0.007 0.16 0.35 7 -0.46 31 38
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 -0.043 0.18 0.36 4 -0.67 22 26
HIF1A/ARNT 0.031 0.01 -10000 0 -10000 0 0
SHB 0.021 0.007 -10000 0 -10000 0 0
VEGFA 0.024 0.004 -10000 0 -10000 0 0
VEGFC 0.019 0.038 -10000 0 -0.56 2 2
FAK1/Vinculin -0.042 0.21 0.31 4 -0.65 34 38
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.036 0.2 -10000 0 -0.7 26 26
PTPN6 0.022 0.006 -10000 0 -10000 0 0
EPAS1 -0.078 0.23 -10000 0 -0.56 86 86
mol:L-citrulline -0.015 0.17 0.35 8 -0.49 31 39
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.03 0.18 -10000 0 -0.43 67 67
VEGFR2 homodimer/VEGFA homodimer -0.041 0.19 -10000 0 -0.45 70 70
VEGFR2/3 heterodimer -0.073 0.22 -10000 0 -0.48 90 90
VEGFB 0.023 0.002 -10000 0 -10000 0 0
MAPK11 -0.043 0.18 0.42 6 -0.61 28 34
VEGFR2 homodimer -0.076 0.22 -10000 0 -0.53 78 78
FLT1 0.022 0.006 -10000 0 -10000 0 0
NEDD4 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.05 0.18 0.34 10 -0.61 25 35
MAPK1 -0.048 0.18 0.34 11 -0.62 25 36
VEGFA145/NRP2 0.03 0.036 -10000 0 -0.4 3 3
VEGFR1/2 heterodimer -0.06 0.2 -10000 0 -0.46 80 80
KDR -0.076 0.22 -10000 0 -0.53 78 78
VEGFA165/NRP1/VEGFR2 homodimer -0.037 0.18 -10000 0 -0.71 22 22
SRC 0.022 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.047 0.18 0.37 9 -0.64 24 33
PI3K -0.037 0.16 -10000 0 -0.63 22 22
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.038 0.18 -10000 0 -0.44 66 66
FES -0.046 0.19 0.36 2 -0.71 22 24
GAB1 -0.048 0.18 -10000 0 -0.62 29 29
VEGFR2 homodimer/VEGFA homodimer/Src -0.042 0.19 -10000 0 -0.43 77 77
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
SOS1 0.023 0.003 -10000 0 -10000 0 0
ARNT 0.022 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.069 0.2 0.32 5 -0.48 57 62
VEGFR2 homodimer/VEGFA homodimer/Yes -0.042 0.19 -10000 0 -0.44 74 74
PI3K/GAB1 -0.007 0.17 -10000 0 -0.55 25 25
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.019 0.17 -10000 0 -0.63 21 21
PRKACA 0.022 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.06 0.21 -10000 0 -0.47 80 80
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
CDC42 -0.043 0.18 0.36 4 -0.69 22 26
actin cytoskeleton reorganization -0.041 0.18 -10000 0 -0.44 69 69
PTK2 -0.058 0.22 0.32 5 -0.66 40 45
EDG1 -0.059 0.17 -10000 0 -0.67 22 22
mol:DAG -0.043 0.18 0.36 4 -0.67 22 26
CaM/Ca2+ -0.033 0.17 -10000 0 -0.62 22 22
MAP2K3 -0.047 0.14 -10000 0 -0.57 22 22
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.036 0.18 -10000 0 -0.7 22 22
PLCG1 -0.043 0.18 0.36 4 -0.68 22 26
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.031 0.18 -10000 0 -0.43 65 65
IQGAP1 0.023 0.003 -10000 0 -10000 0 0
YES1 0.022 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.043 0.19 -10000 0 -0.43 77 77
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.041 0.18 -10000 0 -0.43 73 73
cell migration -0.056 0.2 0.36 3 -0.6 40 43
mol:PI-3-4-5-P3 -0.034 0.15 -10000 0 -0.57 22 22
FYN 0.022 0.027 -10000 0 -0.56 1 1
VEGFB/NRP1 -0.039 0.17 -10000 0 -0.64 22 22
mol:NO -0.015 0.17 0.35 8 -0.49 31 39
PXN 0.023 0.002 -10000 0 -10000 0 0
HRAS/GTP -0.038 0.15 -10000 0 -0.57 22 22
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.044 0.18 -10000 0 -0.7 22 22
VHL 0.021 0.006 -10000 0 -10000 0 0
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
NOS3 -0.021 0.19 0.37 7 -0.56 31 38
VEGFR2 homodimer/VEGFA homodimer/Sck -0.044 0.19 -10000 0 -0.46 67 67
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA -0.055 0.17 0.35 4 -0.63 23 27
PRKCB -0.067 0.18 0.35 4 -0.65 26 30
VCL 0.022 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.039 0.18 -10000 0 -0.68 22 22
VEGFR1/2 heterodimer/VEGFA homodimer -0.044 0.19 -10000 0 -0.44 74 74
VEGFA165/NRP2 0.03 0.036 -10000 0 -0.4 3 3
MAPKKK cascade -0.037 0.15 -10000 0 -0.56 22 22
NRP2 0.019 0.046 -10000 0 -0.56 3 3
VEGFC homodimer 0.019 0.038 -10000 0 -0.56 2 2
NCK1 0.019 0.009 -10000 0 -10000 0 0
ROCK1 0.023 0.003 -10000 0 -10000 0 0
FAK1/Paxillin -0.041 0.21 0.35 6 -0.64 36 42
MAP3K13 -0.038 0.15 -10000 0 -0.6 22 22
PDPK1 -0.034 0.13 0.26 2 -0.51 22 24
IL6-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
BCL2L1 -0.15 0.23 -10000 0 -0.68 16 16
CRP -0.15 0.23 -10000 0 -0.62 27 27
cell cycle arrest -0.18 0.26 -10000 0 -0.65 46 46
TIMP1 -0.12 0.21 -10000 0 -0.61 16 16
IL6ST -0.009 0.098 -10000 0 -0.56 14 14
Rac1/GDP -0.069 0.16 -10000 0 -0.42 51 51
AP1 0.039 0.15 -10000 0 -0.48 8 8
GAB2 0.015 0.092 -10000 0 -0.55 12 12
TNFSF11 -0.16 0.23 -10000 0 -0.7 14 14
HSP90B1 -0.002 0.09 -10000 0 -0.76 5 5
GAB1 0.026 0.01 -10000 0 -10000 0 0
MAPK14 -0.046 0.14 -10000 0 -0.56 18 18
AKT1 0.041 0.071 0.3 5 -0.36 3 8
FOXO1 0.039 0.068 0.33 2 -0.35 2 4
MAP2K6 -0.058 0.14 -10000 0 -0.4 47 47
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
MAP2K4 -0.092 0.17 -10000 0 -0.46 49 49
MITF -0.066 0.15 -10000 0 -0.42 51 51
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.022 0.004 -10000 0 -10000 0 0
A2M -0.43 0.65 -10000 0 -1.4 157 157
CEBPB 0.026 0.005 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.028 0.12 0.26 5 -0.44 13 18
STAT3 -0.19 0.27 -10000 0 -0.69 46 46
STAT1 -0.004 0.096 -10000 0 -0.83 6 6
CEBPD -0.16 0.24 -10000 0 -0.68 21 21
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
PI3K 0.017 0.018 -10000 0 -10000 0 0
JUN 0.022 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.061 0.15 -10000 0 -0.4 51 51
MAPK11 -0.046 0.14 -10000 0 -0.56 18 18
STAT3 (dimer)/FOXO1 -0.2 0.3 0.4 1 -0.64 97 98
GRB2/SOS1/GAB family 0.005 0.16 -10000 0 -0.46 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.05 0.15 -10000 0 -0.38 62 62
GRB2 0.027 0.008 -10000 0 -10000 0 0
JAK2 0.02 0.007 -10000 0 -10000 0 0
LBP -0.094 0.19 -10000 0 -0.64 7 7
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
JAK1 0.014 0.02 -10000 0 -10000 0 0
MYC -0.14 0.23 -10000 0 -0.68 14 14
FGG -0.46 0.53 -10000 0 -1 224 224
macrophage differentiation -0.18 0.26 -10000 0 -0.65 46 46
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.034 0.16 -10000 0 -0.36 76 76
JUNB -0.15 0.23 -10000 0 -0.7 14 14
FOS -0.042 0.18 -10000 0 -0.56 53 53
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.067 0.16 -10000 0 -0.42 55 55
STAT1/PIAS1 -0.07 0.16 -10000 0 -0.41 54 54
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.069 -10000 0 -0.37 4 4
STAT3 (dimer) -0.18 0.27 -10000 0 -0.68 46 46
PRKCD -0.11 0.2 0.31 2 -0.52 43 45
IL6R 0.001 0.088 -10000 0 -0.56 11 11
SOCS3 -0.034 0.15 -10000 0 -0.8 8 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.077 -10000 0 -0.35 14 14
Rac1/GTP -0.078 0.17 -10000 0 -0.44 51 51
HCK 0.02 0.046 -10000 0 -0.56 3 3
MAPKKK cascade 0.048 0.13 -10000 0 -0.53 9 9
bone resorption -0.15 0.22 -10000 0 -0.66 14 14
IRF1 -0.16 0.23 -10000 0 -0.68 16 16
mol:GDP -0.07 0.15 -10000 0 -0.42 51 51
SOS1 0.03 0.011 -10000 0 -10000 0 0
VAV1 -0.072 0.16 -10000 0 -0.43 51 51
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.035 0.17 -10000 0 -0.6 24 24
PTPN11 0.008 0.058 -10000 0 -0.82 2 2
IL6/IL6RA -0.056 0.17 -10000 0 -0.44 74 74
gp130 (dimer)/TYK2/TYK2/LMO4 0.017 0.073 -10000 0 -0.35 14 14
gp130 (dimer)/JAK2/JAK2/LMO4 0.016 0.072 -10000 0 -0.35 14 14
IL6 -0.082 0.21 -10000 0 -0.56 76 76
PIAS3 0.022 0.004 -10000 0 -10000 0 0
PTPRE 0.02 0.042 -10000 0 -0.55 2 2
PIAS1 0.023 0.002 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.058 0.15 -10000 0 -0.35 75 75
LMO4 0.009 0.026 0.22 1 -10000 0 1
STAT3 (dimer)/PIAS3 -0.17 0.26 -10000 0 -0.67 44 44
MCL1 0.05 0.08 0.45 2 -10000 0 2
Glypican 2 network

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
MDK 0.028 0.038 0.28 10 -9999 0 10
GPC2 0.058 0.088 0.26 72 -9999 0 72
GPC2/Midkine 0.058 0.063 0.28 12 -9999 0 12
neuron projection morphogenesis 0.057 0.063 0.28 12 -9999 0 12
Coregulation of Androgen receptor activity

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
NRIP1 0.022 0.006 -10000 0 -10000 0 0
SVIL 0.022 0.004 -10000 0 -10000 0 0
ZNF318 0.022 0.005 -10000 0 -10000 0 0
JMJD2C 0.006 0.012 0.06 1 -10000 0 1
T-DHT/AR/Ubc9 -0.079 0.16 -10000 0 -0.38 99 99
CARM1 0.022 0.004 -10000 0 -10000 0 0
PRDX1 0.023 0.004 -10000 0 -10000 0 0
PELP1 0.022 0.006 -10000 0 -10000 0 0
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.022 0.006 -10000 0 -10000 0 0
PTK2B 0.021 0.007 -10000 0 -10000 0 0
MED1 0.023 0.003 -10000 0 -10000 0 0
MAK -0.017 0.14 -10000 0 -0.56 32 32
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.023 0.004 -10000 0 -10000 0 0
GSN 0.023 0.003 -10000 0 -10000 0 0
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
NCOA6 0.022 0.005 -10000 0 -10000 0 0
DNA-PK 0.043 0.013 -10000 0 -10000 0 0
NCOA4 0.022 0.005 -10000 0 -10000 0 0
PIAS3 0.022 0.004 -10000 0 -10000 0 0
cell proliferation -0.075 0.22 -10000 0 -0.76 41 41
XRCC5 0.022 0.004 -10000 0 -10000 0 0
UBE3A 0.023 0.004 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.09 0.18 -10000 0 -0.39 108 108
FHL2 -0.029 0.073 -10000 0 -0.35 3 3
RANBP9 0.023 0.004 -10000 0 -10000 0 0
JMJD1A -0.037 0.064 -10000 0 -0.13 154 154
CDK6 0.023 0.024 0.38 2 -10000 0 2
TGFB1I1 0.023 0.003 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.074 0.16 0.26 1 -0.38 93 94
XRCC6 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR -0.097 0.18 -10000 0 -0.4 99 99
CTDSP1 0.022 0.004 -10000 0 -10000 0 0
CTDSP2 0.022 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.003 -10000 0 -10000 0 0
TCF4 0.021 0.027 -10000 0 -0.56 1 1
CDKN2A 0.095 0.14 0.24 200 -0.3 19 219
SRF 0.026 0.005 -10000 0 -10000 0 0
NKX3-1 -0.11 0.17 -10000 0 -0.59 29 29
KLK3 0.013 0.044 -10000 0 -10000 0 0
TMF1 0.021 0.007 -10000 0 -10000 0 0
HNRNPA1 0.023 0.002 -10000 0 -10000 0 0
AOF2 0 0.001 -10000 0 -10000 0 0
APPL1 -0.009 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.078 0.16 -10000 0 -0.38 98 98
AR -0.12 0.24 -10000 0 -0.58 98 98
UBA3 0.021 0.007 -10000 0 -10000 0 0
PATZ1 0.022 0.005 -10000 0 -10000 0 0
PAWR 0.023 0.003 -10000 0 -10000 0 0
PRKDC 0.022 0.005 -10000 0 -10000 0 0
PA2G4 0.023 0.002 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.071 0.15 -10000 0 -0.35 99 99
RPS6KA3 0.022 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.08 0.16 -10000 0 -0.38 99 99
LATS2 0.02 0.027 -10000 0 -0.56 1 1
T-DHT/AR/PRX1 -0.071 0.15 -10000 0 -0.35 99 99
Cyclin D3/CDK11 p58 0.017 0.003 -10000 0 -10000 0 0
VAV3 0.021 0.027 -10000 0 -0.56 1 1
KLK2 -0.036 0.091 -10000 0 -0.49 6 6
CASP8 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.062 0.16 -10000 0 -0.35 97 97
TMPRSS2 -0.33 0.47 -10000 0 -0.99 156 156
CCND1 0.013 0.067 0.38 1 -0.56 6 7
PIAS1 0.023 0.002 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.03 -10000 0 -0.066 116 116
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.023 0.005 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.074 0.16 0.24 2 -0.37 93 95
CMTM2 -0.049 0.19 -10000 0 -0.56 57 57
SNURF 0.005 0.098 -10000 0 -0.56 14 14
ZMIZ1 -0.004 0.051 -10000 0 -0.62 1 1
CCND3 0.022 0.004 -10000 0 -10000 0 0
TGIF1 0.022 0.005 -10000 0 -10000 0 0
FKBP4 0.022 0.017 0.38 1 -10000 0 1
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.21 0.27 -10000 0 -0.76 31 31
PCK1 -0.1 0.17 -10000 0 -0.67 10 10
HNF4A -0.25 0.34 -10000 0 -0.9 57 57
KCNJ11 -0.22 0.31 -10000 0 -0.94 22 22
AKT1 -0.015 0.097 -10000 0 -0.45 1 1
response to starvation -0.008 0.03 -10000 0 -0.19 3 3
DLK1 -0.2 0.29 -10000 0 -0.74 31 31
NKX2-1 -0.7 0.7 -10000 0 -1.4 249 249
ACADM -0.21 0.27 -10000 0 -0.75 32 32
TAT -0.11 0.2 0.4 1 -0.71 19 20
CEBPB 0.023 0.005 -10000 0 -10000 0 0
CEBPA 0.021 0.027 -10000 0 -0.56 1 1
TTR -0.025 0.18 0.71 1 -0.72 14 15
PKLR -0.2 0.27 -10000 0 -0.76 30 30
APOA1 -0.36 0.5 -10000 0 -1.3 68 68
CPT1C -0.21 0.27 -10000 0 -0.76 30 30
ALAS1 -0.11 0.17 -10000 0 -0.54 7 7
TFRC -0.091 0.2 -10000 0 -0.75 10 10
FOXF1 0.047 0.18 0.24 46 -0.44 45 91
NF1 0.026 0.003 -10000 0 -10000 0 0
HNF1A (dimer) 0.036 0.031 0.25 8 -10000 0 8
CPT1A -0.2 0.28 -10000 0 -0.76 28 28
HMGCS1 -0.17 0.28 -10000 0 -0.76 23 23
NR3C1 0.027 0.008 -10000 0 -10000 0 0
CPT1B -0.21 0.27 -10000 0 -0.75 32 32
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.012 -10000 0 -10000 0 0
GCK -0.21 0.27 -10000 0 -0.76 31 31
CREB1 0.026 0.008 -10000 0 -10000 0 0
IGFBP1 -0.1 0.16 -10000 0 -0.86 2 2
PDX1 -0.1 0.18 -10000 0 -0.77 2 2
UCP2 -0.21 0.27 -10000 0 -0.77 28 28
ALDOB -0.21 0.28 -10000 0 -0.78 19 19
AFP 0.046 0.077 0.32 2 -10000 0 2
BDH1 -0.12 0.27 0.53 1 -0.75 26 27
HADH -0.21 0.28 -10000 0 -0.73 30 30
F2 -0.28 0.36 -10000 0 -0.95 42 42
HNF1A 0.036 0.031 0.26 8 -10000 0 8
G6PC 0.023 0.06 -10000 0 -10000 0 0
SLC2A2 -0.092 0.18 -10000 0 -0.84 2 2
INS -0.023 0.006 -10000 0 -10000 0 0
FOXA1 0.11 0.12 0.27 84 -0.37 10 94
FOXA3 0.03 0.1 0.36 4 -0.55 13 17
FOXA2 -0.24 0.33 -10000 0 -0.82 33 33
ABCC8 -0.22 0.3 -10000 0 -0.81 37 37
ALB 0.046 0.075 0.36 1 -10000 0 1
LPA4-mediated signaling events

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
ADCY4 -0.029 0.086 -10000 0 -0.36 29 29
ADCY5 -0.036 0.098 -10000 0 -0.36 39 39
ADCY6 -0.009 0.022 -10000 0 -0.35 2 2
ADCY7 -0.008 0.016 -10000 0 -0.35 1 1
ADCY1 -0.01 0.027 -10000 0 -0.35 3 3
ADCY2 -0.009 0.084 0.27 17 -0.35 16 33
ADCY3 -0.008 0.016 -10000 0 -0.35 1 1
ADCY8 -0.099 0.15 -10000 0 -0.35 125 125
PRKCE -0.006 0.019 -10000 0 -0.41 1 1
ADCY9 -0.009 0.022 -10000 0 -0.35 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.017 0.12 0.24 33 -0.28 19 52
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.022 0.005 -10000 0 -10000 0 0
CCL5 0.012 0.079 -10000 0 -0.56 9 9
SDCBP 0.022 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.023 0.065 0.26 7 -0.33 5 12
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.031 0.071 0.26 6 -0.32 6 12
Syndecan-1/Syntenin 0.032 0.069 0.26 6 -0.32 5 11
MAPK3 0.025 0.063 0.24 6 -0.34 3 9
HGF/MET -0.055 0.18 0.26 1 -0.41 96 97
TGFB1/TGF beta receptor Type II 0.022 0.005 -10000 0 -10000 0 0
BSG 0.022 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.03 0.07 0.26 6 -0.32 6 12
Syndecan-1/RANTES 0.026 0.089 0.26 6 -0.38 11 17
Syndecan-1/CD147 0.043 0.07 0.26 6 -0.33 4 10
Syndecan-1/Syntenin/PIP2 0.03 0.066 0.24 6 -0.31 5 11
LAMA5 0.021 0.027 -10000 0 -0.56 1 1
positive regulation of cell-cell adhesion 0.029 0.064 0.24 6 -0.3 5 11
MMP7 0.02 0.091 0.24 20 -0.56 9 29
HGF -0.092 0.23 -10000 0 -0.56 94 94
Syndecan-1/CASK 0.015 0.063 0.2 6 -0.3 7 13
Syndecan-1/HGF/MET -0.018 0.15 0.29 3 -0.31 78 81
regulation of cell adhesion 0.015 0.059 0.23 5 -0.34 3 8
HPSE 0.022 0.005 -10000 0 -10000 0 0
positive regulation of cell migration 0.023 0.065 0.26 7 -0.33 5 12
SDC1 0.025 0.06 0.24 6 -0.27 8 14
Syndecan-1/Collagen 0.023 0.065 0.26 7 -0.33 5 12
PPIB 0.023 0.002 -10000 0 -10000 0 0
MET 0.021 0.041 0.38 1 -0.56 2 3
PRKACA 0.022 0.005 -10000 0 -10000 0 0
MMP9 0.033 0.047 0.24 24 -10000 0 24
MAPK1 0.021 0.061 0.22 4 -0.34 3 7
homophilic cell adhesion 0.023 0.067 0.24 9 -0.32 5 14
MMP1 0.15 0.11 0.24 291 -0.29 4 295
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.016 0.17 0.32 11 -0.57 26 37
FYN -0.011 0.22 0.29 14 -0.72 32 46
LAT/GRAP2/SLP76 -0.005 0.18 0.27 4 -0.6 32 36
IKBKB 0.022 0.018 0.38 1 -10000 0 1
AKT1 -0.004 0.15 0.24 13 -0.44 35 48
B2M 0.022 0.011 -10000 0 -10000 0 0
IKBKG 0.003 0.044 0.097 9 -0.14 19 28
MAP3K8 0.021 0.027 -10000 0 -0.56 1 1
mol:Ca2+ -0.013 0.016 0.087 2 -0.088 8 10
integrin-mediated signaling pathway 0.029 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.017 0.21 0.29 10 -0.66 36 46
TRPV6 0.005 0.16 1.1 8 -0.55 8 16
CD28 0.018 0.054 -10000 0 -0.57 4 4
SHC1 -0.01 0.21 0.3 17 -0.72 28 45
receptor internalization -0.024 0.22 0.23 3 -0.71 36 39
PRF1 -0.061 0.33 -10000 0 -1.1 42 42
KRAS 0.021 0.006 -10000 0 -10000 0 0
GRB2 0.023 0.004 -10000 0 -10000 0 0
COT/AKT1 0.01 0.12 0.24 10 -0.36 32 42
LAT -0.014 0.2 0.26 7 -0.72 28 35
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D 0.011 0.081 -10000 0 -0.57 9 9
CD3E 0.012 0.077 -10000 0 -0.57 8 8
CD3G -0.012 0.14 -10000 0 -0.57 28 28
RASGRP2 -0.017 0.061 -10000 0 -0.17 64 64
RASGRP1 -0.005 0.14 0.25 10 -0.44 33 43
HLA-A 0.02 0.029 -10000 0 -0.57 1 1
RASSF5 0.023 0.004 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.029 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.057 0.16 18 -0.13 22 40
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.06 -10000 0 -0.24 23 23
PRKCA 0 0.087 0.16 14 -0.29 25 39
GRAP2 -0.006 0.12 -10000 0 -0.56 23 23
mol:IP3 -0.016 0.12 0.24 5 -0.44 29 34
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.025 0.19 -10000 0 -0.73 26 26
ORAI1 -0.014 0.13 0.36 2 -0.89 9 11
CSK -0.014 0.2 0.27 7 -0.75 27 34
B7 family/CD28 -0.012 0.23 -10000 0 -0.82 29 29
CHUK 0.022 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.035 0.23 0.25 1 -0.77 34 35
PTPN6 -0.013 0.21 0.25 5 -0.75 27 32
VAV1 -0.017 0.2 0.26 6 -0.74 28 34
Monovalent TCR/CD3 -0.022 0.16 -10000 0 -0.52 35 35
CBL 0.023 0.004 -10000 0 -10000 0 0
LCK -0.012 0.22 0.29 13 -0.74 31 44
PAG1 -0.013 0.21 0.28 9 -0.75 27 36
RAP1A 0.022 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.034 0.24 0.27 3 -0.77 34 37
CD80 0.002 0.1 -10000 0 -0.56 15 15
CD86 0.013 0.066 -10000 0 -0.57 6 6
PDK1/CARD11/BCL10/MALT1 -0.008 0.076 -10000 0 -0.28 25 25
HRAS 0.022 0.004 -10000 0 -10000 0 0
GO:0035030 -0.028 0.17 0.24 1 -0.6 33 34
CD8A 0.013 0.072 -10000 0 -0.57 7 7
CD8B 0.01 0.092 0.24 4 -0.57 11 15
PTPRC -0.013 0.14 -10000 0 -0.56 29 29
PDK1/PKC theta -0.017 0.18 0.26 8 -0.54 36 44
CSK/PAG1 -0.012 0.2 0.29 12 -0.71 27 39
SOS1 0.023 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.03 0.032 -10000 0 -0.36 2 2
GRAP2/SLP76 -0.007 0.21 0.29 3 -0.7 33 36
STIM1 -0.003 0.03 -10000 0 -10000 0 0
RAS family/GTP 0.022 0.069 0.18 22 -0.19 17 39
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.028 0.24 0.23 3 -0.77 36 39
mol:DAG -0.027 0.1 -10000 0 -0.39 30 30
RAP1A/GDP 0.009 0.027 0.08 14 -0.067 7 21
PLCG1 0.022 0.004 -10000 0 -10000 0 0
CD247 0.008 0.089 -10000 0 -0.57 11 11
cytotoxic T cell degranulation -0.054 0.31 -10000 0 -0.98 42 42
RAP1A/GTP -0.006 0.023 -10000 0 -0.065 61 61
mol:PI-3-4-5-P3 -0.007 0.17 0.27 11 -0.53 36 47
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.013 0.16 0.25 5 -0.59 29 34
NRAS 0.022 0.005 -10000 0 -10000 0 0
ZAP70 0.013 0.075 -10000 0 -0.56 8 8
GRB2/SOS1 0.033 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.016 0.17 -10000 0 -0.59 30 30
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.019 0.1 -10000 0 -0.55 13 13
CARD11 0.022 0.033 0.31 2 -0.56 1 3
PRKCB -0.007 0.1 0.16 14 -0.32 35 49
PRKCE -0.003 0.084 0.16 7 -0.28 27 34
PRKCQ -0.022 0.2 0.27 8 -0.61 38 46
LCP2 0.014 0.065 -10000 0 -0.56 6 6
BCL10 0.022 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.001 0.13 0.22 16 -0.38 33 49
IKK complex 0.013 0.053 0.14 31 -0.12 13 44
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.006 0.095 0.18 16 -0.28 31 47
PDPK1 -0.002 0.14 0.25 11 -0.43 32 43
TCR/CD3/MHC I/CD8/Fyn -0.028 0.23 -10000 0 -0.81 30 30
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.031 0.087 -10000 0 -0.34 22 22
ER alpha/Gai/GDP/Gbeta gamma -0.038 0.19 -10000 0 -0.58 40 40
AKT1 -0.025 0.2 -10000 0 -0.82 26 26
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.02 0.2 -10000 0 -0.83 26 26
mol:Ca2+ -0.094 0.18 -10000 0 -0.41 113 113
IGF1R 0.022 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.014 0.077 -10000 0 -0.35 20 20
SHC1 0.022 0.005 -10000 0 -10000 0 0
apoptosis 0.022 0.19 0.78 26 -10000 0 26
RhoA/GTP 0.007 0.057 -10000 0 -0.28 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.008 0.16 -10000 0 -0.48 36 36
regulation of stress fiber formation 0.008 0.067 0.45 1 -0.22 3 4
E2/ERA-ERB (dimer) 0.014 0.075 -10000 0 -0.35 19 19
KRAS 0.021 0.006 -10000 0 -10000 0 0
G13/GTP 0.014 0.069 -10000 0 -0.31 20 20
pseudopodium formation -0.008 0.067 0.22 3 -0.45 1 4
E2/ER alpha (dimer)/PELP1 0.013 0.076 -10000 0 -0.35 20 20
GRB2 0.023 0.004 -10000 0 -10000 0 0
GNG2 0.016 0.059 -10000 0 -0.56 5 5
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.025 0.18 -10000 0 -0.56 36 36
E2/ER beta (dimer) 0.016 0.004 -10000 0 -10000 0 0
mol:GDP -0.004 0.085 -10000 0 -0.39 21 21
mol:NADP -0.025 0.18 -10000 0 -0.56 36 36
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 -0.098 0.19 -10000 0 -0.43 113 113
IGF-1R heterotetramer 0.022 0.004 -10000 0 -10000 0 0
PLCB1 -0.091 0.19 -10000 0 -0.43 112 112
PLCB2 -0.098 0.2 -10000 0 -0.44 117 117
IGF1 0.005 0.1 0.24 1 -0.56 15 16
mol:L-citrulline -0.025 0.18 -10000 0 -0.56 36 36
RHOA 0.021 0.007 -10000 0 -10000 0 0
Gai/GDP -0.042 0.21 -10000 0 -0.63 52 52
JNK cascade 0.016 0.004 -10000 0 -10000 0 0
BCAR1 0.022 0.006 -10000 0 -10000 0 0
ESR2 0.022 0.005 -10000 0 -10000 0 0
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
ESR1 -0.002 0.12 -10000 0 -0.56 20 20
Gq family/GDP/Gbeta gamma -0.07 0.21 -10000 0 -0.68 34 34
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.015 0.075 -10000 0 -0.45 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.007 0.16 -10000 0 -0.48 37 37
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
E2/ER alpha (dimer) -0.001 0.086 -10000 0 -0.4 21 21
STRN 0.023 0.003 -10000 0 -10000 0 0
GNAL 0.019 0.046 -10000 0 -0.56 3 3
PELP1 0.022 0.006 -10000 0 -10000 0 0
MAPK11 0.01 0.003 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
HBEGF -0.036 0.19 0.3 8 -0.62 33 41
cAMP biosynthetic process 0.01 0.066 -10000 0 -0.3 19 19
SRC -0.034 0.18 0.26 2 -0.54 39 41
PI3K 0.017 0.017 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
G13/GDP/Gbeta gamma 0.017 0.095 -10000 0 -0.42 17 17
SOS1 0.023 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.026 0.12 -10000 0 -0.4 36 36
Gs family/GTP 0.016 0.069 -10000 0 -0.31 19 19
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.038 0.016 -10000 0 -10000 0 0
vasodilation -0.023 0.17 -10000 0 -0.53 36 36
mol:DAG -0.098 0.19 -10000 0 -0.43 113 113
Gs family/GDP/Gbeta gamma 0.001 0.088 -10000 0 -0.42 15 15
MSN -0.009 0.071 0.23 3 -0.49 1 4
Gq family/GTP -0.092 0.21 -10000 0 -0.46 113 113
mol:PI-3-4-5-P3 -0.018 0.19 -10000 0 -0.79 26 26
NRAS 0.022 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.023 0.17 0.53 36 -10000 0 36
GRB2/SOS1 0.033 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.085 -10000 0 -0.38 20 20
NOS3 -0.028 0.19 -10000 0 -0.6 36 36
GNA11 0.022 0.004 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.16 0.32 1 -0.63 26 27
E2/ER alpha (dimer)/PELP1/Src -0.014 0.17 -10000 0 -0.5 40 40
ruffle organization -0.008 0.067 0.22 3 -0.45 1 4
ROCK2 -0.006 0.074 0.24 3 -0.27 12 15
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.022 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
MMP9 -0.028 0.17 0.32 8 -0.58 27 35
MMP2 -0.028 0.17 0.34 2 -0.59 29 31
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.28 0.23 0.62 1 -1.2 2 3
PLK1 0.12 0.096 -10000 0 -10000 0 0
BIRC5 0.15 0.071 -10000 0 -0.5 1 1
HSPA1B 0.28 0.23 0.64 4 -1.2 2 6
MAP2K1 0.07 0.042 -10000 0 -10000 0 0
BRCA2 0.28 0.23 0.61 2 -1.2 2 4
FOXM1 0.3 0.27 0.64 11 -1.4 3 14
XRCC1 0.28 0.24 0.68 9 -1.2 2 11
FOXM1B/p19 0.16 0.27 0.61 8 -1.3 3 11
Cyclin D1/CDK4 0.23 0.25 0.61 16 -1.1 3 19
CDC2 0.29 0.24 0.6 13 -1.1 3 16
TGFA 0.26 0.23 0.57 20 -0.98 3 23
SKP2 0.32 0.26 0.7 41 -1.1 2 43
CCNE1 0.087 0.11 0.29 106 -10000 0 106
CKS1B 0.29 0.24 0.7 13 -1.2 2 15
RB1 0.16 0.2 0.45 38 -0.79 6 44
FOXM1C/SP1 0.28 0.24 0.6 1 -1.2 3 4
AURKB 0.1 0.18 -10000 0 -0.77 11 11
CENPF 0.3 0.24 0.71 9 -1.2 2 11
CDK4 0.042 0.025 0.38 1 -10000 0 1
MYC 0.23 0.22 0.54 12 -0.9 3 15
CHEK2 0.068 0.043 -10000 0 -10000 0 0
ONECUT1 0.28 0.24 0.59 28 -1.1 3 31
CDKN2A 0.075 0.14 0.22 200 -0.32 19 219
LAMA4 0.27 0.26 0.61 2 -1.2 6 8
FOXM1B/HNF6 0.28 0.26 0.64 11 -1.4 3 14
FOS 0.18 0.45 0.77 4 -0.95 55 59
SP1 0.024 0.002 -10000 0 -10000 0 0
CDC25B 0.29 0.24 0.7 11 -1.2 2 13
response to radiation 0.04 0.03 -10000 0 -10000 0 0
CENPB 0.29 0.24 0.7 11 -1.2 2 13
CENPA 0.31 0.24 0.68 12 -1.2 2 14
NEK2 0.3 0.24 0.66 16 -1.2 2 18
HIST1H2BA 0.28 0.23 0.68 2 -1.2 2 4
CCNA2 0.087 0.1 0.26 123 -0.3 1 124
EP300 0.022 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.28 0.25 -10000 0 -1.5 2 2
CCNB2 0.3 0.24 0.64 2 -1.2 2 4
CCNB1 0.29 0.24 0.63 6 -1.3 2 8
ETV5 0.36 0.29 0.69 88 -1.1 5 93
ESR1 0.24 0.34 0.67 4 -1.1 20 24
CCND1 0.22 0.25 0.6 8 -1.2 3 11
GSK3A 0.059 0.036 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.15 0.11 0.32 98 -10000 0 98
CDK2 0.032 0.013 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.049 0.036 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.25 0.24 0.57 1 -1.2 3 4
GAS1 0.27 0.28 0.69 2 -1.1 8 10
MMP2 0.28 0.26 0.69 2 -1.2 5 7
RB1/FOXM1C 0.24 0.26 0.59 28 -1.2 3 31
CREBBP 0.022 0.005 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.045 0.11 -10000 0 -0.39 11 11
epithelial cell differentiation -0.023 0.089 -10000 0 -0.38 8 8
ITCH 0.037 0.022 -10000 0 -10000 0 0
WWP1 -0.039 0.08 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
EGFR 0.022 0.084 0.36 11 -0.56 6 17
PRL 0.002 0.036 0.24 8 -10000 0 8
neuron projection morphogenesis -0.031 0.075 -10000 0 -0.36 4 4
PTPRZ1 0.16 0.14 0.24 312 -0.49 8 320
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.01 0.09 -10000 0 -0.38 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.035 0.083 -10000 0 -0.35 11 11
ADAM17 0.037 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.055 0.094 -10000 0 -0.3 5 5
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.18 -10000 0 -0.4 117 117
NCOR1 0.022 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.03 0.087 -10000 0 -0.35 11 11
GRIN2B -0.035 0.08 -10000 0 -0.33 10 10
ErbB4/ErbB2/betacellulin -0.042 0.11 -10000 0 -0.35 33 33
STAT1 0.022 0.004 -10000 0 -10000 0 0
HBEGF 0.006 0.095 -10000 0 -0.56 13 13
PRLR 0.018 0.1 0.29 20 -0.56 10 30
E4ICDs/ETO2 -0.041 0.1 -10000 0 -0.38 7 7
axon guidance -0.038 0.073 -10000 0 -0.37 4 4
NEDD4 0.037 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.026 0.079 0.28 8 -0.42 10 18
CBFA2T3 0.015 0.065 -10000 0 -0.56 6 6
ErbB4/ErbB2/HBEGF -0.027 0.088 -10000 0 -0.34 11 11
MAPK3 -0.023 0.082 -10000 0 -0.37 4 4
STAT1 (dimer) -0.037 0.093 -10000 0 -10000 0 0
MAPK1 -0.022 0.08 -10000 0 -0.37 4 4
JAK2 0.02 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.034 0.082 -10000 0 -0.34 10 10
NRG1 -0.005 0.068 -10000 0 -0.41 12 12
NRG3 -0.13 0.25 -10000 0 -0.56 117 117
NRG2 -0.039 0.17 -10000 0 -0.56 46 46
NRG4 0.048 0.071 0.24 57 -0.29 1 58
heart development -0.038 0.073 -10000 0 -0.37 4 4
neural crest cell migration -0.034 0.081 -10000 0 -0.34 10 10
ERBB2 0.008 0.029 0.31 2 -10000 0 2
WWOX/E4ICDs -0.036 0.092 -10000 0 -0.26 4 4
SHC1 0.022 0.005 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.018 0.12 0.29 2 -0.38 5 7
apoptosis 0.16 0.24 0.51 130 -10000 0 130
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.069 0.14 -10000 0 -0.39 48 48
ErbB4/ErbB2/epiregulin -0.072 0.15 -10000 0 -0.36 81 81
ErbB4/ErbB4/betacellulin/betacellulin -0.061 0.13 -10000 0 -0.38 40 40
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.02 0.11 0.37 1 -0.41 10 11
MDM2 -0.041 0.09 0.24 8 -0.26 5 13
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.021 0.072 -10000 0 -0.33 11 11
STAT5A -0.038 0.07 -10000 0 -0.38 3 3
ErbB4/EGFR/neuregulin 1 beta -0.027 0.1 0.28 2 -0.41 13 15
DLG4 0.022 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.032 0.01 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.036 0.085 -10000 0 -10000 0 0
STAT5A (dimer) -0.02 0.098 -10000 0 -0.43 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.026 0.078 -10000 0 -0.38 3 3
LRIG1 0.02 0.027 -10000 0 -0.56 1 1
EREG -0.078 0.23 0.25 14 -0.56 87 101
BTC -0.021 0.15 -10000 0 -0.56 35 35
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.037 0.072 -10000 0 -0.37 4 4
ERBB4 -0.055 0.094 -10000 0 -0.3 5 5
STAT5B 0.023 0.003 -10000 0 -10000 0 0
YAP1 -0.01 0.077 -10000 0 -0.52 9 9
GRB2 0.023 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.014 0.091 0.33 2 -10000 0 2
glial cell differentiation 0.036 0.084 -10000 0 -10000 0 0
WWOX 0.022 0.006 -10000 0 -10000 0 0
cell proliferation -0.06 0.12 -10000 0 -0.41 28 28
Glucocorticoid receptor regulatory network

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
PCK2 -0.01 0.095 -10000 0 -0.5 2 2
SMARCC2 0.024 0.002 -10000 0 -10000 0 0
SMARCC1 0.022 0.007 -10000 0 -10000 0 0
TBX21 -0.072 0.3 0.5 1 -0.9 49 50
SUMO2 0.022 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.026 0.005 -10000 0 -10000 0 0
FKBP4 0.022 0.017 0.38 1 -10000 0 1
FKBP5 0.023 0.003 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.009 0.11 0.32 8 -10000 0 8
PRL 0.016 0.094 0.42 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 0 0.26 0.52 42 -0.41 34 76
RELA -0.061 0.13 -10000 0 -0.29 59 59
FGG -0.24 0.34 0.47 13 -0.6 201 214
GR beta/TIF2 -0.001 0.12 0.31 19 -0.33 1 20
IFNG 0.029 0.19 -10000 0 -0.9 8 8
apoptosis -0.007 0.11 0.5 2 -0.54 5 7
CREB1 0.026 0.011 -10000 0 -10000 0 0
histone acetylation 0 0.11 0.32 1 -0.36 13 14
BGLAP 0.022 0.11 -10000 0 -0.53 1 1
GR/PKAc 0.01 0.11 0.32 8 -10000 0 8
NF kappa B1 p50/RelA -0.12 0.24 -10000 0 -0.42 157 157
SMARCD1 0.024 0.002 -10000 0 -10000 0 0
MDM2 0.003 0.081 0.24 21 -10000 0 21
GATA3 0.011 0.097 0.24 3 -0.56 13 16
AKT1 0.019 0.005 -10000 0 -10000 0 0
CSF2 -0.12 0.36 -10000 0 -1.2 50 50
GSK3B 0.019 0.01 -10000 0 -10000 0 0
NR1I3 0.002 0.12 0.62 2 -0.69 1 3
CSN2 -0.05 0.17 0.37 17 -0.38 34 51
BRG1/BAF155/BAF170/BAF60A 0.056 0.021 -10000 0 -10000 0 0
NFATC1 0.021 0.027 -10000 0 -0.56 1 1
POU2F1 0.023 0.007 -10000 0 -10000 0 0
CDKN1A 0.009 0.042 -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 0.04 0.072 0.24 45 -0.38 3 48
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.025 0.12 0.32 7 -10000 0 7
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.01 0.14 0.52 2 -0.81 9 11
JUN 0.041 0.1 0.38 2 -0.4 5 7
IL4 0.009 0.11 -10000 0 -0.49 2 2
CDK5R1 0.027 0.03 0.24 9 -10000 0 9
PRKACA 0.022 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.15 -10000 0 -0.4 80 80
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.015 0.11 0.32 8 -10000 0 8
cortisol/GR alpha (monomer) -0.007 0.3 0.6 43 -0.47 38 81
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.001 0.2 -10000 0 -0.55 53 53
AP-1/NFAT1-c-4 0.073 0.19 0.38 2 -0.5 12 14
AFP 0.043 0.094 -10000 0 -0.43 1 1
SUV420H1 0.022 0.004 -10000 0 -10000 0 0
IRF1 -0.001 0.13 0.4 10 -0.39 1 11
TP53 0.031 0.008 -10000 0 -10000 0 0
PPP5C 0.023 0.004 -10000 0 -10000 0 0
KRT17 0.069 0.18 -10000 0 -0.62 6 6
KRT14 0.044 0.13 0.46 1 -0.9 2 3
TBP 0.027 0.005 -10000 0 -10000 0 0
CREBBP -0.013 0.045 0.34 1 -10000 0 1
HDAC1 0.022 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.024 -10000 0 -10000 0 0
AP-1 0.074 0.19 0.38 2 -0.5 12 14
MAPK14 0.022 0.008 -10000 0 -10000 0 0
MAPK10 0.013 0.07 -10000 0 -0.56 7 7
MAPK11 0.022 0.008 -10000 0 -10000 0 0
KRT5 0.071 0.18 -10000 0 -0.72 5 5
interleukin-1 receptor activity 0.007 0.023 -10000 0 -10000 0 0
NCOA1 0.024 0.004 -10000 0 -10000 0 0
STAT1 0.026 0.005 -10000 0 -10000 0 0
CGA 0.016 0.11 -10000 0 -0.54 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.035 0.19 0.46 36 -0.36 13 49
MAPK3 0.022 0.008 -10000 0 -10000 0 0
MAPK1 0.021 0.009 -10000 0 -10000 0 0
ICAM1 -0.14 0.39 -10000 0 -1.1 52 52
NFKB1 -0.059 0.13 -10000 0 -0.3 57 57
MAPK8 0.033 0.14 0.3 3 -0.37 17 20
MAPK9 0.02 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.009 0.11 0.5 2 -0.57 5 7
BAX 0.007 0.041 -10000 0 -10000 0 0
POMC -0.026 0.2 0.53 1 -1 6 7
EP300 -0.013 0.046 0.34 1 -10000 0 1
cortisol/GR alpha (dimer)/p53 0 0.25 0.53 35 -0.41 30 65
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.069 0.23 14 -0.2 1 15
SGK1 -0.006 0.075 -10000 0 -10000 0 0
IL13 0.011 0.16 -10000 0 -0.61 12 12
IL6 -0.21 0.48 -10000 0 -1.1 92 92
PRKACG -0.01 0.019 0.24 1 -10000 0 1
IL5 0.009 0.14 -10000 0 -0.64 6 6
IL2 0.026 0.16 -10000 0 -0.59 7 7
CDK5 0.022 0.005 -10000 0 -10000 0 0
PRKACB 0.023 0.004 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
IL8 -0.07 0.24 -10000 0 -0.68 34 34
CDK5R1/CDK5 0.035 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.063 0.2 -10000 0 -0.44 55 55
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.01 0.24 0.51 38 -0.38 28 66
SMARCA4 0.023 0.004 -10000 0 -10000 0 0
chromatin remodeling -0.001 0.14 0.36 16 -0.39 1 17
NF kappa B1 p50/RelA/Cbp -0.091 0.2 0.37 1 -0.48 58 59
JUN (dimer) 0.041 0.1 0.38 2 -0.4 5 7
YWHAH 0.022 0.004 -10000 0 -10000 0 0
VIPR1 -0.29 0.46 -10000 0 -0.91 164 164
NR3C1 -0.01 0.17 0.45 21 -10000 0 21
NR4A1 -0.054 0.2 -10000 0 -0.55 68 68
TIF2/SUV420H1 0.031 0.022 -10000 0 -0.41 1 1
MAPKKK cascade -0.007 0.11 0.5 2 -0.54 5 7
cortisol/GR alpha (dimer)/Src-1 0.004 0.26 0.52 41 -0.41 34 75
PBX1 0.021 0.038 -10000 0 -0.56 2 2
POU1F1 0.004 0.027 0.24 3 -10000 0 3
SELE -0.33 0.56 -10000 0 -1.1 149 149
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.001 0.14 0.37 16 -0.39 1 17
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.01 0.24 0.51 38 -0.38 28 66
mol:cortisol -0.012 0.16 0.33 44 -0.24 44 88
MMP1 0.076 0.11 -10000 0 -0.54 6 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.17 0.27 -10000 0 -0.56 155 155
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.022 0.005 -10000 0 -10000 0 0
TCEB1 0.022 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.012 0.065 0.25 1 -0.28 13 14
HIF1A -0.003 0.049 -10000 0 -0.27 15 15
COPS5 0.022 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.059 0.025 -10000 0 -10000 0 0
FIH (dimer) 0.022 0.005 -10000 0 -10000 0 0
CDKN2A 0.096 0.14 0.24 200 -0.3 19 219
ARNT/IPAS -0.11 0.2 -10000 0 -0.41 142 142
HIF1AN 0.022 0.005 -10000 0 -10000 0 0
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.01 0.062 -10000 0 -0.31 6 6
CUL2 0.022 0.004 -10000 0 -10000 0 0
OS9 0.023 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.016 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.011 0.063 -10000 0 -0.27 17 17
PHD1-3/OS9 0.069 0.052 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.031 0.062 -10000 0 -0.29 2 2
VHL 0.021 0.006 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.013 0.062 0.25 1 -0.31 5 6
EGLN3 0.055 0.079 0.24 71 -10000 0 71
EGLN2 0.021 0.006 -10000 0 -10000 0 0
EGLN1 0.022 0.004 -10000 0 -10000 0 0
TP53 0.022 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.015 0.17 -10000 0 -0.58 38 38
ARNT 0.022 0.006 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.022 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.056 0.11 0.33 3 -0.33 17 20
Regulation of Androgen receptor activity

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
HDAC1 -0.01 0.003 -10000 0 -10000 0 0
SMARCC1 0.004 0.023 -10000 0 -10000 0 0
REL 0.021 0.007 -10000 0 -10000 0 0
HDAC7 -0.068 0.11 -10000 0 -0.36 5 5
JUN 0.022 0.004 -10000 0 -10000 0 0
EP300 0.022 0.004 -10000 0 -10000 0 0
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
KAT5 0.023 0.001 -10000 0 -10000 0 0
MAPK14 -0.007 0.024 -10000 0 -10000 0 0
FOXO1 0.022 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.055 0.13 -10000 0 -0.37 6 6
MAP2K6 0.007 0.026 0.22 1 -10000 0 1
BRM/BAF57 0.029 0.023 -10000 0 -0.41 1 1
MAP2K4 0.007 0.024 -10000 0 -10000 0 0
SMARCA2 0.019 0.027 -10000 0 -0.56 1 1
PDE9A -0.084 0.22 -10000 0 -0.95 20 20
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
CEBPA 0.02 0.027 -10000 0 -0.56 1 1
EHMT2 0.023 0.003 -10000 0 -10000 0 0
cell proliferation -0.078 0.16 0.33 4 -0.47 36 40
NR0B1 0.072 0.12 0.24 146 -0.29 7 153
EGR1 0.013 0.07 -10000 0 -0.56 7 7
RXRs/9cRA -0.14 0.18 -10000 0 -0.32 231 231
AR/RACK1/Src -0.024 0.079 0.29 4 -0.28 1 5
AR/GR -0.045 0.12 -10000 0 -0.29 83 83
GNB2L1 0.021 0.007 -10000 0 -10000 0 0
PKN1 0.022 0.005 -10000 0 -10000 0 0
RCHY1 0.022 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 -0.007 0.023 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.018 0.083 0.28 1 -0.33 2 3
SRC -0.027 0.038 0.2 4 -10000 0 4
NR3C1 0.022 0.006 -10000 0 -10000 0 0
KLK3 -0.04 0.13 -10000 0 -0.47 10 10
APPBP2 0.007 0.025 -10000 0 -10000 0 0
TRIM24 0.023 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.032 0.075 -10000 0 -0.3 1 1
TMPRSS2 -0.36 0.52 -10000 0 -1.1 159 159
RXRG -0.26 0.29 -10000 0 -0.56 233 233
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.023 0.004 -10000 0 -10000 0 0
RXRB 0.023 0.004 -10000 0 -10000 0 0
CARM1 0.023 0.005 -10000 0 -10000 0 0
NR2C2 0.021 0.006 -10000 0 -10000 0 0
KLK2 -0.012 0.075 0.32 3 -0.36 1 4
AR -0.062 0.12 -10000 0 -0.31 85 85
SENP1 0.023 0.002 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
MDM2 0.023 0.017 0.38 1 -10000 0 1
SRY 0 0.001 -10000 0 -10000 0 0
GATA2 -0.034 0.17 -10000 0 -0.56 45 45
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.14 0.12 0.24 282 -10000 0 282
T-DHT/AR/RACK1/Src -0.025 0.078 0.3 3 -0.29 1 4
positive regulation of transcription -0.034 0.17 -10000 0 -0.56 45 45
DNAJA1 0.007 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.01 0.22 1 -10000 0 1
NCOA1 0.031 0.021 -10000 0 -10000 0 0
SPDEF -0.046 0.19 0.24 4 -0.56 58 62
T-DHT/AR/TIF2 -0.024 0.086 -10000 0 -0.37 15 15
T-DHT/AR/Hsp90 -0.03 0.074 -10000 0 -0.3 1 1
GSK3B 0.017 0.013 -10000 0 -10000 0 0
NR2C1 0.023 0.002 -10000 0 -10000 0 0
mol:T-DHT -0.029 0.035 -10000 0 -10000 0 0
SIRT1 0.022 0.005 -10000 0 -10000 0 0
ZMIZ2 0.022 0.005 -10000 0 -10000 0 0
POU2F1 -0.011 0.061 -10000 0 -0.18 4 4
T-DHT/AR/DAX-1 -0.017 0.11 0.28 3 -0.3 2 5
CREBBP 0.022 0.005 -10000 0 -10000 0 0
SMARCE1 0.023 0.003 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.008 0.12 0.23 1 -0.39 26 27
TBX21 -0.12 0.47 -10000 0 -1.3 56 56
B2M 0.022 0.01 -10000 0 -10000 0 0
TYK2 0.014 0.031 -10000 0 -10000 0 0
IL12RB1 -0.019 0.14 -10000 0 -0.59 28 28
GADD45B -0.066 0.36 -10000 0 -1.1 41 41
IL12RB2 0.037 0.075 0.24 45 -0.28 1 46
GADD45G -0.049 0.32 -10000 0 -1 33 33
natural killer cell activation 0 0.016 -10000 0 -10000 0 0
RELB 0.023 0.017 0.38 1 -10000 0 1
RELA 0.023 0.001 -10000 0 -10000 0 0
IL18 0.016 0.05 -10000 0 -0.57 3 3
IL2RA 0.021 0.042 0.24 3 -0.56 2 5
IFNG 0.016 0.056 0.24 2 -0.56 4 6
STAT3 (dimer) -0.046 0.29 -10000 0 -0.78 48 48
HLA-DRB5 -0.038 0.17 -10000 0 -0.56 46 46
FASLG -0.08 0.39 -10000 0 -1.2 43 43
NF kappa B2 p52/RelB -0.057 0.34 -10000 0 -0.95 46 46
CD4 0.001 0.095 -10000 0 -0.56 13 13
SOCS1 0.021 0.027 -10000 0 -0.56 1 1
EntrezGene:6955 -0.002 0.009 -10000 0 -10000 0 0
CD3D 0.006 0.081 -10000 0 -0.56 9 9
CD3E 0.007 0.076 -10000 0 -0.56 8 8
CD3G -0.017 0.14 -10000 0 -0.56 28 28
IL12Rbeta2/JAK2 0.035 0.065 0.22 1 -10000 0 1
CCL3 -0.066 0.34 -10000 0 -1 39 39
CCL4 -0.069 0.35 -10000 0 -1.1 39 39
HLA-A 0.021 0.028 -10000 0 -0.56 1 1
IL18/IL18R 0.03 0.12 -10000 0 -0.44 24 24
NOS2 -0.092 0.42 -10000 0 -1.2 52 52
IL12/IL12R/TYK2/JAK2/SPHK2 0.009 0.12 0.23 1 -0.39 24 25
IL1R1 -0.064 0.34 -10000 0 -1 39 39
IL4 -0.007 0.03 -10000 0 -10000 0 0
JAK2 0.013 0.029 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.043 0.27 -10000 0 -1.1 23 23
RAB7A -0.019 0.28 -10000 0 -0.81 37 37
lysosomal transport -0.014 0.27 -10000 0 -0.76 37 37
FOS -0.18 0.47 -10000 0 -1.1 83 83
STAT4 (dimer) -0.052 0.33 0.42 1 -0.91 48 49
STAT5A (dimer) -0.06 0.34 -10000 0 -0.95 46 46
GZMA -0.07 0.35 -10000 0 -1.1 38 38
GZMB -0.071 0.36 -10000 0 -1.1 37 37
HLX 0.023 0.004 -10000 0 -10000 0 0
LCK -0.074 0.37 -10000 0 -1 46 46
TCR/CD3/MHC II/CD4 -0.079 0.28 -10000 0 -0.74 48 48
IL2/IL2R 0.044 0.072 -10000 0 -0.45 8 8
MAPK14 -0.056 0.35 -10000 0 -0.98 45 45
CCR5 -0.074 0.36 -10000 0 -1.2 37 37
IL1B 0.001 0.096 -10000 0 -0.59 11 11
STAT6 0.007 0.091 -10000 0 -10000 0 0
STAT4 0.013 0.075 -10000 0 -0.56 8 8
STAT3 0.023 0.003 -10000 0 -10000 0 0
STAT1 0.022 0.004 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
NFKB2 0.022 0.005 -10000 0 -10000 0 0
IL12B 0.013 0.029 -10000 0 -10000 0 0
CD8A 0.014 0.071 -10000 0 -0.56 7 7
CD8B 0.011 0.091 0.24 4 -0.57 11 15
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.008 0.12 0.38 26 -0.22 1 27
IL2RB 0.019 0.046 -10000 0 -0.56 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.041 0.3 0.41 1 -0.81 48 49
IL2RG 0.014 0.07 -10000 0 -0.56 7 7
IL12 0.012 0.06 -10000 0 -0.42 6 6
STAT5A 0.023 0.003 -10000 0 -10000 0 0
CD247 0.003 0.089 -10000 0 -0.57 11 11
IL2 0.001 0.02 -10000 0 -10000 0 0
SPHK2 0.023 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.003 0.069 -10000 0 -0.57 6 6
IL12/IL12R/TYK2/JAK2 -0.099 0.4 -10000 0 -1.1 48 48
MAP2K3 -0.063 0.36 -10000 0 -1 44 44
RIPK2 0.022 0.005 -10000 0 -10000 0 0
MAP2K6 -0.054 0.34 -10000 0 -0.99 42 42
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.028 0.16 -10000 0 -0.56 37 37
IL18RAP -0.006 0.12 -10000 0 -0.57 22 22
IL12Rbeta1/TYK2 -0.003 0.12 -10000 0 -0.45 28 28
EOMES -0.059 0.25 -10000 0 -0.92 28 28
STAT1 (dimer) -0.042 0.28 -10000 0 -0.79 42 42
T cell proliferation -0.026 0.24 0.42 1 -0.66 44 45
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.014 0.063 -10000 0 -0.57 5 5
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.045 0.27 -10000 0 -0.72 48 48
ATF2 -0.047 0.31 -10000 0 -0.91 42 42
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 0.01 0.075 0.28 1 -0.29 19 20
FZD6 0.022 0.005 -10000 0 -10000 0 0
WNT6 0.056 0.084 0.24 80 -0.29 1 81
WNT4 0.019 0.057 0.24 4 -0.56 4 8
FZD3 0.021 0.007 -10000 0 -10000 0 0
WNT5A 0.024 0.032 0.24 8 -0.29 1 9
WNT11 0.007 0.11 0.25 10 -0.56 17 27
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.074 -10000 0 -0.35 13 13
fibroblast growth factor receptor signaling pathway 0.029 0.074 -10000 0 -0.35 13 13
LAMA1 0.086 0.1 0.25 138 -0.29 1 139
PRNP 0.022 0.005 -10000 0 -10000 0 0
GPC1/SLIT2 -0.057 0.18 -10000 0 -0.41 94 94
SMAD2 -0.031 0.072 0.18 4 -0.32 24 28
GPC1/PrPc/Cu2+ 0.035 0.03 -10000 0 -10000 0 0
GPC1/Laminin alpha1 0.082 0.084 0.31 23 -0.2 1 24
TDGF1 0.014 0.024 0.24 3 -10000 0 3
CRIPTO/GPC1 0.038 0.035 -10000 0 -10000 0 0
APP/GPC1 0.039 0.033 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.013 0.01 -10000 0 -10000 0 0
FLT1 0.022 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.024 0.098 -10000 0 -0.35 25 25
SERPINC1 0.014 0.031 0.24 6 -10000 0 6
FYN -0.014 0.017 -10000 0 -0.32 1 1
FGR -0.033 0.079 -10000 0 -0.35 27 27
positive regulation of MAPKKK cascade -0.018 0.1 0.3 2 -0.36 21 23
SLIT2 -0.093 0.23 -10000 0 -0.56 94 94
GPC1/NRG 0.026 0.078 -10000 0 -0.41 12 12
NRG1 0.006 0.091 -10000 0 -0.56 12 12
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.048 0.032 -10000 0 -10000 0 0
LYN -0.015 0.024 -10000 0 -0.34 2 2
mol:Spermine -0.008 0.011 -10000 0 -10000 0 0
cell growth 0.029 0.074 -10000 0 -0.35 13 13
BMP signaling pathway -0.033 0.047 -10000 0 -0.24 24 24
SRC -0.013 0.011 -10000 0 -10000 0 0
TGFBR1 0.023 0.004 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.26 0.24 2 -0.56 131 133
GPC1 0.033 0.047 0.24 24 -10000 0 24
TGFBR1 (dimer) 0.023 0.004 -10000 0 -10000 0 0
VEGFA 0.023 0.004 -10000 0 -10000 0 0
BLK -0.017 0.054 -10000 0 -0.36 10 10
HCK -0.015 0.029 -10000 0 -0.36 3 3
FGF2 0.006 0.095 -10000 0 -0.56 13 13
FGFR1 0.017 0.028 -10000 0 -0.56 1 1
VEGFR1 homodimer 0.022 0.006 -10000 0 -10000 0 0
TGFBR2 -0.01 0.13 -10000 0 -0.56 26 26
cell death 0.039 0.033 -10000 0 -10000 0 0
ATIII/GPC1 0.039 0.037 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.088 0.2 -10000 0 -0.42 131 131
LCK -0.015 0.019 -10000 0 -0.36 1 1
neuron differentiation 0.026 0.078 -10000 0 -0.41 12 12
PrPc/Cu2+ 0.016 0.004 -10000 0 -10000 0 0
APP 0.022 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.01 0.13 -10000 0 -0.56 26 26
Nectin adhesion pathway

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
PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
alphaV beta3 Integrin 0.026 0.058 -10000 0 -0.41 8 8
PTK2 0.012 0.14 -10000 0 -0.46 28 28
positive regulation of JNK cascade 0.002 0.1 -10000 0 -0.32 32 32
CDC42/GDP 0.019 0.14 -10000 0 -0.43 35 35
Rac1/GDP 0.019 0.14 -10000 0 -0.42 34 34
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.011 0.13 -10000 0 -0.4 31 31
nectin-3/I-afadin 0 0.11 -10000 0 -0.41 31 31
RAPGEF1 0.003 0.14 0.28 1 -0.47 30 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.003 0.15 -10000 0 -0.53 30 30
PDGFB-D/PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
TLN1 -0.032 0.1 -10000 0 -0.42 23 23
Rap1/GTP 0 0.1 -10000 0 -0.34 28 28
IQGAP1 0.023 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0 0.11 -10000 0 -0.41 31 31
PVR 0.022 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0.005 0.17 -10000 0 -0.52 36 36
MLLT4 0.023 0.004 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.018 0.07 -10000 0 -0.3 12 12
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.1 0.077 0.26 1 -0.2 1 2
positive regulation of lamellipodium assembly 0.007 0.11 -10000 0 -0.33 33 33
PVRL1 0.12 0.11 0.24 228 -0.29 1 229
PVRL3 -0.017 0.14 -10000 0 -0.56 31 31
PVRL2 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
CDH1 0.022 0.005 -10000 0 -10000 0 0
CLDN1 0.064 0.12 0.31 84 -0.56 2 86
JAM-A/CLDN1 0.041 0.1 -10000 0 -0.33 15 15
SRC -0.009 0.17 -10000 0 -0.59 30 30
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
nectin-1(dimer)/I-afadin/I-afadin 0.1 0.077 0.26 1 -0.2 1 2
FARP2 0.004 0.17 -10000 0 -0.53 33 33
RAC1 0.022 0.004 -10000 0 -10000 0 0
CTNNA1 0.021 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.013 0.099 -10000 0 -0.35 31 31
nectin-1/I-afadin 0.1 0.077 0.26 1 -0.2 1 2
nectin-2/I-afadin 0.033 0.008 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.03 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.062 0.13 -10000 0 -0.37 30 30
CDC42/GTP/IQGAP1/filamentous actin 0.03 0.007 -10000 0 -10000 0 0
F11R 0.022 0.006 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.002 0.1 -10000 0 -0.32 32 32
alphaV/beta3 Integrin/Talin 0.008 0.13 0.27 6 -0.44 22 28
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.033 0.008 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.033 0.008 -10000 0 -10000 0 0
PIP5K1C -0.031 0.11 -10000 0 -0.34 45 45
VAV2 0.006 0.17 -10000 0 -0.53 37 37
RAP1/GDP 0.018 0.13 -10000 0 -0.39 34 34
ITGAV 0.023 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.013 0.099 -10000 0 -0.35 31 31
nectin-3(dimer)/I-afadin/I-afadin 0 0.11 -10000 0 -0.41 31 31
Rac1/GTP 0.013 0.13 -10000 0 -0.41 33 33
PTPRM -0.028 0.12 -10000 0 -0.35 49 49
E-cadherin/beta catenin/alpha catenin 0.1 0.063 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.029 0.058 0.3 6 -0.2 19 25
TP53 -0.002 0.046 -10000 0 -0.18 24 24
Senescence -0.002 0.046 -10000 0 -0.18 24 24
Apoptosis -0.002 0.046 -10000 0 -0.18 24 24
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.002 0.075 0.23 35 -0.21 6 41
MDM4 0.022 0.004 -10000 0 -10000 0 0
Syndecan-3-mediated signaling 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
CTTN 0.02 0.008 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.03 0.076 -10000 0 -0.35 8 8
Syndecan-3/Neurocan 0.028 0.07 -10000 0 -0.37 8 8
POMC 0.039 0.08 0.25 42 -0.56 3 45
EGFR 0.022 0.084 0.36 11 -0.56 6 17
Syndecan-3/EGFR 0.02 0.07 0.29 3 -0.34 10 13
AGRP -0.24 0.28 -10000 0 -0.56 207 207
NCSTN 0.022 0.005 -10000 0 -10000 0 0
PSENEN 0.021 0.007 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.002 -10000 0 -10000 0 0
APH1A 0.022 0.006 -10000 0 -10000 0 0
NCAN 0.03 0.061 0.24 34 -10000 0 34
long-term memory 0.027 0.063 -10000 0 -0.36 9 9
Syndecan-3/IL8 0.022 0.07 -10000 0 -0.35 11 11
PSEN1 0.022 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.028 0.013 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
limb bud formation 0.002 0.053 -10000 0 -0.38 9 9
MC4R 0.026 0.051 0.25 21 -10000 0 21
SRC 0.022 0.004 -10000 0 -10000 0 0
PTN 0.012 0.085 0.24 3 -0.56 10 13
FGFR/FGF/Syndecan-3 0.002 0.054 -10000 0 -0.39 9 9
neuron projection morphogenesis 0.03 0.091 0.29 9 -0.34 7 16
Syndecan-3/AgRP -0.11 0.16 -10000 0 -0.29 176 176
Syndecan-3/AgRP/MC4R -0.1 0.16 0.32 1 -0.38 14 15
Fyn/Cortactin 0.028 0.024 -10000 0 -0.41 1 1
SDC3 0.002 0.054 -10000 0 -0.39 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.022 0.069 -10000 0 -0.35 11 11
IL8 0.026 0.063 0.26 16 -0.56 3 19
Syndecan-3/Fyn/Cortactin 0.027 0.064 -10000 0 -0.36 9 9
Syndecan-3/CASK -0.001 0.055 -10000 0 -0.37 9 9
alpha-MSH/MC4R 0.049 0.066 0.28 6 -0.42 3 9
Gamma Secretase 0.056 0.028 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.022 0.005 -10000 0 -10000 0 0
VLDLR 0.019 0.027 -10000 0 -0.56 1 1
LRPAP1 0.021 0.006 -10000 0 -10000 0 0
NUDC 0.022 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.021 0.14 -10000 0 -0.35 76 76
CaM/Ca2+ 0.016 0.004 -10000 0 -10000 0 0
KATNA1 0.023 0.003 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.054 0.12 -10000 0 -0.32 76 76
IQGAP1/CaM 0.032 0.009 -10000 0 -10000 0 0
DAB1 0.028 0.06 0.25 30 -10000 0 30
IQGAP1 0.023 0.003 -10000 0 -10000 0 0
PLA2G7 0.018 0.053 -10000 0 -0.56 4 4
CALM1 0.022 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.032 0.014 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.023 0.002 -10000 0 -10000 0 0
CDK5R1 0.027 0.029 0.24 9 -10000 0 9
LIS1/Poliovirus Protein 3A -0.007 0.002 -10000 0 -10000 0 0
CDK5R2 0.073 0.098 0.24 121 -0.29 2 123
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.017 0.15 0.35 2 -0.35 75 77
YWHAE 0.022 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.016 0.12 0.31 2 -0.32 8 10
MAP1B 0.005 0.01 0.21 1 -10000 0 1
RAC1 0.009 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.048 0.12 0.28 1 -0.29 71 72
RELN -0.07 0.21 0.24 3 -0.56 76 79
PAFAH/LIS1 0.019 0.031 -10000 0 -0.35 3 3
LIS1/CLIP170 0.022 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.011 0.097 -10000 0 -0.3 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.036 0.13 -10000 0 -0.3 69 69
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.035 0.12 0.34 1 -0.31 17 18
LIS1/IQGAP1 0.021 0.008 -10000 0 -10000 0 0
RHOA 0.009 0.004 -10000 0 -10000 0 0
PAFAH1B1 -0.009 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.025 0.33 3 -10000 0 3
PAFAH1B2 0.023 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.015 0.027 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.008 0.12 0.3 2 -0.32 7 9
LRP8 0.024 0.017 0.24 3 -10000 0 3
NDEL1/Katanin 60 -0.019 0.12 0.31 2 -0.32 10 12
P39/CDK5 -0.019 0.14 0.31 6 -0.3 73 79
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.008 -10000 0 -10000 0 0
CDK5 -0.054 0.11 0.18 16 -0.3 76 92
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.019 0.007 -10000 0 -10000 0 0
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.006 0.13 0.28 3 -0.31 67 70
RELN/VLDLR -0.01 0.14 -10000 0 -0.32 74 74
CDC42 0.009 0.004 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.016 0.3 0.48 1 -0.92 24 25
HDAC7 0.024 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.091 0.3 -10000 0 -0.91 11 11
SMAD4 0.022 0.009 -10000 0 -10000 0 0
ID2 0.014 0.3 0.48 1 -0.92 24 25
AP1 -0.023 0.14 -10000 0 -0.42 53 53
ABCG2 -0.02 0.35 0.48 1 -0.97 33 34
HIF1A 0.02 0.074 -10000 0 -0.42 1 1
TFF3 -0.009 0.33 -10000 0 -0.99 27 27
GATA2 -0.039 0.17 -10000 0 -0.56 45 45
AKT1 0.02 0.068 -10000 0 -10000 0 0
response to hypoxia 0.003 0.066 -10000 0 -0.27 7 7
MCL1 0.008 0.29 0.48 1 -0.95 20 21
NDRG1 0.015 0.29 0.48 1 -0.94 20 21
SERPINE1 0.015 0.29 0.48 1 -0.92 22 23
FECH 0.014 0.29 0.48 1 -0.94 22 23
FURIN 0.016 0.29 0.48 1 -0.94 22 23
NCOA2 0.022 0.027 -10000 0 -0.56 1 1
EP300 0.022 0.074 -10000 0 -0.3 4 4
HMOX1 0.016 0.3 0.48 1 -0.92 24 25
BHLHE40 0.014 0.29 0.48 1 -0.94 22 23
BHLHE41 0.01 0.3 0.48 1 -1 22 23
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.064 0.13 -10000 0 -0.45 5 5
ENG 0.014 0.12 0.35 2 -0.64 6 8
JUN 0.018 0.017 -10000 0 -10000 0 0
RORA 0.016 0.3 0.48 1 -0.92 24 25
ABCB1 -0.11 0.39 -10000 0 -1.1 60 60
TFRC -0.015 0.26 -10000 0 -0.9 19 19
CXCR4 0.017 0.3 0.48 1 -0.92 24 25
TF 0.006 0.29 -10000 0 -0.92 25 25
CITED2 0.011 0.3 0.48 1 -0.99 22 23
HIF1A/ARNT 0.14 0.4 0.62 5 -1.1 22 27
LDHA 0.021 0.14 -10000 0 -0.99 5 5
ETS1 0.009 0.31 0.48 1 -1 23 24
PGK1 0.014 0.3 0.48 1 -0.93 23 24
NOS2 0.006 0.33 0.48 1 -0.97 27 28
ITGB2 0.003 0.32 -10000 0 -1 25 25
ALDOA 0.017 0.3 0.48 1 -0.93 23 24
Cbp/p300/CITED2 0.027 0.31 -10000 0 -1 20 20
FOS -0.046 0.18 -10000 0 -0.56 53 53
HK2 0.015 0.29 0.48 1 -0.93 24 25
SP1 0.008 0.051 -10000 0 -0.2 1 1
GCK 0.037 0.11 -10000 0 -10000 0 0
HK1 0.016 0.3 0.48 1 -0.93 23 24
NPM1 0.013 0.29 0.48 1 -0.93 23 24
EGLN1 0.015 0.29 0.48 1 -0.93 23 24
CREB1 0.026 0.004 -10000 0 -10000 0 0
PGM1 0.014 0.29 0.48 1 -0.93 23 24
SMAD3 0.023 0.008 -10000 0 -10000 0 0
EDN1 -0.1 0.37 0.41 1 -1.1 50 51
IGFBP1 0.015 0.29 0.47 1 -0.94 21 22
VEGFA 0.026 0.23 -10000 0 -0.78 10 10
HIF1A/JAB1 0.031 0.058 -10000 0 -0.3 1 1
CP -0.008 0.29 0.48 1 -0.95 26 27
CXCL12 -0.004 0.34 0.48 1 -1.1 29 30
COPS5 0.023 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.033 0.014 -10000 0 -10000 0 0
BNIP3 0.016 0.3 0.48 1 -0.92 24 25
EGLN3 0.026 0.3 0.48 1 -0.92 24 25
CA9 0.082 0.34 0.52 7 -0.96 23 30
TERT 0.054 0.3 0.51 8 -0.91 21 29
ENO1 0.015 0.29 0.48 1 -0.94 22 23
PFKL 0.014 0.29 -10000 0 -0.93 23 23
NCOA1 0.023 0.004 -10000 0 -10000 0 0
ADM 0.015 0.3 0.48 1 -0.92 24 25
ARNT 0.021 0.07 -10000 0 -0.32 1 1
HNF4A 0.027 0.031 0.26 8 -10000 0 8
ADFP 0.005 0.29 -10000 0 -0.91 25 25
SLC2A1 0.082 0.27 0.42 4 -0.76 14 18
LEP 0.028 0.3 0.48 1 -0.92 23 24
HIF1A/ARNT/Cbp/p300 0.087 0.3 -10000 0 -0.91 13 13
EPO 0.053 0.19 -10000 0 -0.92 2 2
CREBBP 0.021 0.078 -10000 0 -0.31 7 7
HIF1A/ARNT/Cbp/p300/HDAC7 0.12 0.32 -10000 0 -0.89 13 13
PFKFB3 0.015 0.29 0.48 1 -0.91 24 25
NT5E 0.015 0.3 0.48 1 -0.93 24 25
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.005 0.096 -10000 0 -0.41 23 23
PDGFRB 0.02 0.028 -10000 0 -0.56 1 1
SPHK1 0 0.054 -10000 0 -0.73 2 2
mol:S1P -0.004 0.053 -10000 0 -0.64 2 2
S1P1/S1P/Gi -0.049 0.16 -10000 0 -0.43 61 61
GNAO1 0.017 0.034 0.23 2 -0.56 1 3
PDGFB-D/PDGFRB/PLCgamma1 -0.032 0.15 0.25 3 -0.39 59 62
PLCG1 -0.051 0.15 -10000 0 -0.41 61 61
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.028 -10000 0 -0.56 1 1
GNAI2 0.017 0.016 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.017 0.031 -10000 0 -0.57 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.025 0.074 -10000 0 -0.35 23 23
S1P1/S1P -0.018 0.081 -10000 0 -0.31 21 21
negative regulation of cAMP metabolic process -0.048 0.16 -10000 0 -0.42 61 61
MAPK3 -0.072 0.21 -10000 0 -0.56 67 67
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.005 -10000 0 -10000 0 0
KDR -0.011 0.13 -10000 0 -0.56 24 24
PLCB2 -0.009 0.091 0.25 4 -0.31 14 18
RAC1 0.022 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.012 0.072 -10000 0 -0.33 9 9
receptor internalization -0.018 0.076 -10000 0 -0.29 21 21
PTGS2 -0.1 0.33 0.34 1 -0.96 56 57
Rac1/GTP -0.012 0.072 -10000 0 -0.32 11 11
RHOA 0.021 0.007 -10000 0 -10000 0 0
VEGFA 0.019 0.013 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.048 0.16 -10000 0 -0.42 61 61
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.012 0.061 -10000 0 -0.56 5 5
MAPK1 -0.064 0.2 -10000 0 -0.54 63 63
S1P1/S1P/PDGFB-D/PDGFRB -0.009 0.095 0.28 1 -0.33 21 22
ABCC1 0.019 0.017 0.24 1 -10000 0 1
Caspase cascade in apoptosis

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
TOP1 -0.026 0.16 0.28 1 -0.51 35 36
ACTA1 -0.036 0.15 0.26 2 -0.53 30 32
NUMA1 -0.029 0.16 0.28 1 -0.53 35 36
SPTAN1 -0.038 0.15 0.3 1 -0.54 29 30
LIMK1 -0.036 0.15 0.3 1 -0.52 30 31
BIRC3 0.015 0.065 -10000 0 -0.56 6 6
BIRC2 0.022 0.004 -10000 0 -10000 0 0
BAX 0.023 0.004 -10000 0 -10000 0 0
CASP10 -0.031 0.097 -10000 0 -0.45 22 22
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.023 0.003 -10000 0 -10000 0 0
PTK2 -0.026 0.15 0.26 1 -0.49 36 37
DIABLO 0.023 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.037 0.14 0.29 1 -0.53 29 30
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
GSN -0.039 0.15 0.29 1 -0.54 29 30
MADD 0.023 0.004 -10000 0 -10000 0 0
TFAP2A 0.082 0.19 -10000 0 -0.68 22 22
BID -0.008 0.051 -10000 0 -0.26 18 18
MAP3K1 -0.038 0.16 -10000 0 -0.56 36 36
TRADD 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.029 0.15 0.3 1 -0.55 27 28
CASP9 0.022 0.005 -10000 0 -10000 0 0
DNA repair 0.003 0.048 0.21 7 -0.17 2 9
neuron apoptosis -0.009 0.15 -10000 0 -0.75 16 16
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.036 0.17 0.29 1 -0.57 32 33
APAF1 0.023 0.002 -10000 0 -10000 0 0
CASP6 -0.035 0.22 -10000 0 -1 21 21
TRAF2 0.023 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.038 0.14 0.32 2 -0.52 29 31
CASP7 -0.004 0.066 0.32 5 -0.26 6 11
KRT18 0.008 0.047 -10000 0 -0.62 1 1
apoptosis -0.043 0.16 0.41 1 -0.56 34 35
DFFA -0.038 0.15 0.3 1 -0.53 30 31
DFFB -0.037 0.15 0.3 1 -0.53 30 31
PARP1 -0.003 0.048 0.17 2 -0.21 7 9
actin filament polymerization 0.031 0.14 0.49 29 -0.3 8 37
TNF 0.011 0.084 0.24 1 -0.56 10 11
CYCS -0.002 0.062 0.2 4 -0.25 16 20
SATB1 -0.036 0.2 -10000 0 -0.92 22 22
SLK -0.038 0.15 0.32 1 -0.53 30 31
p15 BID/BAX 0.006 0.066 0.2 3 -0.3 11 14
CASP2 0.006 0.053 0.2 2 -0.38 2 4
JNK cascade 0.038 0.16 0.56 36 -10000 0 36
CASP3 -0.038 0.16 0.32 1 -0.54 32 33
LMNB2 -0.005 0.13 0.24 2 -0.44 24 26
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CASP4 0.021 0.027 -10000 0 -0.56 1 1
Mammalian IAPs/DIABLO 0.052 0.045 -10000 0 -0.33 6 6
negative regulation of DNA binding 0.082 0.18 -10000 0 -0.67 22 22
stress fiber formation -0.037 0.14 0.31 1 -0.52 30 31
GZMB -0.034 0.12 -10000 0 -0.52 23 23
CASP1 0.008 0.041 -10000 0 -0.58 2 2
LMNB1 -0.026 0.19 0.24 1 -0.63 32 33
APP -0.009 0.15 -10000 0 -0.76 16 16
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.004 0.002 -10000 0 -10000 0 0
VIM -0.041 0.17 0.4 1 -0.54 38 39
LMNA 0.003 0.1 0.24 2 -0.43 15 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.01 0.057 -10000 0 -0.35 3 3
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.038 0.15 0.3 1 -0.53 30 31
APAF-1/Caspase 9 -0.007 0.13 -10000 0 -0.64 19 19
nuclear fragmentation during apoptosis -0.028 0.16 0.27 1 -0.52 35 36
CFL2 -0.033 0.14 0.31 8 -0.5 29 37
GAS2 -0.068 0.17 -10000 0 -0.43 67 67
positive regulation of apoptosis -0.01 0.15 0.25 2 -0.56 23 25
PRF1 -0.002 0.12 -10000 0 -0.56 20 20
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 -0.008 0.024 0.24 1 -10000 0 1
RFC1 -0.006 0.03 0.22 5 -10000 0 5
PRKDC -0.003 0.045 0.22 13 -10000 0 13
RIPK1 0.024 0.006 -10000 0 -10000 0 0
CASP7 -0.015 0.12 0.45 1 -0.61 17 18
FASLG/FAS/FADD/FAF1 -0.006 0.065 0.22 5 -0.29 18 23
MAP2K4 -0.021 0.15 0.29 6 -0.42 25 31
mol:ceramide -0.019 0.098 -10000 0 -0.38 20 20
GSN -0.008 0.024 0.24 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.089 -10000 0 -0.35 21 21
FAS 0.013 0.033 -10000 0 -0.57 1 1
BID -0.014 0.056 0.52 4 -10000 0 4
MAP3K1 0.01 0.14 0.32 9 -0.47 20 29
MAP3K7 0.017 0.015 -10000 0 -10000 0 0
RB1 -0.006 0.022 0.23 2 -10000 0 2
CFLAR 0.024 0.006 -10000 0 -10000 0 0
HGF/MET -0.038 0.16 0.25 1 -0.36 94 95
ARHGDIB 0 0.053 0.22 21 -0.19 4 25
FADD 0.013 0.018 -10000 0 -10000 0 0
actin filament polymerization 0.018 0.046 -10000 0 -0.24 1 1
NFKB1 -0.035 0.14 -10000 0 -0.67 16 16
MAPK8 -0.05 0.2 0.36 2 -0.44 78 80
DFFA -0.008 0.026 0.24 1 -10000 0 1
DNA fragmentation during apoptosis -0.015 0.046 0.23 3 -10000 0 3
FAS/FADD/MET 0.026 0.044 0.25 1 -0.36 3 4
CFLAR/RIP1 0.034 0.011 -10000 0 -10000 0 0
FAIM3 0.019 0.054 0.24 1 -0.56 4 5
FAF1 0.014 0.022 -10000 0 -10000 0 0
PARP1 -0.006 0.036 0.22 6 -10000 0 6
DFFB -0.007 0.03 0.23 3 -10000 0 3
CHUK -0.031 0.13 -10000 0 -0.61 16 16
FASLG -0.009 0.12 -10000 0 -0.56 19 19
FAS/FADD 0.018 0.033 -10000 0 -0.44 1 1
HGF -0.092 0.23 -10000 0 -0.56 94 94
LMNA -0.011 0.044 0.19 8 -10000 0 8
CASP6 -0.006 0.026 0.23 3 -10000 0 3
CASP10 0.013 0.033 -10000 0 -0.56 1 1
CASP3 -0.003 0.017 0.25 2 -10000 0 2
PTPN13 0.017 0.053 -10000 0 -0.56 4 4
CASP8 -0.015 0.046 0.46 4 -10000 0 4
IL6 -0.2 0.5 -10000 0 -1.2 86 86
MET 0.021 0.041 0.38 1 -0.56 2 3
ICAD/CAD -0.009 0.027 0.2 3 -10000 0 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.019 0.099 -10000 0 -0.38 20 20
activation of caspase activity by cytochrome c -0.014 0.056 0.52 4 -10000 0 4
PAK2 0.061 0.11 0.22 146 -10000 0 146
BCL2 0.023 0.011 0.24 1 -10000 0 1
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.041 0.094 -10000 0 -0.27 22 22
NT3 (dimer)/TRKC -0.095 0.2 -10000 0 -0.41 138 138
NT3 (dimer)/TRKB 0.042 0.13 0.32 2 -0.38 30 32
SHC/Grb2/SOS1/GAB1/PI3K 0.009 0.023 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
BDNF -0.049 0.19 -10000 0 -0.56 59 59
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
DYNLT1 0.023 0.003 -10000 0 -10000 0 0
NTRK1 0.014 0.065 -10000 0 -0.56 6 6
NTRK2 0.023 0.16 0.24 76 -0.56 28 104
NTRK3 -0.14 0.26 0.24 2 -0.56 136 138
NT-4/5 (dimer)/TRKB 0.045 0.13 0.28 4 -0.38 33 37
neuron apoptosis 0.043 0.18 0.42 52 -10000 0 52
SHC 2-3/Grb2 -0.047 0.19 -10000 0 -0.46 52 52
SHC1 0.022 0.005 -10000 0 -10000 0 0
SHC2 0.005 0.12 -10000 0 -0.42 19 19
SHC3 -0.075 0.23 -10000 0 -0.53 84 84
STAT3 (dimer) 0.022 0.044 -10000 0 -0.36 6 6
NT3 (dimer)/TRKA 0.043 0.07 0.25 1 -0.36 9 10
RIN/GDP -0.028 0.093 0.25 5 -0.26 10 15
GIPC1 0.022 0.005 -10000 0 -10000 0 0
KRAS 0.021 0.006 -10000 0 -10000 0 0
DNAJA3 0.03 0.059 0.23 1 -0.25 5 6
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.001 0.093 0.37 1 -0.81 6 7
MAGED1 0.023 0.004 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.013 0.075 -10000 0 -0.56 8 8
SHC/GRB2/SOS1 0.042 0.014 -10000 0 -10000 0 0
GRB2 0.023 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.017 0.1 0.25 1 -0.35 31 32
TRKA/NEDD4-2 0.026 0.05 -10000 0 -0.41 6 6
ELMO1 0.013 0.075 -10000 0 -0.56 8 8
RhoG/GTP/ELMO1/DOCK1 0.022 0.05 -10000 0 -0.35 8 8
NGF 0.013 0.078 0.28 3 -0.56 8 11
HRAS 0.022 0.004 -10000 0 -10000 0 0
DOCK1 0.022 0.005 -10000 0 -10000 0 0
GAB2 0.008 0.091 -10000 0 -0.56 12 12
RIT2 -0.015 0.01 -10000 0 -10000 0 0
RIT1 0.022 0.005 -10000 0 -10000 0 0
FRS2 0.022 0.005 -10000 0 -10000 0 0
DNM1 0.024 0.014 0.24 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.036 0.067 -10000 0 -0.26 9 9
mol:GDP -0.043 0.13 0.31 5 -0.36 19 24
NGF (dimer) 0.013 0.078 0.28 3 -0.56 8 11
RhoG/GDP 0.009 0.056 -10000 0 -0.36 10 10
RIT1/GDP -0.024 0.091 0.26 5 -0.27 8 13
TIAM1 0.023 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.005 0.18 0.25 1 -0.4 74 75
KIDINS220/CRKL/C3G 0.032 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.03 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2 0.043 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.051 0.022 -10000 0 -10000 0 0
RIT1/GTP 0.016 0.004 -10000 0 -10000 0 0
NT3 (dimer) 0.016 0.061 0.24 2 -0.56 5 7
RAP1/GDP -0.026 0.074 -10000 0 -0.24 7 7
KIDINS220/CRKL 0.022 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.049 0.19 -10000 0 -0.56 59 59
ubiquitin-dependent protein catabolic process 0.03 0.07 0.25 1 -0.35 14 15
Schwann cell development -0.04 0.031 -10000 0 -10000 0 0
EHD4 0.023 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.053 0.02 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.012 0.053 -10000 0 -0.33 3 3
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.098 0.21 -10000 0 -0.36 164 164
ABL1 0.023 0.003 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.033 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.015 0.093 -10000 0 -0.38 11 11
STAT3 0.022 0.044 -10000 0 -0.36 6 6
axon guidance -0.1 0.2 -10000 0 -0.34 164 164
MAPK3 -0.027 0.085 0.18 16 -0.32 30 46
MAPK1 -0.027 0.083 0.18 14 -0.32 29 43
CDC42/GDP -0.023 0.095 0.26 5 -0.28 7 12
NTF3 0.016 0.061 0.24 2 -0.56 5 7
NTF4 0.013 0.075 -10000 0 -0.56 8 8
NGF (dimer)/TRKA/FAIM 0.026 0.067 0.25 1 -0.36 12 13
PI3K 0.017 0.017 -10000 0 -10000 0 0
FRS3 0.022 0.004 -10000 0 -10000 0 0
FAIM 0.019 0.009 -10000 0 -10000 0 0
GAB1 0.022 0.006 -10000 0 -10000 0 0
RASGRF1 -0.13 0.15 -10000 0 -0.3 134 134
SOS1 0.023 0.003 -10000 0 -10000 0 0
MCF2L -0.11 0.16 0.25 1 -0.36 128 129
RGS19 0.023 0.004 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.023 0.081 0.37 1 -0.44 3 4
Rac1/GDP -0.024 0.093 0.26 4 -0.26 10 14
NGF (dimer)/TRKA/GRIT 0.018 0.066 0.24 1 -0.35 14 15
neuron projection morphogenesis 0.034 0.13 -10000 0 -0.78 8 8
NGF (dimer)/TRKA/NEDD4-2 0.031 0.07 0.25 1 -0.36 14 15
MAP2K1 0 0.053 0.35 1 -10000 0 1
NGFR 0.041 0.062 0.24 40 -10000 0 40
NGF (dimer)/TRKA/GIPC/GAIP 0.012 0.05 -10000 0 -0.28 12 12
RAS family/GTP/PI3K 0.009 0.01 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.061 0.023 -10000 0 -10000 0 0
NRAS 0.022 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.033 0.008 -10000 0 -10000 0 0
PRKCI 0.013 0.011 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
MAPKKK cascade -0.028 0.14 -10000 0 -0.57 24 24
RASA1 0.021 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.027 0.05 -10000 0 -0.41 6 6
SQSTM1 0.021 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.007 0.17 0.25 1 -0.38 70 71
NGF (dimer)/TRKA/p62/Atypical PKCs 0.026 0.061 -10000 0 -0.31 9 9
MATK 0 0.11 -10000 0 -0.56 18 18
NEDD4L 0.022 0.005 -10000 0 -10000 0 0
RAS family/GDP -0.038 0.058 -10000 0 -0.24 2 2
NGF (dimer)/TRKA 0.005 0.049 0.19 1 -0.26 8 9
Rac1/GTP -0.11 0.1 -10000 0 -0.27 67 67
FRS2 family/SHP2/CRK family 0.058 0.026 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.023 0.002 -10000 0 -10000 0 0
GNAT1/GTP 0.016 0.021 0.16 7 -0.19 1 8
Metarhodopsin II/Arrestin 0.023 0.013 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.021 0.053 -10000 0 -0.33 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.008 0.036 0.24 7 -0.29 1 8
GRK1 -0.004 0.031 0.38 2 -10000 0 2
CNG Channel 0.027 0.08 -10000 0 -0.29 23 23
mol:Na + 0.058 0.059 -10000 0 -10000 0 0
mol:ADP -0.004 0.031 0.38 2 -10000 0 2
RGS9-1/Gbeta5/R9AP -0.008 0.14 -10000 0 -0.36 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.075 0.07 0.26 21 -10000 0 21
CNGB1 0.041 0.063 0.24 43 -10000 0 43
RDH5 0.021 0.038 -10000 0 -0.56 2 2
SAG -0.013 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0 0.089 0.35 13 -10000 0 13
Na + (4 Units) 0.044 0.044 -10000 0 -10000 0 0
RGS9 -0.041 0.18 -10000 0 -0.56 52 52
GNB1/GNGT1 0.078 0.079 0.26 18 -0.41 1 19
GNAT1/GDP 0.001 0.12 -10000 0 -0.32 58 58
GUCY2D 0.02 0.009 -10000 0 -10000 0 0
GNGT1 0.094 0.11 0.26 148 -10000 0 148
GUCY2F -0.005 0.019 -10000 0 -10000 0 0
GNB5 0.023 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0 0.07 -10000 0 -0.3 23 23
mol:11-cis-retinal 0.02 0.038 -10000 0 -0.56 2 2
mol:cGMP 0.063 0.063 0.28 3 -10000 0 3
GNB1 0.021 0.027 -10000 0 -0.56 1 1
Rhodopsin 0.027 0.032 -10000 0 -0.42 2 2
SLC24A1 0.023 0.002 -10000 0 -10000 0 0
CNGA1 0.024 0.025 0.24 6 -10000 0 6
Metarhodopsin II 0.022 0.017 0.22 2 -10000 0 2
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.073 0.064 -10000 0 -10000 0 0
RGS9BP 0.009 0.083 -10000 0 -0.56 10 10
Metarhodopsin II/Transducin 0.024 0.046 0.17 14 -0.27 1 15
GCAP Family/Ca ++ 0.064 0.06 -10000 0 -10000 0 0
PDE6A/B 0.016 0.081 -10000 0 -0.38 17 17
mol:Pi -0.008 0.13 -10000 0 -0.36 58 58
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.072 0.07 0.24 18 -0.32 1 19
PDE6B 0.017 0.054 0.24 1 -0.56 4 5
PDE6A 0.008 0.088 0.24 2 -0.56 11 13
PDE6G 0.013 0.075 -10000 0 -0.56 8 8
RHO 0 0.025 0.24 2 -10000 0 2
PDE6 -0.003 0.14 -10000 0 -0.33 69 69
GUCA1A 0.077 0.099 0.24 126 -0.29 2 128
GC2/GCAP Family 0.072 0.063 -10000 0 -10000 0 0
GUCA1C -0.016 0.006 -10000 0 -10000 0 0
GUCA1B 0.022 0.005 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.025 0.096 -10000 0 -0.35 26 26
MAP4K1 0.016 0.053 -10000 0 -0.56 4 4
MAP3K8 0.021 0.027 -10000 0 -0.56 1 1
PRKCB -0.005 0.12 -10000 0 -0.56 23 23
DBNL 0.022 0.005 -10000 0 -10000 0 0
CRKL 0.022 0.005 -10000 0 -10000 0 0
MAP3K1 0 0.081 -10000 0 -0.49 7 7
JUN -0.035 0.2 -10000 0 -0.66 39 39
MAP3K7 -0.007 0.09 -10000 0 -0.46 9 9
GRAP2 -0.006 0.12 -10000 0 -0.56 23 23
CRK 0.022 0.006 -10000 0 -10000 0 0
MAP2K4 0.003 0.096 0.25 5 -0.51 9 14
LAT 0.023 0.003 -10000 0 -10000 0 0
LCP2 0.014 0.065 -10000 0 -0.56 6 6
MAPK8 -0.034 0.21 -10000 0 -0.7 40 40
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.002 0.094 -10000 0 -0.34 26 26
LAT/GRAP2/SLP76/HPK1/HIP-55 0.032 0.094 -10000 0 -0.33 25 25
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.027 0.047 -10000 0 -0.41 5 5
Necdin/E2F1 0.027 0.047 -10000 0 -0.41 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.059 0.076 -10000 0 -0.31 13 13
NGF (dimer)/p75(NTR)/BEX1 0.016 0.14 0.29 5 -0.36 48 53
NT-4/5 (dimer)/p75(NTR) 0.038 0.073 0.26 2 -0.41 8 10
IKBKB 0.022 0.018 0.38 1 -10000 0 1
AKT1 0.053 0.1 0.31 4 -0.32 6 10
IKBKG 0.023 0.004 -10000 0 -10000 0 0
BDNF -0.049 0.19 -10000 0 -0.56 59 59
MGDIs/NGR/p75(NTR)/LINGO1 0.065 0.061 0.32 7 -0.36 1 8
FURIN 0.023 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.001 0.15 0.25 2 -0.36 63 65
LINGO1 0.043 0.063 0.24 43 -10000 0 43
Sortilin/TRAF6/NRIF 0.022 0.033 -10000 0 -0.29 4 4
proBDNF (dimer) -0.049 0.19 -10000 0 -0.56 59 59
NTRK1 0.014 0.065 -10000 0 -0.56 6 6
RTN4R 0.021 0.029 0.24 1 -0.56 1 2
neuron apoptosis -0.047 0.15 0.3 1 -0.53 18 19
IRAK1 0.023 0.004 -10000 0 -10000 0 0
SHC1 -0.019 0.051 0.23 3 -0.36 8 11
ARHGDIA 0.022 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.005 -10000 0 -10000 0 0
Gamma Secretase 0.056 0.028 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.054 0.077 -10000 0 -0.33 13 13
MAGEH1 0.023 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.05 0.088 0.25 3 -0.35 17 20
Mammalian IAPs/DIABLO 0.052 0.045 -10000 0 -0.33 6 6
proNGF (dimer) 0.013 0.078 0.28 3 -0.56 8 11
MAGED1 0.023 0.004 -10000 0 -10000 0 0
APP 0.022 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.013 0.075 -10000 0 -0.56 8 8
ZNF274 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.017 0.051 0.2 3 -0.31 8 11
NGF 0.013 0.078 0.28 3 -0.56 8 11
cell cycle arrest -0.016 0.068 0.21 7 -0.3 13 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.015 0.048 -10000 0 -0.26 7 7
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.049 0.066 0.25 2 -0.36 8 10
NCSTN 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0.047 0.068 0.25 3 -0.36 8 11
PSENEN 0.021 0.007 -10000 0 -10000 0 0
mol:ceramide -0.022 0.059 0.2 3 -0.33 13 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.01 0.036 0.24 1 -10000 0 1
p75(NTR)/beta APP 0.044 0.042 0.26 2 -10000 0 2
BEX1 -0.02 0.17 0.24 21 -0.56 41 62
mol:GDP -0.015 0.05 0.22 3 -0.36 8 11
NGF (dimer) 0.043 0.082 -10000 0 -0.35 16 16
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.074 0.06 0.32 7 -0.33 1 8
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
RAC1/GTP 0.041 0.06 0.22 3 -0.31 8 11
MYD88 0.021 0.007 -10000 0 -10000 0 0
CHUK 0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.048 0.068 0.25 3 -0.36 8 11
RHOB 0.021 0.027 -10000 0 -0.56 1 1
RHOA 0.021 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.032 0.009 -10000 0 -10000 0 0
NT3 (dimer) 0.016 0.061 0.24 2 -0.56 5 7
TP53 -0.049 0.11 0.33 2 -0.3 63 65
PRDM4 -0.021 0.059 0.2 3 -0.33 13 16
BDNF (dimer) 0.061 0.18 0.31 14 -0.36 64 78
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
SORT1 0.016 0.059 -10000 0 -0.56 5 5
activation of caspase activity 0.053 0.073 -10000 0 -0.31 13 13
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.054 0.077 0.25 3 -0.33 13 16
RHOC 0.022 0.005 -10000 0 -10000 0 0
XIAP 0.023 0.003 -10000 0 -10000 0 0
MAPK10 -0.032 0.1 0.34 4 -0.43 7 11
DIABLO 0.023 0.002 -10000 0 -10000 0 0
SMPD2 -0.022 0.059 0.2 3 -0.33 13 16
APH1B 0.023 0.002 -10000 0 -10000 0 0
APH1A 0.022 0.006 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.044 0.08 0.25 3 -0.36 13 16
PSEN1 0.022 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.038 0.062 0.26 1 -0.41 5 6
MAPK8 -0.029 0.098 0.31 4 -0.42 4 8
MAPK9 -0.03 0.096 0.35 2 -0.39 6 8
APAF1 0.023 0.002 -10000 0 -10000 0 0
NTF3 0.016 0.061 0.24 2 -0.56 5 7
NTF4 0.013 0.075 -10000 0 -0.56 8 8
NDN 0.016 0.059 -10000 0 -0.56 5 5
RAC1/GDP 0.017 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.052 0.061 -10000 0 -0.3 9 9
p75 CTF/Sortilin/TRAF6/NRIF 0.049 0.041 -10000 0 -0.33 4 4
RhoA-B-C/GTP 0.047 0.067 0.25 3 -0.36 8 11
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.019 0.14 -10000 0 -0.32 63 63
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.012 0.14 0.25 2 -0.33 63 65
PRKACB 0.023 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.023 0.15 -10000 0 -0.4 61 61
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.015 0.065 -10000 0 -0.56 6 6
BIRC2 0.022 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.004 0.074 0.23 3 -0.32 13 16
BAD -0.031 0.1 0.3 5 -0.4 5 10
RIPK2 0.022 0.005 -10000 0 -10000 0 0
NGFR 0.041 0.062 0.24 40 -10000 0 40
CYCS -0.021 0.057 -10000 0 -0.31 12 12
ADAM17 0.022 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.056 0.068 0.25 3 -0.34 8 11
BCL2L11 -0.031 0.1 0.31 4 -0.4 5 9
BDNF (dimer)/p75(NTR) -0.012 0.16 0.26 2 -0.42 59 61
PI3K 0.03 0.064 0.25 1 -0.33 6 7
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.054 0.077 -10000 0 -0.33 13 13
NDNL2 0.023 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
PRKCI 0.013 0.011 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.037 0.075 0.26 3 -0.42 8 11
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.054 0.077 0.25 3 -0.33 13 16
TRAF6 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
PLG -0.005 0.026 0.24 3 -10000 0 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.031 0.12 0.21 2 -0.32 69 71
SQSTM1 0.021 0.007 -10000 0 -10000 0 0
NGFRAP1 0.023 0.003 -10000 0 -10000 0 0
CASP3 -0.033 0.099 0.3 4 -0.35 9 13
E2F1 0.022 0.005 -10000 0 -10000 0 0
CASP9 0.022 0.005 -10000 0 -10000 0 0
IKK complex 0.046 0.081 -10000 0 -0.34 7 7
NGF (dimer)/TRKA 0.019 0.077 0.26 1 -0.41 14 15
MMP7 0.02 0.091 0.24 20 -0.56 9 29
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.06 0.076 -10000 0 -0.32 13 13
MMP3 0.15 0.12 0.24 284 -0.29 4 288
APAF-1/Caspase 9 -0.035 0.05 -10000 0 -0.36 3 3
PDGFR-alpha signaling pathway

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
PDGFRA 0.011 0.06 0.36 1 -0.57 4 5
PDGF/PDGFRA/CRKL 0.021 0.043 0.25 1 -0.35 4 5
positive regulation of JUN kinase activity 0.044 0.04 -10000 0 -0.31 4 4
CRKL 0.022 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.048 0.16 0.25 1 -0.4 76 77
AP1 -0.11 0.31 0.3 1 -0.96 54 55
mol:IP3 -0.014 0.037 0.3 1 -0.41 2 3
PLCG1 -0.014 0.037 0.3 1 -0.42 2 3
PDGF/PDGFRA/alphaV Integrin 0.021 0.047 0.25 1 -0.41 4 5
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.037 0.3 1 -0.41 2 3
CAV3 -0.089 0.19 -10000 0 -0.56 69 69
CAV1 -0.13 0.26 -10000 0 -0.56 125 125
SHC/Grb2/SOS1 0.046 0.041 -10000 0 -0.31 4 4
PDGF/PDGFRA/Shf 0.022 0.046 0.25 1 -0.4 4 5
FOS -0.11 0.3 0.3 1 -0.94 54 55
JUN -0.022 0.025 -10000 0 -10000 0 0
oligodendrocyte development 0.021 0.046 0.25 1 -0.41 4 5
GRB2 0.023 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:DAG -0.014 0.037 0.3 1 -0.41 2 3
PDGF/PDGFRA 0.011 0.06 0.36 1 -0.57 4 5
actin cytoskeleton reorganization 0.021 0.046 0.25 1 -0.4 4 5
SRF -0.005 0.014 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.017 0.04 0.24 1 -0.35 3 4
PDGF/PDGFRA/Crk/C3G 0.031 0.043 0.24 1 -0.32 4 5
JAK1 -0.012 0.04 0.28 1 -0.4 4 5
ELK1/SRF -0.01 0.051 0.3 1 -0.3 3 4
SHB 0.021 0.007 -10000 0 -10000 0 0
SHF 0.023 0.003 -10000 0 -10000 0 0
CSNK2A1 0.024 0.02 -10000 0 -10000 0 0
GO:0007205 -0.012 0.041 0.3 1 -0.4 3 4
SOS1 0.023 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.044 0.04 -10000 0 -0.31 4 4
PDGF/PDGFRA/SHB 0.021 0.046 0.25 1 -0.4 4 5
PDGF/PDGFRA/Caveolin-1 -0.094 0.2 0.25 1 -0.42 128 129
ITGAV 0.023 0.003 -10000 0 -10000 0 0
ELK1 -0.017 0.044 0.23 2 -0.36 3 5
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.021 0.045 0.25 1 -0.39 4 5
JAK-STAT cascade -0.012 0.04 0.28 1 -0.4 4 5
cell proliferation 0.022 0.046 0.25 1 -0.4 4 5
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 -0.017 0.15 -10000 0 -0.38 52 52
MAP3K8 0.017 0.029 -10000 0 -0.56 1 1
FOS -0.012 0.12 -10000 0 -0.5 13 13
PRKCA 0.016 0.041 -10000 0 -0.56 2 2
PTPN7 0.017 0.036 0.38 1 -0.56 1 2
HRAS 0.022 0.004 -10000 0 -10000 0 0
PRKCB -0.01 0.12 -10000 0 -0.56 23 23
NRAS 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.025 -10000 0 -10000 0 0
MAPK3 0.002 0.095 -10000 0 -0.6 8 8
MAP2K1 -0.015 0.12 -10000 0 -0.45 27 27
ELK1 0.016 0.02 -10000 0 -10000 0 0
BRAF -0.012 0.1 -10000 0 -0.43 24 24
mol:GTP -0.001 0.002 -10000 0 -0.005 54 54
MAPK1 0.002 0.089 -10000 0 -0.47 9 9
RAF1 -0.015 0.11 -10000 0 -0.48 24 24
KRAS 0.021 0.006 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
Jak2/Leptin Receptor -0.018 0.15 -10000 0 -0.44 36 36
PTP1B/AKT1 0 0.087 -10000 0 -0.32 19 19
FYN 0.022 0.027 -10000 0 -0.56 1 1
p210 bcr-abl/PTP1B -0.011 0.091 0.2 1 -0.32 23 24
EGFR 0.02 0.084 0.35 11 -0.57 6 17
EGF/EGFR 0.004 0.1 0.24 9 -0.34 24 33
CSF1 0.017 0.053 -10000 0 -0.56 4 4
AKT1 0.022 0.007 -10000 0 -10000 0 0
INSR 0.022 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.005 0.097 0.24 6 -0.33 19 25
Insulin Receptor/Insulin 0.013 0.087 -10000 0 -0.34 11 11
HCK 0.018 0.046 -10000 0 -0.56 3 3
CRK 0.022 0.006 -10000 0 -10000 0 0
TYK2 -0.012 0.087 0.2 2 -0.32 19 21
EGF 0.015 0.073 0.24 3 -0.57 7 10
YES1 0.022 0.006 -10000 0 -10000 0 0
CAV1 -0.048 0.13 0.24 3 -0.39 37 40
TXN 0.023 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.011 0.091 -10000 0 -0.34 14 14
cell migration 0.011 0.091 0.32 23 -0.2 1 24
STAT3 0.023 0.003 -10000 0 -10000 0 0
PRLR 0.018 0.1 0.29 20 -0.56 10 30
ITGA2B 0.006 0.098 -10000 0 -0.56 14 14
CSF1R 0.014 0.065 -10000 0 -0.56 6 6
Prolactin Receptor/Prolactin 0.025 0.079 0.28 8 -0.42 10 18
FGR -0.011 0.13 -10000 0 -0.56 27 27
PTP1B/p130 Cas 0.003 0.087 -10000 0 -0.32 18 18
Crk/p130 Cas 0.012 0.089 -10000 0 -0.34 12 12
DOK1 -0.011 0.1 -10000 0 -0.35 29 29
JAK2 -0.016 0.14 0.23 1 -0.43 41 42
Jak2/Leptin Receptor/Leptin 0.03 0.12 0.28 1 -0.41 13 14
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
PTPN1 -0.011 0.091 0.2 1 -0.32 24 25
LYN 0.02 0.038 -10000 0 -0.56 2 2
CDH2 0.034 0.061 0.25 27 -0.56 1 28
SRC 0.013 0.073 -10000 0 -0.62 5 5
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
CAT1/PTP1B -0.02 0.14 0.26 3 -0.43 35 38
CAPN1 0.023 0.003 -10000 0 -10000 0 0
CSK 0.023 0.002 -10000 0 -10000 0 0
PI3K 0.01 0.067 -10000 0 -0.34 6 6
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.11 0.26 1 -0.38 13 14
negative regulation of transcription -0.016 0.14 0.23 1 -0.43 41 42
FCGR2A 0.011 0.079 -10000 0 -0.56 9 9
FER 0.021 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.013 0.094 -10000 0 -0.42 22 22
BLK 0.013 0.091 0.24 12 -0.56 10 22
Insulin Receptor/Insulin/Shc 0.04 0.014 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
LEPR -0.01 0.13 -10000 0 -0.56 27 27
BCAR1 0.022 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.022 0.004 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.016 0.14 0.27 1 -0.44 29 30
PRL 0.005 0.036 0.24 8 -10000 0 8
SOCS3 0.015 0.11 -10000 0 -1.2 4 4
SPRY2 0.018 0.047 -10000 0 -0.56 3 3
Insulin Receptor/Insulin/IRS1 0.04 0.012 -10000 0 -10000 0 0
CSF1/CSF1R 0.005 0.1 -10000 0 -0.35 22 22
Ras protein signal transduction 0.011 0.1 0.58 13 -10000 0 13
IRS1 0.023 0.004 -10000 0 -10000 0 0
INS 0.011 0.015 -10000 0 -10000 0 0
LEP 0.057 0.085 0.24 83 -0.29 1 84
STAT5B -0.008 0.11 -10000 0 -0.37 29 29
STAT5A -0.008 0.11 -10000 0 -0.38 28 28
GRB2 0.023 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.003 0.088 -10000 0 -0.33 18 18
CSN2 0.017 0.066 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
LAT 0.002 0.1 -10000 0 -0.5 16 16
YBX1 0.026 0.005 -10000 0 -10000 0 0
LCK 0.021 0.027 -10000 0 -0.56 1 1
SHC1 0.022 0.005 -10000 0 -10000 0 0
NOX4 0.023 0.017 0.37 1 -10000 0 1
BCR signaling pathway

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
JUN -0.011 0.11 -10000 0 -0.4 21 21
IKBKB 0.025 0.078 0.29 6 -0.31 5 11
AKT1 0.047 0.11 0.24 52 -0.24 9 61
IKBKG 0.023 0.069 0.25 4 -0.31 5 9
CALM1 -0.005 0.094 0.26 1 -0.38 17 18
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
MAP3K1 -0.007 0.14 -10000 0 -0.53 20 20
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.096 0.28 1 -0.4 17 18
DOK1 0.023 0.004 -10000 0 -10000 0 0
AP-1 -0.017 0.078 0.21 1 -0.25 12 13
LYN 0.02 0.038 -10000 0 -0.56 2 2
BLNK 0.021 0.027 -10000 0 -0.56 1 1
SHC1 0.022 0.005 -10000 0 -10000 0 0
BCR complex 0.022 0.086 0.34 1 -0.42 15 16
CD22 -0.039 0.16 0.23 2 -0.46 48 50
CAMK2G -0.006 0.09 0.31 2 -0.38 14 16
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
SHC/GRB2/SOS1 0.016 0.06 -10000 0 -0.32 12 12
GO:0007205 -0.006 0.1 0.28 1 -0.41 18 19
SYK 0.022 0.004 -10000 0 -10000 0 0
ELK1 -0.009 0.098 0.25 2 -0.39 18 20
NFATC1 -0.015 0.1 0.28 2 -0.46 14 16
B-cell antigen/BCR complex 0.022 0.086 0.34 1 -0.42 15 16
PAG1/CSK 0.028 0.046 -10000 0 -0.41 5 5
NFKBIB 0.022 0.044 0.15 5 -0.12 19 24
HRAS -0.007 0.093 0.24 2 -0.36 18 20
NFKBIA 0.022 0.043 0.15 5 -0.12 20 25
NF-kappa-B/RelA/I kappa B beta 0.025 0.038 0.16 4 -10000 0 4
RasGAP/Csk 0.046 0.084 0.31 1 -0.35 16 17
mol:GDP -0.009 0.1 0.27 1 -0.39 20 21
PTEN 0.021 0.006 -10000 0 -10000 0 0
CD79B 0.019 0.047 0.24 1 -0.56 3 4
NF-kappa-B/RelA/I kappa B alpha 0.025 0.037 0.16 4 -10000 0 4
GRB2 0.023 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.008 0.14 0.33 1 -0.51 23 24
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 -0.005 0.095 0.28 1 -0.41 16 17
CSK 0.023 0.002 -10000 0 -10000 0 0
FOS -0.036 0.12 0.33 2 -0.4 20 22
CHUK 0.013 0.086 0.26 3 -0.32 12 15
IBTK 0.023 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.014 0.093 -10000 0 -0.39 12 12
PTPN6 -0.038 0.15 0.25 1 -0.44 45 46
RELA 0.023 0.002 -10000 0 -10000 0 0
BCL2A1 0.017 0.032 0.17 2 -0.12 3 5
VAV2 -0.013 0.13 0.25 1 -0.6 15 16
ubiquitin-dependent protein catabolic process 0.023 0.044 0.15 5 -0.12 19 24
BTK -0.088 0.33 -10000 0 -1.1 46 46
CD19 -0.018 0.12 0.26 2 -0.52 18 20
MAP4K1 0.016 0.053 -10000 0 -0.56 4 4
CD72 0.021 0.012 0.24 1 -10000 0 1
PAG1 0.016 0.059 -10000 0 -0.56 5 5
MAPK14 -0.005 0.12 0.23 1 -0.45 20 21
SH3BP5 0.015 0.059 -10000 0 -0.56 5 5
PIK3AP1 -0.003 0.11 0.3 1 -0.48 17 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.009 0.14 -10000 0 -0.55 23 23
RAF1 -0.008 0.085 0.23 2 -0.35 15 17
RasGAP/p62DOK/SHIP 0.045 0.084 0.28 1 -0.36 15 16
CD79A 0.012 0.1 0.24 13 -0.56 13 26
re-entry into mitotic cell cycle -0.017 0.078 0.21 1 -0.25 12 13
RASA1 0.021 0.006 -10000 0 -10000 0 0
MAPK3 -0.01 0.074 0.24 1 -0.33 10 11
MAPK1 -0.003 0.08 0.26 4 -0.34 8 12
CD72/SHP1 -0.006 0.15 0.29 5 -0.54 23 28
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.004 0.12 -10000 0 -0.45 19 19
actin cytoskeleton organization -0.009 0.11 0.29 1 -0.54 13 14
NF-kappa-B/RelA 0.051 0.074 0.27 5 -0.2 3 8
Calcineurin 0.016 0.09 -10000 0 -0.38 11 11
PI3K -0.017 0.091 -10000 0 -0.41 17 17
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.003 0.092 0.26 3 -0.42 14 17
SOS1 0.023 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.013 0.19 -10000 0 -0.68 29 29
DAPP1 -0.029 0.2 -10000 0 -0.77 28 28
cytokine secretion -0.013 0.096 0.25 3 -0.43 14 17
mol:DAG -0.005 0.095 0.28 1 -0.41 16 17
PLCG2 0.022 0.005 -10000 0 -10000 0 0
MAP2K1 -0.01 0.081 0.25 1 -0.34 13 14
B-cell antigen/BCR complex/FcgammaRIIB 0.03 0.09 0.32 1 -0.41 16 17
mol:PI-3-4-5-P3 0.003 0.084 0.24 1 -0.31 13 14
ETS1 -0.013 0.097 0.27 3 -0.37 20 23
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.048 0.083 0.31 1 -0.35 15 16
B-cell antigen/BCR complex/LYN -0.011 0.12 0.28 2 -0.4 34 36
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.004 -10000 0 -10000 0 0
RAC1 -0.011 0.12 -10000 0 -0.58 13 13
B-cell antigen/BCR complex/LYN/SYK 0.013 0.16 0.34 2 -0.53 25 27
CARD11 -0.007 0.1 0.26 2 -0.42 16 18
FCGR2B 0.015 0.065 -10000 0 -0.56 6 6
PPP3CA 0.022 0.005 -10000 0 -10000 0 0
BCL10 0.022 0.004 -10000 0 -10000 0 0
IKK complex 0.026 0.049 0.16 23 -0.13 4 27
PTPRC -0.013 0.14 -10000 0 -0.56 29 29
PDPK1 0.029 0.091 0.22 44 -0.24 7 51
PPP3CB 0.022 0.005 -10000 0 -10000 0 0
PPP3CC 0.021 0.007 -10000 0 -10000 0 0
POU2F2 0.02 0.026 0.16 2 -10000 0 2
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
CDC42/GTP -0.008 0.097 -10000 0 -0.29 33 33
PLCG1 -0.013 0.085 -10000 0 -0.3 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
G12/G13 0.033 0.008 -10000 0 -10000 0 0
cell migration -0.008 0.095 -10000 0 -0.28 33 33
S1PR5 0.024 0.036 0.24 6 -0.56 1 7
S1PR4 -0.023 0.16 -10000 0 -0.56 37 37
MAPK3 -0.012 0.084 -10000 0 -0.29 29 29
MAPK1 -0.011 0.08 -10000 0 -0.3 26 26
S1P/S1P5/Gi 0.017 0.037 -10000 0 -0.23 5 5
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
CDC42/GDP 0.017 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.03 0.024 -10000 0 -0.35 1 1
RHOA -0.029 0.083 0.18 13 -0.3 35 48
S1P/S1P4/Gi -0.006 0.089 -10000 0 -0.3 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
S1P/S1P4/G12/G13 0.012 0.097 -10000 0 -0.32 35 35
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.052 0.19 -10000 0 -0.56 61 61
GNB1/GNG2 0.017 0.094 0.26 1 -0.36 6 7
mol:DAG -0.004 0.077 0.22 2 -0.37 4 6
PLCG1 -0.004 0.078 0.22 2 -0.38 4 6
YES1 -0.004 0.07 0.27 2 -0.34 6 8
FZD3 0.021 0.007 -10000 0 -10000 0 0
FZD6 0.022 0.005 -10000 0 -10000 0 0
G protein 0.013 0.09 -10000 0 -0.39 4 4
MAP3K7 -0.027 0.095 0.19 2 -0.4 13 15
mol:Ca2+ -0.003 0.075 0.22 2 -0.36 4 6
mol:IP3 -0.004 0.077 0.22 2 -0.37 4 6
NLK 0.005 0.073 -10000 0 -0.79 4 4
GNB1 0.021 0.027 -10000 0 -0.56 1 1
CAMK2A -0.02 0.1 0.2 2 -0.43 14 16
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.01 0.075 0.28 1 -0.29 19 20
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
GNAS -0.003 0.071 0.25 3 -0.34 6 9
GO:0007205 -0.011 0.074 0.21 2 -0.38 4 6
WNT6 0.056 0.084 0.24 80 -0.29 1 81
WNT4 0.019 0.057 0.24 4 -0.56 4 8
NFAT1/CK1 alpha -0.015 0.14 0.28 1 -0.42 21 22
GNG2 0.016 0.059 -10000 0 -0.56 5 5
WNT5A 0.024 0.032 0.24 8 -0.29 1 9
WNT11 0.007 0.11 0.25 10 -0.56 17 27
CDC42 -0.004 0.066 0.25 2 -0.36 4 6
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.021 0.033 -10000 0 -10000 0 0
BIRC5 0.21 0.084 0.24 406 -0.29 1 407
NFKBIA -0.022 0.026 0.24 1 -10000 0 1
CPEB1 -0.014 0.14 -10000 0 -0.56 29 29
AKT1 -0.023 0.023 -10000 0 -10000 0 0
NDEL1 0.022 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.019 0.03 -10000 0 -10000 0 0
NDEL1/TACC3 -0.007 0.042 -10000 0 -10000 0 0
GADD45A 0.022 0.004 -10000 0 -10000 0 0
GSK3B -0.02 0.02 -10000 0 -10000 0 0
PAK1/Aurora A -0.02 0.036 0.31 1 -10000 0 1
MDM2 0.023 0.017 0.38 1 -10000 0 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.019 0.094 0.3 35 -10000 0 35
TP53 -0.01 0.044 0.22 1 -0.22 17 18
DLG7 -0.021 0.022 0.15 2 -10000 0 2
AURKAIP1 0.022 0.005 -10000 0 -10000 0 0
ARHGEF7 0.022 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.008 0.044 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.019 0.029 -10000 0 -10000 0 0
AURKA -0.024 0.03 0.2 2 -10000 0 2
AURKB 0.08 0.06 0.16 14 -0.17 4 18
CDC25B -0.011 0.019 -10000 0 -10000 0 0
G2/M transition checkpoint -0.02 0.023 -10000 0 -10000 0 0
mRNA polyadenylation -0.038 0.081 -10000 0 -0.33 29 29
Aurora A/CPEB -0.038 0.081 -10000 0 -0.33 29 29
Aurora A/TACC1/TRAP/chTOG -0.004 0.047 -10000 0 -10000 0 0
BRCA1 0.023 0.003 -10000 0 -10000 0 0
centrosome duplication -0.02 0.036 0.31 1 -10000 0 1
regulation of centrosome cycle -0.007 0.041 -10000 0 -10000 0 0
spindle assembly -0.004 0.046 -10000 0 -10000 0 0
TDRD7 0.023 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.081 0.27 6 -10000 0 6
CENPA 0.1 0.052 0.17 75 -10000 0 75
Aurora A/PP2A -0.021 0.033 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.012 0.031 0.24 1 -10000 0 1
negative regulation of DNA binding -0.01 0.044 0.22 1 -0.22 17 18
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.032 0.009 -10000 0 -10000 0 0
RASA1 0.021 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A -0.02 0.023 -10000 0 -10000 0 0
mitotic prometaphase -0.02 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.03 0.2 2 -10000 0 2
TACC1 0.018 0.028 -10000 0 -0.56 1 1
TACC3 0.022 0.02 0.31 2 -10000 0 2
Aurora A/Antizyme1 -0.01 0.045 -10000 0 -10000 0 0
Aurora A/RasGAP -0.018 0.029 -10000 0 -10000 0 0
OAZ1 0.022 0.004 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.022 0.019 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.043 0.017 0.25 1 -10000 0 1
Importin alpha/Importin beta/TPX2 -0.019 0.094 0.3 35 -10000 0 35
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.016 0.083 0.22 27 -10000 0 27
PAK1 0.023 0.017 0.38 1 -10000 0 1
CKAP5 0.022 0.004 -10000 0 -10000 0 0
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 -0.005 0.005 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.013 0.13 -10000 0 -0.42 43 43
STXBP1 0.019 0.046 -10000 0 -0.56 3 3
ACh/CHRNA1 0.014 0.053 0.19 8 -0.29 8 16
RAB3GAP2/RIMS1/UNC13B 0.002 0.12 -10000 0 -0.36 42 42
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.037 0.17 0.24 1 -0.56 46 47
mol:ACh 0 0.031 0.096 7 -0.15 10 17
RAB3GAP2 0.022 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0 0.098 -10000 0 -0.28 42 42
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.014 0.053 0.19 8 -0.29 8 16
UNC13B 0.018 0.038 -10000 0 -0.56 2 2
CHRNA1 0.02 0.067 0.24 9 -0.56 5 14
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.021 0.04 0.18 16 -0.15 3 19
SNAP25 -0.002 0.042 -10000 0 -0.3 9 9
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 0.031 0.041 0.25 16 -10000 0 16
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.018 0.03 -10000 0 -0.35 3 3
STX1A/SNAP25 fragment 1/VAMP2 0 0.098 -10000 0 -0.28 42 42
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 0.022 0.004 -10000 0 -10000 0 0
EGFR 0.022 0.084 0.36 11 -0.56 6 17
EGF/EGFR 0.005 0.12 -10000 0 -0.33 45 45
EGF/EGFR dimer/SHC/GRB2/SOS1 0.049 0.073 -10000 0 -0.34 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.018 0.046 -10000 0 -0.56 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.015 0.072 0.24 3 -0.56 7 10
EGF/EGFR dimer/SHC 0.033 0.075 0.25 7 -0.38 12 19
mol:GDP 0.044 0.07 -10000 0 -0.33 12 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.025 0.16 -10000 0 -0.56 39 39
GRB2/SOS1 0.033 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.029 0.06 -10000 0 -0.31 12 12
SHC1 0.022 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.042 0.067 -10000 0 -0.32 12 12
FRAP1 -0.018 0.054 0.16 7 -0.32 12 19
EGF/EGFR dimer 0.024 0.083 0.26 8 -0.44 12 20
SOS1 0.023 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.009 0.13 -10000 0 -0.4 44 44
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.023 0.004 -10000 0 -10000 0 0
SPHK1 0.023 0.004 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
mol:S1P 0.011 0.003 -10000 0 -10000 0 0
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
mol:Sphinganine-1-P -0.01 0.002 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.043 0.032 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
G12/G13 0.033 0.008 -10000 0 -10000 0 0
S1PR3 0.023 0.004 -10000 0 -10000 0 0
S1PR2 0.022 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.003 0.024 -10000 0 -0.2 3 3
S1PR5 0.024 0.036 0.24 6 -0.56 1 7
S1PR4 -0.023 0.16 -10000 0 -0.56 37 37
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
S1P/S1P5/G12 0.033 0.037 -10000 0 -0.23 3 3
S1P/S1P3/Gq -0.049 0.14 -10000 0 -0.28 113 113
S1P/S1P4/Gi -0.004 0.092 -10000 0 -0.31 29 29
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.022 0.004 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
GNA11 0.022 0.004 -10000 0 -10000 0 0
ABCC1 0.023 0.01 0.24 1 -10000 0 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.006 0.062 -10000 0 -0.32 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.07 0.32 2 -0.33 1 3
alphaV/beta3 Integrin/Osteopontin/Src 0.11 0.083 0.27 1 -10000 0 1
AP1 0.006 0.12 -10000 0 -0.5 3 3
ILK -0.015 0.059 -10000 0 -0.34 8 8
bone resorption -0.013 0.059 -10000 0 -0.33 1 1
PTK2B 0.021 0.007 -10000 0 -10000 0 0
PYK2/p130Cas 0.1 0.095 0.29 2 -0.31 8 10
ITGAV 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.032 0.022 -10000 0 -0.41 1 1
alphaV/beta3 Integrin/Osteopontin 0.11 0.099 0.26 1 -0.37 8 9
MAP3K1 -0.015 0.059 -10000 0 -0.34 8 8
JUN 0.022 0.005 -10000 0 -10000 0 0
MAPK3 -0.015 0.058 0.38 1 -0.32 8 9
MAPK1 -0.015 0.057 0.38 1 -0.32 8 9
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.024 0.053 -10000 0 -0.33 8 8
ITGB3 0.015 0.075 -10000 0 -0.56 8 8
NFKBIA -0.009 0.052 0.35 1 -0.33 5 6
FOS -0.042 0.18 -10000 0 -0.56 53 53
CD44 0.021 0.027 -10000 0 -0.56 1 1
CHUK 0.022 0.005 -10000 0 -10000 0 0
PLAU 0.002 0.066 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.01 0.076 -10000 0 -10000 0 0
BCAR1 0.022 0.006 -10000 0 -10000 0 0
RELA 0.023 0.001 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.03 0.058 -10000 0 -0.41 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.017 0.059 -10000 0 -0.34 8 8
VAV3 -0.025 0.059 0.38 1 -0.35 8 9
MAP3K14 -0.013 0.06 -10000 0 -0.34 8 8
ROCK2 0.023 0.004 -10000 0 -10000 0 0
SPP1 0.13 0.12 0.24 246 -0.28 6 252
RAC1 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.016 0.057 -10000 0 -0.33 8 8
MMP2 -0.046 0.1 -10000 0 -0.63 4 4
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.024 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.047 0.25 1 -0.36 6 7
forebrain development -0.1 0.16 -10000 0 -0.51 24 24
GNAO1 0.015 0.033 0.24 2 -0.57 1 3
SMO/beta Arrestin2 0.007 0.03 0.24 1 -10000 0 1
SMO 0.004 0.032 0.37 2 -10000 0 2
ARRB2 0.005 0.019 -10000 0 -10000 0 0
GLI3/SPOP 0.025 0.095 -10000 0 -0.41 9 9
mol:GTP -0.003 0.004 -10000 0 -10000 0 0
GSK3B 0.02 0.008 -10000 0 -10000 0 0
GNAI2 0.014 0.013 -10000 0 -10000 0 0
SIN3/HDAC complex 0.055 0.023 -10000 0 -10000 0 0
GNAI1 0.015 0.029 -10000 0 -0.56 1 1
XPO1 -0.001 0.024 -10000 0 -10000 0 0
GLI1/Su(fu) -0.1 0.16 -10000 0 -0.55 22 22
SAP30 0.022 0.007 -10000 0 -10000 0 0
mol:GDP 0.004 0.032 0.37 2 -10000 0 2
MIM/GLI2A -0.041 0.069 -10000 0 -10000 0 0
IFT88 0.022 0.006 -10000 0 -10000 0 0
GNAI3 0.016 0.012 -10000 0 -10000 0 0
GLI2 0.016 0.076 0.26 1 -0.34 9 10
GLI3 0.013 0.097 -10000 0 -0.4 12 12
CSNK1D 0.022 0.004 -10000 0 -10000 0 0
CSNK1E 0.022 0.004 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.022 0.006 -10000 0 -10000 0 0
GNG2 0.016 0.059 -10000 0 -0.56 5 5
Gi family/GTP -0.01 0.051 -10000 0 -0.27 7 7
SIN3B 0.023 0.005 -10000 0 -10000 0 0
SIN3A 0.024 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.011 0.11 -10000 0 -0.42 21 21
GLI2/Su(fu) 0.011 0.089 0.21 1 -0.39 12 13
FOXA2 -0.53 0.56 -10000 0 -1.1 242 242
neural tube patterning -0.1 0.16 -10000 0 -0.51 24 24
SPOP 0.023 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.007 0.046 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
CSNK1G2 0.022 0.005 -10000 0 -10000 0 0
CSNK1G3 0.021 0.006 -10000 0 -10000 0 0
MTSS1 -0.041 0.069 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.1 0.16 -10000 0 -0.51 24 24
SUFU 0.004 0.016 -10000 0 -10000 0 0
LGALS3 0.022 0.005 -10000 0 -10000 0 0
catabolic process 0.027 0.12 -10000 0 -0.47 17 17
GLI3A/CBP 0.005 0.03 -10000 0 -0.36 1 1
KIF3A 0.021 0.006 -10000 0 -10000 0 0
GLI1 -0.11 0.16 -10000 0 -0.53 23 23
RAB23 0.023 0.004 -10000 0 -10000 0 0
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
IFT172 0.023 0.003 -10000 0 -10000 0 0
RBBP7 0.023 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.01 0.042 -10000 0 -10000 0 0
GNAZ 0.01 0.06 -10000 0 -0.56 5 5
RBBP4 0.023 0.004 -10000 0 -10000 0 0
CSNK1G1 0.023 0.002 -10000 0 -10000 0 0
PIAS1 0.023 0.002 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.024 0.081 0.23 1 -0.34 11 12
STK36 -0.001 0.025 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.01 0.066 -10000 0 -0.37 9 9
PTCH1 -0.1 0.17 -10000 0 -0.74 14 14
MIM/GLI1 -0.22 0.28 -10000 0 -0.51 222 222
CREBBP 0.005 0.03 -10000 0 -0.36 1 1
Su(fu)/SIN3/HDAC complex 0.007 0.089 -10000 0 -0.4 16 16
Ephrin B reverse signaling

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.02 0.027 -10000 0 -0.56 1 1
EPHB2 0.026 0.028 0.24 8 -10000 0 8
EFNB1 -0.004 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.063 0.054 0.29 1 -10000 0 1
Ephrin B2/EPHB1-2 0.052 0.057 0.24 16 -0.33 1 17
neuron projection morphogenesis 0.044 0.039 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 0.06 0.057 0.3 1 -10000 0 1
DNM1 0.024 0.014 0.24 2 -10000 0 2
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.019 0.1 -10000 0 -0.43 25 25
YES1 -0.023 0.16 -10000 0 -0.66 26 26
Ephrin B1/EPHB1-2/NCK2 0.06 0.057 0.3 1 -10000 0 1
PI3K 0 0.092 -10000 0 -0.43 16 16
mol:GDP 0.058 0.055 0.3 1 -10000 0 1
ITGA2B 0.005 0.098 -10000 0 -0.56 14 14
endothelial cell proliferation 0.027 0.02 -10000 0 -0.35 1 1
FYN -0.022 0.16 -10000 0 -0.66 26 26
MAP3K7 -0.021 0.11 -10000 0 -0.46 26 26
FGR -0.029 0.16 -10000 0 -0.68 25 25
TIAM1 0.023 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
RGS3 0.023 0.004 -10000 0 -10000 0 0
cell adhesion -0.016 0.098 -10000 0 -0.4 18 18
LYN -0.022 0.15 -10000 0 -0.67 25 25
Ephrin B1/EPHB1-2/Src Family Kinases -0.023 0.14 -10000 0 -0.6 26 26
Ephrin B1/EPHB1-2 -0.02 0.11 -10000 0 -0.51 24 24
SRC -0.02 0.15 -10000 0 -0.65 26 26
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
EPHB1 0.052 0.088 0.28 59 -10000 0 59
EPHB4 0.022 0.006 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.02 -10000 0 -0.35 1 1
alphaIIb/beta3 Integrin 0.013 0.094 -10000 0 -0.41 22 22
BLK -0.025 0.16 -10000 0 -0.67 25 25
HCK -0.022 0.15 -10000 0 -0.65 26 26
regulation of stress fiber formation -0.058 0.056 -10000 0 -0.3 1 1
MAPK8 -0.019 0.097 -10000 0 -0.42 24 24
Ephrin B1/EPHB1-2/RGS3 0.06 0.057 0.3 1 -10000 0 1
endothelial cell migration -0.01 0.099 0.3 2 -0.37 25 27
NCK2 0.023 0.002 -10000 0 -10000 0 0
PTPN13 0.016 0.063 -10000 0 -0.67 4 4
regulation of focal adhesion formation -0.058 0.056 -10000 0 -0.3 1 1
chemotaxis -0.058 0.056 -10000 0 -0.3 1 1
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.054 0.047 0.25 1 -10000 0 1
angiogenesis -0.021 0.12 -10000 0 -0.5 25 25
LCK -0.019 0.15 -10000 0 -0.66 25 25
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.018 0.007 -10000 0 -10000 0 0
epithelial cell differentiation 0.044 0.016 -10000 0 -10000 0 0
CYFIP2 0.009 0.083 -10000 0 -0.56 10 10
ENAH 0.009 0.07 0.28 10 -10000 0 10
EGFR 0.022 0.084 0.36 11 -0.56 6 17
EPHA2 0.018 0.046 -10000 0 -0.56 3 3
MYO6 -0.008 0.026 -10000 0 -10000 0 0
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.033 0.057 -10000 0 -0.36 8 8
AQP5 -0.14 0.23 -10000 0 -0.48 141 141
CTNND1 0.023 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.009 0.023 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.085 0.13 -10000 0 -0.29 130 130
EGF 0.015 0.072 0.24 3 -0.56 7 10
NCKAP1 0.023 0.004 -10000 0 -10000 0 0
AQP3 -0.06 0.17 -10000 0 -0.48 65 65
cortical microtubule organization 0.044 0.016 -10000 0 -10000 0 0
GO:0000145 -0.009 0.022 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.049 0.018 -10000 0 -10000 0 0
MLLT4 0.023 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.019 0.023 -10000 0 -0.28 3 3
ARF6 0.022 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.039 -10000 0 -0.33 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.001 0.009 -10000 0 -10000 0 0
PVRL2 0.022 0.004 -10000 0 -10000 0 0
ZYX -0.009 0.024 -10000 0 -10000 0 0
ARF6/GTP 0.046 0.041 -10000 0 -0.31 3 3
CDH1 0.022 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.03 0.062 -10000 0 -0.32 12 12
RhoA/GDP 0.045 0.017 -10000 0 -10000 0 0
actin cytoskeleton organization -0.011 0.021 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.022 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
IGF1R 0.022 0.004 -10000 0 -10000 0 0
IGF1 0.005 0.1 0.24 1 -0.56 15 16
DIAPH1 -0.015 0.16 -10000 0 -0.57 20 20
Wnt receptor signaling pathway -0.044 0.016 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.019 0.023 -10000 0 -0.27 3 3
CTNNA1 0.021 0.006 -10000 0 -10000 0 0
VCL -0.011 0.021 -10000 0 -10000 0 0
EFNA1 0.022 0.005 -10000 0 -10000 0 0
LPP -0.008 0.015 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.036 0.031 -10000 0 -0.29 3 3
SEC6/SEC8 -0.015 0.01 -10000 0 -10000 0 0
MGAT3 -0.087 0.13 -10000 0 -0.3 130 130
HGF/MET -0.025 0.13 -10000 0 -0.28 93 93
HGF -0.092 0.23 -10000 0 -0.56 94 94
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.018 0.007 -10000 0 -10000 0 0
actin cable formation 0.047 0.1 0.31 27 -10000 0 27
KIAA1543 -0.009 0.021 0.16 5 -10000 0 5
KIFC3 -0.01 0.022 -10000 0 -10000 0 0
NCK1 0.019 0.009 -10000 0 -10000 0 0
EXOC3 0.018 0.01 -10000 0 -10000 0 0
ACTN1 -0.009 0.025 -10000 0 -10000 0 0
NCK1/GIT1 0.028 0.013 -10000 0 -10000 0 0
mol:GDP 0.044 0.016 -10000 0 -10000 0 0
EXOC4 0.023 0.004 -10000 0 -10000 0 0
STX4 -0.009 0.025 -10000 0 -10000 0 0
PIP5K1C -0.009 0.024 -10000 0 -10000 0 0
LIMA1 0.023 0.002 -10000 0 -10000 0 0
ABI1 0.022 0.004 -10000 0 -10000 0 0
ROCK1 0.019 0.086 0.3 19 -10000 0 19
adherens junction assembly -0.014 0.094 0.28 3 -0.65 7 10
IGF-1R heterotetramer/IGF1 0.03 0.056 -10000 0 -0.29 13 13
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.033 0.008 -10000 0 -10000 0 0
MET 0.021 0.041 0.38 1 -0.56 2 3
PLEKHA7 -0.01 0.022 -10000 0 -10000 0 0
mol:GTP 0.041 0.038 -10000 0 -0.33 3 3
establishment of epithelial cell apical/basal polarity 0.025 0.084 0.31 8 -10000 0 8
cortical actin cytoskeleton stabilization 0.018 0.007 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.011 0.021 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.018 0.007 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.023 0.006 -10000 0 -10000 0 0
HSPA8 0.022 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.016 0.098 -10000 0 -0.4 20 20
AKT1 0.014 0.03 -10000 0 -10000 0 0
GSC 0.02 0.074 -10000 0 -10000 0 0
NKX2-5 0.11 0.14 0.24 222 -0.28 23 245
muscle cell differentiation -0.029 0.1 0.48 8 -10000 0 8
SMAD2-3/SMAD4/SP1 0.054 0.071 -10000 0 -10000 0 0
SMAD4 0.017 0.038 -10000 0 -10000 0 0
CBFB 0.022 0.005 -10000 0 -10000 0 0
SAP18 0.022 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.043 0.025 -10000 0 -0.36 1 1
SMAD3/SMAD4/VDR 0.053 0.051 -10000 0 -0.31 1 1
MYC 0.022 0.013 -10000 0 -10000 0 0
CDKN2B -0.21 0.47 -10000 0 -1.5 47 47
AP1 0 0.1 -10000 0 -0.29 50 50
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.035 0.067 -10000 0 -0.39 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.012 0.1 -10000 0 -0.34 37 37
SP3 0.024 0.003 -10000 0 -10000 0 0
CREB1 0.023 0.004 -10000 0 -10000 0 0
FOXH1 0.046 0.074 0.27 43 -10000 0 43
SMAD3/SMAD4/GR 0.035 0.047 -10000 0 -10000 0 0
GATA3 0.008 0.097 0.24 2 -0.51 15 17
SKI/SIN3/HDAC complex/NCoR1 -0.001 0.087 -10000 0 -0.4 15 15
MEF2C/TIF2 -0.007 0.095 0.28 2 -0.61 6 8
endothelial cell migration -0.02 0.037 0.49 1 -10000 0 1
MAX 0.021 0.004 -10000 0 -10000 0 0
RBBP7 0.022 0.005 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
RUNX2 0.023 0.003 -10000 0 -10000 0 0
RUNX3 0.022 0.004 -10000 0 -10000 0 0
RUNX1 0.022 0.004 -10000 0 -10000 0 0
CTBP1 0.021 0.007 -10000 0 -10000 0 0
NR3C1 0.021 0.006 -10000 0 -10000 0 0
VDR 0.022 0.027 -10000 0 -0.56 1 1
CDKN1A 0.014 0.052 -10000 0 -0.49 1 1
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.056 0.065 0.28 5 -0.24 2 7
DCP1A 0.021 0.007 -10000 0 -10000 0 0
SKI 0.022 0.005 -10000 0 -10000 0 0
SERPINE1 0.02 0.037 -10000 0 -0.49 1 1
SMAD3/SMAD4/ATF2 0.037 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.037 0.047 -10000 0 -10000 0 0
SAP30 0.021 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.043 0.017 -10000 0 -10000 0 0
JUN -0.009 0.1 -10000 0 -0.29 48 48
SMAD3/SMAD4/IRF7 0.038 0.049 -10000 0 -10000 0 0
TFE3 0.026 0.005 -10000 0 -10000 0 0
COL1A2 0.026 0.029 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.036 0.048 -10000 0 -10000 0 0
DLX1 0.15 0.11 0.24 274 -0.29 1 275
TCF3 0.022 0.004 -10000 0 -10000 0 0
FOS -0.04 0.18 -10000 0 -0.56 53 53
SMAD3/SMAD4/Max 0.034 0.048 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.043 0.014 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.014 0.034 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.036 0.048 -10000 0 -10000 0 0
IRF7 0.023 0.005 -10000 0 -10000 0 0
ESR1 -0.003 0.12 -10000 0 -0.56 20 20
HNF4A 0.021 0.034 0.26 8 -10000 0 8
MEF2C -0.007 0.095 0.37 3 -0.59 6 9
SMAD2-3/SMAD4 0.037 0.061 -10000 0 -0.24 1 1
Cbp/p300/Src-1 0.043 0.015 -10000 0 -10000 0 0
IGHV3OR16-13 0.005 0.04 -10000 0 -0.34 6 6
TGIF2/HDAC complex 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.022 0.006 -10000 0 -10000 0 0
SKIL 0.013 0.011 -10000 0 -10000 0 0
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.002 -10000 0 -10000 0 0
SNIP1 0.023 0.017 0.38 1 -10000 0 1
GCN5L2 0 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.043 0.049 -10000 0 -10000 0 0
MSG1/HSC70 0.032 0.023 -10000 0 -0.41 1 1
SMAD2 0.017 0.03 -10000 0 -10000 0 0
SMAD3 0.016 0.036 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.036 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.005 0.065 0.2 1 -0.4 8 9
NCOR1 0.022 0.005 -10000 0 -10000 0 0
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
NCOA1 0.023 0.003 -10000 0 -10000 0 0
MYOD/E2A 0.049 0.057 0.26 1 -0.18 4 5
SMAD2-3/SMAD4/SP1/MIZ-1 0.063 0.076 -10000 0 -10000 0 0
IFNB1 0.009 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.025 0.1 -10000 0 -0.58 6 6
CITED1 0.021 0.029 0.24 1 -0.56 1 2
SMAD2-3/SMAD4/ARC105 0.044 0.062 -10000 0 -10000 0 0
RBL1 0.022 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.026 0.16 -10000 0 -0.52 41 41
RUNX1-3/PEBPB2 0.043 0.014 -10000 0 -10000 0 0
SMAD7 0.004 0.11 -10000 0 -0.92 1 1
MYC/MIZ-1 0.032 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4 0.012 0.039 -10000 0 -10000 0 0
IL10 0.001 0.077 -10000 0 -0.38 14 14
PIASy/HDAC complex 0.02 0.011 -10000 0 -10000 0 0
PIAS3 0.022 0.004 -10000 0 -10000 0 0
CDK2 0.023 0.003 -10000 0 -10000 0 0
IL5 0 0.07 -10000 0 -0.34 15 15
CDK4 0.024 0.017 0.38 1 -10000 0 1
PIAS4 0.02 0.011 -10000 0 -10000 0 0
ATF3 0.023 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1 0.043 0.054 -10000 0 -10000 0 0
FOXG1 0.027 0.079 0.24 50 -0.29 1 51
FOXO3 0.002 0.031 -10000 0 -10000 0 0
FOXO1 0.003 0.029 -10000 0 -10000 0 0
FOXO4 0.002 0.031 -10000 0 -10000 0 0
heart looping -0.006 0.094 0.36 3 -0.58 6 9
CEBPB 0.017 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.11 0.094 0.27 6 -10000 0 6
MYOD1 0.03 0.089 0.24 65 -0.29 4 69
SMAD3/SMAD4/HNF4 0.038 0.053 0.27 1 -10000 0 1
SMAD3/SMAD4/GATA3 0.027 0.088 -10000 0 -0.37 16 16
SnoN/SIN3/HDAC complex/NCoR1 0.013 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.051 0.054 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.055 0.056 -10000 0 -10000 0 0
MED15 0.022 0.005 -10000 0 -10000 0 0
SP1 0.024 0.015 -10000 0 -10000 0 0
SIN3B 0.022 0.005 -10000 0 -10000 0 0
SIN3A 0.023 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.11 0.12 0.35 14 -0.36 5 19
ITGB5 0.014 0.039 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.004 0.074 -10000 0 -0.38 11 11
SMAD3/SMAD4/AR -0.048 0.17 -10000 0 -0.38 98 98
AR -0.098 0.23 -10000 0 -0.56 98 98
negative regulation of cell growth 0.014 0.047 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.051 0.073 0.27 1 -10000 0 1
E2F5 0.022 0.005 -10000 0 -10000 0 0
E2F4 0.022 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.066 0.062 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.011 0.11 -10000 0 -0.37 39 39
TFDP1 0.024 0.029 0.38 3 -10000 0 3
SMAD3/SMAD4/AP1 0.015 0.11 -10000 0 -0.29 48 48
SMAD3/SMAD4/RUNX2 0.037 0.048 -10000 0 -10000 0 0
TGIF2 0.022 0.005 -10000 0 -10000 0 0
TGIF1 0.022 0.005 -10000 0 -10000 0 0
ATF2 0.023 0.003 -10000 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 -0.015 0.14 -10000 0 -0.57 21 21
Syndecan-4/Syndesmos 0.02 0.095 -10000 0 -0.62 6 6
positive regulation of JNK cascade 0.007 0.12 -10000 0 -0.56 10 10
Syndecan-4/ADAM12 0.048 0.12 0.31 2 -0.64 6 8
CCL5 0.012 0.079 -10000 0 -0.56 9 9
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
DNM2 0.022 0.004 -10000 0 -10000 0 0
ITGA5 0.023 0.002 -10000 0 -10000 0 0
SDCBP 0.022 0.005 -10000 0 -10000 0 0
PLG 0.018 0.022 0.22 3 -10000 0 3
ADAM12 0.078 0.098 0.24 127 -0.29 2 129
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.022 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.053 0.12 0.31 2 -0.63 6 8
Syndecan-4/CXCL12/CXCR4 0.008 0.13 -10000 0 -0.59 10 10
Syndecan-4/Laminin alpha3 0.011 0.099 -10000 0 -0.57 6 6
MDK 0.028 0.038 0.28 10 -10000 0 10
Syndecan-4/FZD7 0.02 0.094 -10000 0 -0.6 6 6
Syndecan-4/Midkine 0.021 0.099 0.34 5 -0.59 6 11
FZD7 0.023 0.017 0.38 1 -10000 0 1
Syndecan-4/FGFR1/FGF 0.014 0.097 -10000 0 -0.56 6 6
THBS1 0.016 0.065 -10000 0 -0.56 6 6
integrin-mediated signaling pathway 0.02 0.095 -10000 0 -0.6 6 6
positive regulation of MAPKKK cascade 0.007 0.12 -10000 0 -0.56 10 10
Syndecan-4/TACI 0.02 0.1 -10000 0 -0.58 7 7
CXCR4 0.023 0.003 -10000 0 -10000 0 0
cell adhesion 0.006 0.054 0.19 5 -0.31 11 16
Syndecan-4/Dynamin 0.019 0.096 -10000 0 -0.62 6 6
Syndecan-4/TSP1 0.015 0.11 -10000 0 -0.68 8 8
Syndecan-4/GIPC 0.019 0.093 -10000 0 -0.72 4 4
Syndecan-4/RANTES 0.013 0.11 -10000 0 -0.57 9 9
ITGB1 0.022 0.004 -10000 0 -10000 0 0
LAMA1 0.086 0.1 0.25 138 -0.29 1 139
LAMA3 0.008 0.087 -10000 0 -0.56 11 11
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA 0.003 0.1 0.77 8 -0.49 1 9
Syndecan-4/alpha-Actinin 0.02 0.095 -10000 0 -0.62 6 6
TFPI -0.022 0.16 -10000 0 -0.56 37 37
F2 0.026 0.038 0.24 14 -10000 0 14
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.015 0.1 -10000 0 -0.57 6 6
ACTN1 0.022 0.005 -10000 0 -10000 0 0
TNC 0.025 0.039 0.24 8 -0.56 1 9
Syndecan-4/CXCL12 -0.002 0.13 -10000 0 -0.61 11 11
FGF6 -0.017 0.006 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
CXCL12 -0.02 0.15 -10000 0 -0.56 35 35
TNFRSF13B 0.019 0.061 0.24 8 -0.56 4 12
FGF2 0.006 0.095 -10000 0 -0.56 13 13
FGFR1 0.017 0.028 -10000 0 -0.56 1 1
Syndecan-4/PI-4-5-P2 0.002 0.09 -10000 0 -0.62 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.008 0.082 -10000 0 -0.55 10 10
cell migration -0.017 0.01 -10000 0 -10000 0 0
PRKCD 0.018 0.014 -10000 0 -10000 0 0
vasculogenesis 0.016 0.11 -10000 0 -0.65 8 8
SDC4 0.012 0.082 -10000 0 -0.69 4 4
Syndecan-4/Tenascin C 0.02 0.099 -10000 0 -0.63 6 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.025 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.019 0.094 -10000 0 -0.6 6 6
MMP9 0.033 0.047 0.23 24 -10000 0 24
Rac1/GTP 0.006 0.056 0.19 5 -0.32 11 16
cytoskeleton organization 0.02 0.092 -10000 0 -0.6 6 6
GIPC1 0.022 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.003 0.13 -10000 0 -0.62 10 10
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.012 0.062 -10000 0 -0.38 11 11
EPHB2 0.026 0.028 0.24 8 -10000 0 8
Syndecan-2/TACI 0.018 0.049 -10000 0 -0.35 7 7
LAMA1 0.086 0.1 0.25 138 -0.29 1 139
Syndecan-2/alpha2 ITGB1 0.033 0.055 -10000 0 -0.3 11 11
HRAS 0.022 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK 0.004 0.028 -10000 0 -0.34 3 3
ITGA5 0.023 0.002 -10000 0 -10000 0 0
BAX -0.006 0.02 -10000 0 -10000 0 0
EPB41 0.022 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.027 -10000 0 -0.32 3 3
LAMA3 0.008 0.087 -10000 0 -0.56 11 11
EZR 0.023 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.006 0.095 -10000 0 -0.56 13 13
Syndecan-2/MMP2 0.016 0.049 -10000 0 -0.4 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.031 0.01 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.032 -10000 0 -0.35 2 2
Syndecan-2/GM-CSF -0.014 0.11 -10000 0 -0.35 43 43
determination of left/right symmetry 0.006 0.033 -10000 0 -0.4 3 3
Syndecan-2/PKC delta 0.018 0.029 -10000 0 -0.34 3 3
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
MAPK3 -0.017 0.1 0.19 17 -0.32 43 60
MAPK1 -0.016 0.098 0.19 14 -0.32 40 54
Syndecan-2/RACK1 0.029 0.028 -10000 0 -0.29 3 3
NF1 0.023 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.006 0.033 -10000 0 -0.4 3 3
ITGA2 0.021 0.006 -10000 0 -10000 0 0
MAPK8 0.003 0.027 -10000 0 -0.34 3 3
Syndecan-2/alpha2/beta1 Integrin 0.075 0.073 0.26 13 -0.29 3 16
Syndecan-2/Kininogen 0.016 0.036 0.25 6 -10000 0 6
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC 0.015 0.04 0.18 19 -0.29 2 21
Syndecan-2/CASK/Protein 4.1 0.018 0.027 -10000 0 -0.32 3 3
extracellular matrix organization 0.019 0.029 -10000 0 -0.34 3 3
actin cytoskeleton reorganization 0.012 0.061 -10000 0 -0.37 11 11
Syndecan-2/Caveolin-2/Ras 0.023 0.061 -10000 0 -0.34 11 11
Syndecan-2/Laminin alpha3 0.011 0.061 -10000 0 -0.35 13 13
Syndecan-2/RasGAP 0.038 0.03 -10000 0 -0.27 3 3
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
PRKCD 0.021 0.007 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.032 -10000 0 -0.35 2 2
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.025 -10000 0 -0.28 2 2
RHOA 0.021 0.007 -10000 0 -10000 0 0
SDCBP 0.022 0.005 -10000 0 -10000 0 0
TNFRSF13B 0.019 0.061 0.24 8 -0.56 4 12
RASA1 0.021 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.031 0.01 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.019 0.03 -10000 0 -0.35 3 3
TGFB1 0.022 0.005 -10000 0 -10000 0 0
CASP3 0.013 0.042 0.19 18 -0.29 3 21
FN1 0.01 0.083 -10000 0 -0.56 10 10
Syndecan-2/IL8 0.022 0.052 0.25 2 -0.36 6 8
SDC2 0.006 0.033 -10000 0 -0.41 3 3
KNG1 0.007 0.052 0.31 12 -10000 0 12
Syndecan-2/Neurofibromin 0.02 0.03 -10000 0 -0.35 3 3
TRAPPC4 0.023 0.004 -10000 0 -10000 0 0
CSF2 -0.033 0.17 -10000 0 -0.56 43 43
Syndecan-2/TGFB1 0.019 0.029 -10000 0 -0.34 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.027 -10000 0 -0.32 3 3
Syndecan-2/Ezrin 0.03 0.029 -10000 0 -0.3 3 3
PRKACA 0.015 0.046 0.19 22 -0.31 3 25
angiogenesis 0.022 0.051 0.25 2 -0.35 6 8
MMP2 0.017 0.053 -10000 0 -0.56 4 4
IL8 0.026 0.063 0.26 16 -0.56 3 19
calcineurin-NFAT signaling pathway 0.018 0.049 -10000 0 -0.34 7 7
Cellular roles of Anthrax toxin

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
ANTXR1 0.02 0.038 -10000 0 -0.56 2 2
ANTXR2 0.015 0.065 -10000 0 -0.56 6 6
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.01 -10000 0 -0.08 7 7
monocyte activation -0.009 0.1 -10000 0 -0.38 32 32
MAP2K2 -0.008 0.11 -10000 0 -0.57 17 17
MAP2K1 -0.005 0.009 -10000 0 -0.099 2 2
MAP2K7 -0.005 0.008 -10000 0 -0.11 1 1
MAP2K6 -0.005 0.011 0.12 1 -10000 0 1
CYAA -0.011 0.046 -10000 0 -0.39 6 6
MAP2K4 -0.005 0.008 -10000 0 -10000 0 0
IL1B -0.009 0.055 0.24 2 -0.3 14 16
Channel 0.022 0.053 -10000 0 -0.38 7 7
NLRP1 -0.006 0.027 -10000 0 -0.34 3 3
CALM1 0.022 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.07 -10000 0 -0.4 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.01 0.08 7 -10000 0 7
MAPK3 -0.005 0.009 -10000 0 -0.11 2 2
MAPK1 -0.005 0.009 -10000 0 -0.099 2 2
PGR -0.062 0.12 -10000 0 -0.3 92 92
PA/Cellular Receptors 0.023 0.057 -10000 0 -0.41 7 7
apoptosis -0.002 0.01 -10000 0 -0.08 7 7
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.05 -10000 0 -0.35 7 7
macrophage activation -0.007 0.009 -10000 0 -10000 0 0
TNF 0.011 0.084 0.24 1 -0.56 10 11
VCAM1 -0.007 0.1 -10000 0 -0.38 30 30
platelet activation -0.004 0.07 -10000 0 -0.4 14 14
MAPKKK cascade 0 0.02 0.13 2 -0.13 3 5
IL18 -0.005 0.034 -10000 0 -0.27 6 6
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.08 7 7
LEF -0.002 0.01 -10000 0 -0.081 7 7
CASP1 -0.003 0.024 -10000 0 -0.15 7 7
mol:cAMP -0.004 0.071 -10000 0 -0.4 14 14
necrosis -0.002 0.01 -10000 0 -0.08 7 7
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.05 -10000 0 -0.36 7 7
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.016 0.12 -10000 0 -0.69 13 13
oxygen homeostasis 0.002 0.009 -10000 0 -10000 0 0
TCEB2 0.022 0.005 -10000 0 -10000 0 0
TCEB1 0.022 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.012 0.13 0.28 5 -0.36 11 16
EPO 0.034 0.16 0.37 2 -0.54 1 3
FIH (dimer) 0.02 0.019 -10000 0 -10000 0 0
APEX1 0.023 0.023 -10000 0 -10000 0 0
SERPINE1 0.021 0.17 0.4 2 -0.51 4 6
FLT1 -0.036 0.23 -10000 0 -0.81 29 29
ADORA2A 0.009 0.16 0.38 3 -0.49 4 7
germ cell development 0.023 0.17 0.39 2 -0.52 5 7
SLC11A2 0.023 0.17 0.4 2 -0.51 5 7
BHLHE40 0.021 0.17 0.42 1 -0.52 3 4
HIF1AN 0.02 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.027 0.14 0.32 3 -0.41 9 12
ETS1 0.011 0.088 -10000 0 -0.57 10 10
CITED2 0.006 0.17 -10000 0 -1.1 10 10
KDR -0.067 0.32 -10000 0 -1 44 44
PGK1 0.022 0.17 0.4 2 -0.51 4 6
SIRT1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.075 0.22 0.47 2 -0.57 5 7
EPAS1 -0.016 0.12 0.28 6 -0.36 24 30
SP1 0.026 0.003 -10000 0 -10000 0 0
ABCG2 -0.017 0.25 0.42 1 -0.62 53 54
EFNA1 0.02 0.16 -10000 0 -0.51 4 4
FXN 0.008 0.16 0.36 5 -0.5 4 9
POU5F1 0.023 0.17 0.4 2 -0.54 5 7
neuron apoptosis -0.073 0.21 0.56 5 -0.46 2 7
EP300 0.022 0.004 -10000 0 -10000 0 0
EGLN3 0.054 0.082 0.24 71 -10000 0 71
EGLN2 0.018 0.02 -10000 0 -10000 0 0
EGLN1 0.02 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.041 0.016 -10000 0 -10000 0 0
VHL 0.021 0.006 -10000 0 -10000 0 0
ARNT 0.024 0.023 -10000 0 -10000 0 0
SLC2A1 0.023 0.18 0.36 10 -0.49 4 14
TWIST1 0.018 0.17 0.39 8 -0.5 4 12
ELK1 0.025 0.014 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.03 0.15 0.34 1 -0.42 7 8
VEGFA 0.023 0.17 0.4 2 -0.54 2 4
CREBBP 0.022 0.005 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.035 0.065 -10000 0 -0.41 8 8
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.078 -10000 0 -0.34 3 3
AP1 -0.003 0.11 -10000 0 -0.3 56 56
mol:PIP3 -0.001 0.051 -10000 0 -0.32 9 9
AKT1 0.005 0.095 0.26 9 -0.48 2 11
PTK2B -0.019 0.083 -10000 0 -0.35 14 14
RHOA -0.017 0.087 -10000 0 -0.31 34 34
PIK3CB 0.019 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.028 0.068 -10000 0 -0.3 9 9
MAGI3 0.022 0.005 -10000 0 -10000 0 0
RELA 0.023 0.001 -10000 0 -10000 0 0
apoptosis 0.009 0.043 0.19 1 -0.29 8 9
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.004 0.097 0.23 5 -0.34 10 15
NF kappa B1 p50/RelA -0.005 0.079 -10000 0 -0.35 6 6
endothelial cell migration 0.007 0.067 -10000 0 -0.71 4 4
ADCY4 -0.003 0.078 -10000 0 -0.4 8 8
ADCY5 -0.008 0.074 -10000 0 -0.35 8 8
ADCY6 0.008 0.058 -10000 0 -0.36 6 6
ADCY7 0.008 0.054 -10000 0 -0.37 5 5
ADCY1 0.007 0.056 -10000 0 -0.37 5 5
ADCY2 0.004 0.067 0.21 2 -0.36 5 7
ADCY3 0.008 0.056 -10000 0 -0.37 5 5
ADCY8 -0.045 0.1 -10000 0 -0.37 12 12
ADCY9 0.008 0.06 -10000 0 -0.39 6 6
GSK3B 0 0.097 0.23 3 -0.37 8 11
arachidonic acid secretion 0.005 0.062 -10000 0 -0.42 6 6
GNG2 0.016 0.059 -10000 0 -0.56 5 5
TRIP6 0.015 0.008 -10000 0 -10000 0 0
GNAO1 0.01 0.041 -10000 0 -0.36 5 5
HRAS 0.022 0.004 -10000 0 -10000 0 0
NFKBIA -0.019 0.074 -10000 0 -0.34 7 7
GAB1 0.022 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.15 -10000 0 -0.82 15 15
JUN 0.022 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.028 0.029 -10000 0 -0.35 2 2
TIAM1 -0.004 0.17 -10000 0 -0.94 15 15
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 -0.027 0.067 -10000 0 -0.3 9 9
PLCB3 0.012 0.035 0.18 10 -0.32 2 12
FOS -0.042 0.18 -10000 0 -0.56 53 53
positive regulation of mitosis 0.005 0.062 -10000 0 -0.42 6 6
LPA/LPA1-2-3 0.041 0.055 0.24 1 -0.32 8 9
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.022 0.006 -10000 0 -10000 0 0
stress fiber formation -0.001 0.066 -10000 0 -0.38 6 6
GNAZ 0.006 0.052 -10000 0 -0.35 9 9
EGFR/PI3K-beta/Gab1 0.009 0.056 -10000 0 -0.33 9 9
positive regulation of dendritic cell cytokine production 0.039 0.054 0.24 1 -0.32 8 9
LPA/LPA2/MAGI-3 0.029 0.014 -10000 0 -10000 0 0
ARHGEF1 0.009 0.048 0.19 15 -0.31 4 19
GNAI2 0.009 0.037 -10000 0 -0.35 4 4
GNAI3 0.01 0.037 -10000 0 -0.35 4 4
GNAI1 0.01 0.048 -10000 0 -0.42 4 4
LPA/LPA3 0.017 0.047 0.17 10 -0.41 4 14
LPA/LPA2 0.017 0.012 -10000 0 -10000 0 0
LPA/LPA1 0.017 0.042 -10000 0 -0.41 4 4
HB-EGF/EGFR 0.011 0.085 0.26 8 -0.37 18 26
HBEGF -0.022 0.067 -10000 0 -0.41 13 13
mol:DAG -0.027 0.067 -10000 0 -0.3 9 9
cAMP biosynthetic process -0.004 0.067 0.23 1 -0.39 5 6
NFKB1 0.022 0.005 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
LYN -0.018 0.08 0.26 2 -0.36 9 11
GNAQ 0.009 0.035 0.19 1 -0.3 5 6
LPAR2 0.022 0.005 -10000 0 -10000 0 0
LPAR3 0.022 0.063 0.25 10 -0.56 4 14
LPAR1 0.022 0.038 -10000 0 -0.32 4 4
IL8 -0.016 0.12 0.31 2 -0.43 15 17
PTK2 0.004 0.05 0.19 1 -0.32 7 8
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
CASP3 0.009 0.043 0.19 1 -0.3 8 9
EGFR 0.022 0.084 0.36 11 -0.56 6 17
PLCG1 -0.02 0.067 -10000 0 -0.24 16 16
PLD2 0.005 0.052 0.18 11 -0.3 8 19
G12/G13 0.041 0.038 -10000 0 -0.32 4 4
PI3K-beta -0.009 0.075 -10000 0 -0.39 6 6
cell migration 0.014 0.056 0.18 1 -0.24 15 16
SLC9A3R2 0.02 0.038 -10000 0 -0.56 2 2
PXN -0.002 0.067 -10000 0 -0.39 6 6
HRAS/GTP 0.004 0.063 -10000 0 -0.44 6 6
RAC1 0.022 0.004 -10000 0 -10000 0 0
MMP9 0.033 0.047 0.24 24 -10000 0 24
PRKCE 0.021 0.027 -10000 0 -0.56 1 1
PRKCD -0.027 0.064 -10000 0 -0.31 4 4
Gi(beta/gamma) 0.009 0.068 -10000 0 -0.56 4 4
mol:LPA 0 0.015 -10000 0 -0.18 3 3
TRIP6/p130 Cas/FAK1/Paxillin 0.02 0.059 0.26 1 -0.39 2 3
MAPKKK cascade 0.005 0.062 -10000 0 -0.42 6 6
contractile ring contraction involved in cytokinesis -0.022 0.097 -10000 0 -0.32 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.061 0.14 -10000 0 -0.31 108 108
GNA15 0.01 0.031 0.19 1 -0.3 4 5
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
MAPT -0.004 0.099 0.24 4 -0.35 10 14
GNA11 0.01 0.031 0.19 1 -0.3 4 5
Rac1/GTP 0.013 0.16 -10000 0 -0.86 15 15
MMP2 0.007 0.068 -10000 0 -0.72 4 4
ErbB2/ErbB3 signaling events

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
USP8 -0.007 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.061 -10000 0 -0.29 3 3
NFATC4 -0.013 0.056 0.24 3 -0.24 11 14
ERBB2IP 0.021 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.022 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis 0.009 0.059 -10000 0 -0.3 11 11
JUN 0.014 0.059 0.18 1 -0.45 1 2
HRAS 0.022 0.004 -10000 0 -10000 0 0
DOCK7 -0.015 0.062 0.29 1 -0.29 11 12
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.057 -10000 0 -0.32 10 10
AKT1 -0.004 0.005 -10000 0 -10000 0 0
BAD -0.008 0.004 -10000 0 -10000 0 0
MAPK10 -0.011 0.054 0.18 5 -0.25 7 12
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.011 0.063 -10000 0 -0.32 11 11
RAF1 0.018 0.072 0.26 7 -0.36 1 8
ErbB2/ErbB3/neuregulin 2 -0.008 0.1 0.2 2 -0.34 42 44
STAT3 0.013 0.11 -10000 0 -0.79 8 8
cell migration -0.006 0.051 0.21 5 -0.27 2 7
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.014 0.17 -10000 0 -0.5 20 20
FOS -0.03 0.19 0.31 2 -0.48 60 62
NRAS 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.009 0.059 -10000 0 -0.3 11 11
MAPK3 -0.004 0.14 0.32 1 -0.53 13 14
MAPK1 -0.006 0.14 0.32 1 -0.52 18 19
JAK2 -0.016 0.058 -10000 0 -0.29 11 11
NF2 -0.004 0.08 -10000 0 -0.57 9 9
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.012 0.052 0.18 3 -0.27 11 14
NRG1 0.007 0.091 -10000 0 -0.56 12 12
GRB2/SOS1 0.033 0.008 -10000 0 -10000 0 0
MAPK8 0.004 0.066 0.24 1 -0.29 11 12
MAPK9 -0.01 0.042 0.18 3 -10000 0 3
ERBB2 -0.016 0.021 0.29 2 -10000 0 2
ERBB3 0.023 0.003 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
apoptosis 0.005 0.017 -10000 0 -0.17 3 3
STAT3 (dimer) 0.014 0.1 -10000 0 -0.78 8 8
RNF41 -0.01 0.007 -10000 0 -10000 0 0
FRAP1 -0.003 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.024 0.033 -10000 0 -0.22 11 11
ErbB2/ErbB2/HSP90 (dimer) -0.014 0.018 0.21 2 -10000 0 2
CHRNA1 0.004 0.13 0.3 1 -0.52 9 10
myelination -0.003 0.073 0.29 10 -0.25 3 13
PPP3CB -0.014 0.059 0.28 1 -0.28 11 12
KRAS 0.021 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.033 0.057 -10000 0 -0.26 9 9
NRG2 -0.039 0.17 -10000 0 -0.56 46 46
mol:GDP 0.012 0.052 0.18 3 -0.27 11 14
SOS1 0.023 0.003 -10000 0 -10000 0 0
MAP2K2 0.013 0.075 0.26 7 -0.39 1 8
SRC 0.022 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.014 0.064 0.28 1 -0.29 11 12
MAP2K1 -0.008 0.15 -10000 0 -0.47 19 19
heart morphogenesis 0.009 0.059 -10000 0 -0.3 11 11
RAS family/GDP 0.034 0.062 -10000 0 -0.29 2 2
GRB2 0.022 0.004 -10000 0 -10000 0 0
PRKACA -0.001 0.087 -10000 0 -0.6 10 10
CHRNE 0.007 0.016 -10000 0 -0.21 1 1
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.004 0.005 -10000 0 -10000 0 0
nervous system development 0.009 0.059 -10000 0 -0.3 11 11
CDC42 0.022 0.004 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.022 0.006 -10000 0 -10000 0 0
VDR 0.022 0.027 -10000 0 -0.56 1 1
Cbp/p300/PCAF 0.04 0.025 -10000 0 -0.36 1 1
EP300 0.022 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.019 0.047 -10000 0 -0.38 5 5
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
MAPK14 0.023 0.003 -10000 0 -10000 0 0
AKT1 -0.008 0.056 -10000 0 -0.28 3 3
RAR alpha/9cRA/Cyclin H 0.038 0.044 -10000 0 -0.32 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.001 0.089 -10000 0 -0.37 20 20
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.022 0.029 -10000 0 -0.28 1 1
NCOR2 0.022 0.027 -10000 0 -0.56 1 1
VDR/VDR/Vit D3 0.016 0.02 -10000 0 -0.41 1 1
RXRs/RARs/NRIP1/9cRA -0.033 0.11 -10000 0 -0.6 9 9
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
NCOA3 0.023 0.004 -10000 0 -10000 0 0
NCOA1 0.023 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.022 0.027 -10000 0 -0.56 1 1
RARG 0.023 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.03 0.007 -10000 0 -10000 0 0
MAPK3 0.023 0.003 -10000 0 -10000 0 0
MAPK1 0.022 0.006 -10000 0 -10000 0 0
MAPK8 0.023 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.026 0.094 -10000 0 -0.52 6 6
RARA 0.015 0.024 0.2 1 -0.25 2 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.001 0.09 -10000 0 -0.34 25 25
PRKCA 0.022 0.038 -10000 0 -0.56 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.045 0.12 -10000 0 -0.56 14 14
RXRG -0.15 0.18 -10000 0 -0.34 228 228
RXRA 0.013 0.029 -10000 0 -0.33 2 2
RXRB 0.018 0.033 0.25 1 -0.28 4 5
VDR/Vit D3/DNA 0.016 0.02 -10000 0 -0.41 1 1
RBP1 0.028 0.05 0.28 17 -10000 0 17
CRBP1/9-cic-RA 0.02 0.034 0.19 17 -10000 0 17
RARB 0.021 0.027 -10000 0 -0.56 1 1
PRKCG 0.037 0.06 0.24 33 -0.29 2 35
MNAT1 0.022 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.039 0.098 -10000 0 -0.55 9 9
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.022 0.092 -10000 0 -0.49 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.1 -10000 0 -0.37 26 26
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.046 0.12 -10000 0 -0.57 14 14
positive regulation of DNA binding 0.03 0.04 -10000 0 -0.31 2 2
NRIP1 -0.043 0.12 -10000 0 -0.65 7 7
RXRs/RARs -0.048 0.13 -10000 0 -0.58 16 16
RXRs/RXRs/DNA/9cRA -0.037 0.086 -10000 0 -0.5 7 7
PRKACA 0.022 0.005 -10000 0 -10000 0 0
CDK7 0.021 0.006 -10000 0 -10000 0 0
TFIIH 0.042 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.046 0.035 -10000 0 -10000 0 0
CCNH 0.021 0.006 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.04 0.016 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.042 0.074 -10000 0 -0.56 2 2
UGCG 0.016 0.085 -10000 0 -0.7 6 6
AKT1/mTOR/p70S6K/Hsp90/TERT 0.075 0.11 0.28 12 -0.43 11 23
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.017 0.084 -10000 0 -0.69 6 6
mol:DAG -0.018 0.16 -10000 0 -0.8 18 18
CaM/Ca2+/Calcineurin A alpha-beta B1 0.05 0.095 -10000 0 -0.38 10 10
FRAP1 0.048 0.1 -10000 0 -0.43 11 11
FOXO3 0.044 0.1 0.27 2 -0.43 11 13
AKT1 0.047 0.11 -10000 0 -0.46 11 11
GAB2 0.008 0.091 -10000 0 -0.56 12 12
SMPD1 0.005 0.12 -10000 0 -0.69 14 14
SGMS1 0.001 0.13 -10000 0 -0.64 17 17
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 -0.003 0.003 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
cell proliferation 0.033 0.1 -10000 0 -0.46 14 14
EIF3A 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.018 0.019 -10000 0 -10000 0 0
RPS6KB1 0.025 0.044 -10000 0 -0.82 1 1
mol:sphingomyelin -0.018 0.16 -10000 0 -0.8 18 18
natural killer cell activation 0 0 -10000 0 -10000 0 0
JAK3 0.024 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.007 -10000 0 -10000 0 0
JAK1 0.024 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MYC 0.061 0.11 0.38 2 -0.52 3 5
MYB 0.018 0.085 -10000 0 -1.2 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.041 0.09 -10000 0 -0.44 9 9
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.046 0.045 -10000 0 -0.74 1 1
mol:PI-3-4-5-P3 0.044 0.091 -10000 0 -0.43 9 9
Rac1/GDP 0.01 0.01 -10000 0 -10000 0 0
T cell proliferation 0.043 0.087 0.26 2 -0.46 6 8
SHC1 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.006 -10000 0 -0.064 2 2
PRKCZ 0.042 0.087 -10000 0 -0.48 6 6
NF kappa B1 p50/RelA 0.063 0.099 -10000 0 -0.42 7 7
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.008 0.054 -10000 0 -0.46 5 5
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
RELA 0.023 0.001 -10000 0 -10000 0 0
IL2RA 0.021 0.042 0.24 3 -0.56 2 5
IL2RB 0.02 0.046 -10000 0 -0.56 3 3
TERT 0.12 0.13 0.28 187 -0.29 1 188
E2F1 0.024 0.038 -10000 0 -0.41 3 3
SOS1 0.023 0.004 -10000 0 -10000 0 0
RPS6 0.021 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.003 0.03 2 -0.012 14 16
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IL2RG 0.016 0.07 -10000 0 -0.56 7 7
actin cytoskeleton organization 0.043 0.087 0.26 2 -0.46 6 8
GRB2 0.023 0.004 -10000 0 -10000 0 0
IL2 0.021 0.006 -10000 0 -10000 0 0
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.023 0.024 -10000 0 -10000 0 0
LCK 0.023 0.027 -10000 0 -0.56 1 1
BCL2 0.046 0.09 0.32 2 -0.46 3 5
IL27-mediated signaling events

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
TGFB1 0.025 0.008 -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 0.011 0.095 0.42 9 -10000 0 9
IL27/IL27R/JAK1 0.029 0.086 -10000 0 -0.42 1 1
TBX21 -0.047 0.16 -10000 0 -0.5 39 39
IL12B 0.021 0.008 -10000 0 -10000 0 0
IL12A -0.003 0.046 -10000 0 -0.41 6 6
IL6ST 0.002 0.099 -10000 0 -0.57 14 14
IL27RA/JAK1 0.016 0.033 -10000 0 -10000 0 0
IL27 0.017 0.015 -10000 0 -10000 0 0
TYK2 0.022 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.028 0.14 -10000 0 -0.78 1 1
T-helper 2 cell differentiation 0.011 0.095 0.42 9 -10000 0 9
T cell proliferation during immune response 0.011 0.095 0.42 9 -10000 0 9
MAPKKK cascade -0.011 0.095 -10000 0 -0.42 9 9
STAT3 0.023 0.003 -10000 0 -10000 0 0
STAT2 0.023 0.002 -10000 0 -10000 0 0
STAT1 0.02 0.011 -10000 0 -10000 0 0
IL12RB1 -0.012 0.14 -10000 0 -0.56 28 28
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.024 0.098 -10000 0 -0.44 5 5
IL27/IL27R/JAK2/TYK2 -0.011 0.096 -10000 0 -0.42 9 9
positive regulation of T cell mediated cytotoxicity -0.011 0.095 -10000 0 -0.42 9 9
STAT1 (dimer) 0.013 0.13 0.5 3 -0.57 5 8
JAK2 0.02 0.009 -10000 0 -10000 0 0
JAK1 0.02 0.011 -10000 0 -10000 0 0
STAT2 (dimer) -0.004 0.1 -10000 0 -0.4 10 10
T cell proliferation -0.06 0.14 -10000 0 -0.5 19 19
IL12/IL12R/TYK2/JAK2 -0.059 0.24 -10000 0 -0.8 42 42
IL17A -0.027 0.14 -10000 0 -0.78 1 1
mast cell activation 0.011 0.095 0.42 9 -10000 0 9
IFNG 0.002 0.029 -10000 0 -0.11 15 15
T cell differentiation -0.002 0.005 -10000 0 -0.019 14 14
STAT3 (dimer) -0.004 0.1 -10000 0 -0.4 10 10
STAT5A (dimer) -0.004 0.1 -10000 0 -0.4 10 10
STAT4 (dimer) -0.008 0.11 -10000 0 -0.44 9 9
STAT4 0.013 0.075 -10000 0 -0.56 8 8
T cell activation -0.005 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.022 0.069 -10000 0 -10000 0 0
GATA3 -0.042 0.22 0.57 2 -1.3 14 16
IL18 0 0.033 -10000 0 -0.41 3 3
positive regulation of mast cell cytokine production -0.004 0.1 -10000 0 -0.4 10 10
IL27/EBI3 0.029 0.024 -10000 0 -10000 0 0
IL27RA 0.004 0.023 -10000 0 -10000 0 0
IL6 -0.068 0.21 -10000 0 -0.56 76 76
STAT5A 0.023 0.003 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.012 0.018 -10000 0 -10000 0 0
IL1B -0.007 0.062 -10000 0 -0.41 11 11
EBI3 0.02 0.031 0.24 1 -0.56 1 2
TNF -0.006 0.059 -10000 0 -0.41 10 10
IL2 signaling events mediated by STAT5

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
GAB2 0.008 0.091 -10000 0 -0.56 12 12
ELF1 0.024 0.02 -10000 0 -0.36 1 1
CCNA2 0.076 0.099 0.24 123 -0.29 2 125
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
JAK3 0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
JAK1 0.023 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.038 0.095 -10000 0 -0.45 9 9
SHC1 0.022 0.005 -10000 0 -10000 0 0
SP1 0.024 0.031 -10000 0 -0.36 3 3
IL2RA 0.01 0.046 -10000 0 -0.68 2 2
IL2RB 0.019 0.046 -10000 0 -0.56 3 3
SOS1 0.023 0.004 -10000 0 -10000 0 0
IL2RG 0.015 0.07 -10000 0 -0.56 7 7
G1/S transition of mitotic cell cycle 0.034 0.094 0.31 5 -0.64 3 8
PTPN11 0.023 0.002 -10000 0 -10000 0 0
CCND2 0.007 0.065 -10000 0 -0.81 3 3
LCK 0.022 0.027 -10000 0 -0.56 1 1
GRB2 0.023 0.004 -10000 0 -10000 0 0
IL2 0.019 0.006 -10000 0 -10000 0 0
CDK6 0.023 0.024 0.38 2 -10000 0 2
CCND3 0.036 0.092 0.32 5 -0.53 3 8
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.047 0.078 0.2 5 -0.26 8 13
adherens junction organization 0.014 0.099 -10000 0 -0.41 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.062 0.089 0.34 3 -0.26 4 7
FMN1 0.009 0.1 -10000 0 -0.34 27 27
mol:IP3 0.001 0.036 -10000 0 -0.24 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.031 0.082 -10000 0 -0.41 11 11
CTNNB1 0.022 0.007 -10000 0 -10000 0 0
AKT1 0.002 0.042 -10000 0 -0.25 6 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.15 -10000 0 -0.72 17 17
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.08 -10000 0 -0.33 16 16
VASP 0.028 0.074 -10000 0 -0.38 8 8
ZYX 0.025 0.081 -10000 0 -0.39 11 11
JUB 0.026 0.083 -10000 0 -0.34 16 16
EGFR(dimer) 0.034 0.099 0.28 9 -0.35 15 24
E-cadherin/beta catenin-gamma catenin 0.038 0.015 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.011 0.052 -10000 0 -0.26 11 11
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.011 0.053 -10000 0 -0.26 11 11
FYN 0.04 0.079 0.22 6 -0.29 4 10
mol:Ca2+ 0.003 0.037 -10000 0 -0.24 3 3
JUP 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.024 0.008 -10000 0 -10000 0 0
mol:DAG 0.001 0.035 -10000 0 -0.24 3 3
CDH1 0.023 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.064 0.087 0.34 3 -0.26 4 7
establishment of polarity of embryonic epithelium 0.027 0.075 -10000 0 -0.37 9 9
SRC 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
EGFR 0.022 0.084 0.36 11 -0.56 6 17
CASR 0.039 0.077 0.23 5 -0.23 3 8
RhoA/GTP 0.061 0.069 -10000 0 -10000 0 0
AKT2 0.002 0.044 -10000 0 -0.24 10 10
actin cable formation 0.007 0.099 0.24 3 -0.34 22 25
apoptosis -0.051 0.085 0.3 9 -0.22 8 17
CTNNA1 0.025 0.008 -10000 0 -10000 0 0
mol:GDP 0.051 0.088 0.34 3 -0.26 6 9
PIP5K1A 0.024 0.08 -10000 0 -0.34 15 15
PLCG1 0.001 0.036 -10000 0 -0.25 3 3
Rac1/GTP 0.039 0.093 0.3 4 -0.33 15 19
homophilic cell adhesion 0.003 0.004 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.011 0.026 -10000 0 -0.41 2 2
MAP4K4 0.005 0.062 -10000 0 -0.47 2 2
BAG4 0.02 0.019 0.38 1 -10000 0 1
PKC zeta/ceramide 0.014 0.032 0.15 1 -0.18 9 10
NFKBIA 0.022 0.005 -10000 0 -10000 0 0
BIRC3 0.015 0.065 -10000 0 -0.56 6 6
BAX 0.001 0.056 -10000 0 -0.34 12 12
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0.013 0.12 0.65 16 -10000 0 16
BAD -0.003 0.032 0.17 3 -0.18 10 13
SMPD1 0.006 0.054 0.21 3 -0.21 11 14
RB1 -0.003 0.031 0.18 3 -0.18 9 12
FADD/Caspase 8 0.024 0.083 -10000 0 -0.45 3 3
MAP2K4 -0.005 0.032 0.18 4 -0.18 2 6
NSMAF 0.022 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.001 0.044 0.2 13 -0.18 9 22
EGF 0.015 0.072 0.24 3 -0.56 7 10
mol:ceramide -0.001 0.032 0.17 2 -0.19 10 12
MADD 0.023 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.01 0.025 -10000 0 -0.39 2 2
ASAH1 0.021 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle -0.003 0.031 0.18 3 -0.18 9 12
cell proliferation 0.012 0.06 -10000 0 -0.26 13 13
BID 0 0.13 -10000 0 -0.62 16 16
MAP3K1 -0.003 0.032 0.18 3 -0.18 9 12
EIF2A 0.05 0.096 0.19 137 -10000 0 137
TRADD 0.022 0.005 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
MAPK3 -0.001 0.043 0.21 6 -10000 0 6
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.042 0.21 5 -10000 0 5
Cathepsin D/ceramide 0.014 0.033 0.17 1 -0.18 10 11
FADD 0.004 0.057 -10000 0 -0.47 2 2
KSR1 0.001 0.043 0.19 14 -0.18 10 24
MAPK8 -0.004 0.046 -10000 0 -0.24 4 4
PRKRA 0.002 0.042 0.19 15 -0.18 8 23
PDGFA 0.02 0.038 -10000 0 -0.56 2 2
TRAF2 0.023 0.004 -10000 0 -10000 0 0
IGF1 0.005 0.1 0.24 1 -0.56 15 16
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0 0.032 0.17 2 -0.19 10 12
CTSD 0.022 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.032 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.013 0.064 -10000 0 -0.27 13 13
PRKCD 0.021 0.007 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.01 0.025 -10000 0 -0.39 2 2
RelA/NF kappa B1 0.033 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.006 0.055 -10000 0 -0.49 2 2
TNFR1A/BAG4/TNF-alpha 0.028 0.057 0.25 1 -0.35 8 9
mol:Sphingosine-1-phosphate -0.011 0.026 -10000 0 -0.41 2 2
MAP2K1 -0.003 0.043 0.23 4 -10000 0 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.023 0.001 -10000 0 -10000 0 0
CYCS 0 0.039 -10000 0 -0.2 8 8
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.018 0.26 1 -10000 0 1
EIF2AK2 0.002 0.049 0.18 23 -0.18 8 31
TNF-alpha/TNFR1A/FAN 0.034 0.053 -10000 0 -0.36 7 7
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.081 -10000 0 -0.43 8 8
MAP2K2 -0.003 0.043 0.19 13 -10000 0 13
SMPD3 0.002 0.076 0.18 1 -0.27 26 27
TNF 0.011 0.084 0.24 1 -0.56 10 11
PKC zeta/PAR4 0.032 0.008 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.006 0.041 0.24 7 -0.16 4 11
NF kappa B1/RelA/I kappa B alpha 0.06 0.023 -10000 0 -10000 0 0
AIFM1 0 0.036 -10000 0 -0.18 7 7
BCL2 0.023 0.011 0.24 1 -10000 0 1
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.03 0.027 -10000 0 -0.35 1 1
cell-cell adhesion 0.018 0.018 0.27 1 -10000 0 1
Ephrin B/EPHB2/RasGAP 0.06 0.036 -10000 0 -0.31 1 1
ITSN1 0.023 0.004 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.025 0.043 0.24 15 -10000 0 15
Ephrin B1/EPHB1 0.046 0.054 0.24 18 -10000 0 18
HRAS/GDP -0.024 0.09 -10000 0 -0.34 1 1
Ephrin B/EPHB1/GRB7 0.066 0.058 -10000 0 -0.31 1 1
Endophilin/SYNJ1 -0.011 0.026 0.2 1 -0.29 1 2
KRAS 0.021 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.064 0.056 -10000 0 -0.31 1 1
endothelial cell migration 0.022 0.029 -10000 0 -0.3 1 1
GRB2 0.023 0.004 -10000 0 -10000 0 0
GRB7 0.026 0.032 0.38 4 -10000 0 4
PAK1 0.006 0.07 0.31 3 -0.29 3 6
HRAS 0.022 0.004 -10000 0 -10000 0 0
RRAS -0.011 0.024 -10000 0 -0.3 1 1
DNM1 0.024 0.014 0.24 2 -10000 0 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.01 0.069 0.35 1 -0.3 1 2
lamellipodium assembly -0.018 0.018 -10000 0 -0.27 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.022 0.043 0.26 1 -0.26 2 3
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
EPHB2 0.026 0.028 0.24 8 -10000 0 8
EPHB3 0.026 0.066 0.35 18 -10000 0 18
EPHB1 0.052 0.088 0.28 59 -10000 0 59
EPHB4 0.022 0.006 -10000 0 -10000 0 0
mol:GDP -0.038 0.069 -10000 0 -0.32 2 2
Ephrin B/EPHB2 0.049 0.031 -10000 0 -0.31 1 1
Ephrin B/EPHB3 0.034 0.048 -10000 0 -0.31 1 1
JNK cascade 0.038 0.13 0.35 65 -10000 0 65
Ephrin B/EPHB1 0.055 0.053 -10000 0 -0.31 1 1
RAP1/GDP -0.029 0.086 -10000 0 -0.31 2 2
EFNB2 0.02 0.027 -10000 0 -0.56 1 1
EFNB3 0.023 0.015 0.24 2 -10000 0 2
EFNB1 0.023 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.052 0.057 0.24 16 -0.32 1 17
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.04 0.046 -10000 0 -0.32 1 1
Rap1/GTP 0.012 0.026 -10000 0 -10000 0 0
axon guidance 0.029 0.027 -10000 0 -0.35 1 1
MAPK3 0.01 0.039 0.23 4 -10000 0 4
MAPK1 0.011 0.043 0.25 6 -10000 0 6
Rac1/GDP -0.037 0.083 -10000 0 -0.32 2 2
actin cytoskeleton reorganization -0.037 0.044 -10000 0 -10000 0 0
CDC42/GDP -0.038 0.083 -10000 0 -0.32 2 2
PI3K 0.025 0.031 -10000 0 -0.31 1 1
EFNA5 0.02 0.027 -10000 0 -0.56 1 1
Ephrin B2/EPHB4 0.027 0.02 -10000 0 -0.35 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.016 0.035 -10000 0 -0.26 1 1
CDC42 0.022 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.019 0.019 -10000 0 -10000 0 0
PTK2 0.03 0.14 0.54 33 -10000 0 33
MAP4K4 0.038 0.13 0.35 65 -10000 0 65
SRC 0.022 0.004 -10000 0 -10000 0 0
KALRN 0.018 0.038 -10000 0 -0.56 2 2
Intersectin/N-WASP 0.033 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis 0.019 0.1 0.29 49 -10000 0 49
MAP2K1 0.014 0.038 0.24 1 -0.24 1 2
WASL 0.023 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.057 0.047 0.31 1 -10000 0 1
cell migration 0.013 0.072 0.28 5 -10000 0 5
NRAS 0.022 0.005 -10000 0 -10000 0 0
SYNJ1 -0.011 0.026 0.2 1 -0.3 1 2
PXN 0.023 0.002 -10000 0 -10000 0 0
TF -0.014 0.04 0.2 1 -0.29 5 6
HRAS/GTP 0.041 0.036 -10000 0 -0.28 1 1
Ephrin B1/EPHB1-2 0.056 0.055 0.24 18 -10000 0 18
cell adhesion mediated by integrin -0.019 0.051 0.3 1 -0.22 3 4
RAC1 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0.045 0.041 -10000 0 -0.29 1 1
RAC1-CDC42/GTP -0.014 0.02 -10000 0 -10000 0 0
RASA1 0.021 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.03 0.087 -10000 0 -0.33 1 1
ruffle organization 0.012 0.08 0.33 8 -10000 0 8
NCK1 0.019 0.009 -10000 0 -10000 0 0
receptor internalization -0.013 0.025 0.2 1 -0.29 1 2
Ephrin B/EPHB2/KALRN 0.053 0.045 -10000 0 -0.3 3 3
ROCK1 0.085 0.085 0.18 211 -10000 0 211
RAS family/GDP -0.041 0.046 -10000 0 -0.28 1 1
Rac1/GTP -0.018 0.02 -10000 0 -0.28 1 1
Ephrin B/EPHB1/Src/Paxillin 0.02 0.042 -10000 0 -0.26 1 1
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.03 0.007 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.023 0.01 0.24 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.006 0.017 -10000 0 -0.21 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.006 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.023 0.003 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
MAP3K12 0.023 0.002 -10000 0 -10000 0 0
FGR -0.011 0.13 -10000 0 -0.56 27 27
p38 alpha/TAB1 -0.029 0.085 -10000 0 -0.36 22 22
PRKG1 -0.023 0.16 -10000 0 -0.56 37 37
DUSP8 0.014 0.07 -10000 0 -0.56 7 7
PGK/cGMP/p38 alpha -0.01 0.13 -10000 0 -0.36 38 38
apoptosis -0.028 0.081 -10000 0 -0.35 22 22
RAL/GTP 0.03 0.007 -10000 0 -10000 0 0
LYN 0.02 0.038 -10000 0 -0.56 2 2
DUSP1 -0.042 0.18 -10000 0 -0.56 52 52
PAK1 0.023 0.017 0.38 1 -10000 0 1
SRC 0.022 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.053 0.019 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.022 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.029 0.008 -10000 0 -10000 0 0
MAPK11 0.012 0.1 0.23 3 -0.38 11 14
BLK 0.013 0.091 0.24 12 -0.56 10 22
HCK 0.018 0.046 -10000 0 -0.56 3 3
MAP2K3 0.022 0.005 -10000 0 -10000 0 0
DUSP16 0.022 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.027 -10000 0 -0.56 1 1
TRAF6/MEKK3 0.029 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.11 0.21 2 -0.42 19 21
positive regulation of innate immune response 0.011 0.12 0.25 3 -0.43 20 23
LCK 0.021 0.027 -10000 0 -0.56 1 1
p38alpha-beta/MKP7 0.019 0.12 0.26 1 -0.43 17 18
p38alpha-beta/MKP5 0.02 0.12 0.26 2 -0.44 17 19
PGK/cGMP -0.017 0.11 -10000 0 -0.4 38 38
PAK2 0.014 0.011 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.007 0.14 0.26 1 -0.43 26 27
CDC42 0.022 0.004 -10000 0 -10000 0 0
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.022 0.005 -10000 0 -10000 0 0
PAK3 0.012 0.055 0.24 1 -0.56 4 5
TCGA08_rtk_signaling

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
PDGFRA 0.017 0.056 0.38 1 -0.56 4 5
HRAS 0.022 0.004 -10000 0 -10000 0 0
EGFR 0.022 0.084 0.36 11 -0.56 6 17
AKT 0.063 0.075 0.25 20 -0.28 1 21
FOXO3 0.023 0.003 -10000 0 -10000 0 0
AKT1 0.022 0.006 -10000 0 -10000 0 0
FOXO1 0.021 0.006 -10000 0 -10000 0 0
AKT3 0.021 0.027 -10000 0 -0.56 1 1
FOXO4 0.023 0.003 -10000 0 -10000 0 0
MET 0.021 0.041 0.38 1 -0.56 2 3
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PIK3CB 0.019 0.009 -10000 0 -10000 0 0
NRAS 0.022 0.005 -10000 0 -10000 0 0
PIK3CG -0.024 0.16 -10000 0 -0.56 38 38
PIK3R3 0.023 0.004 -10000 0 -10000 0 0
PIK3R2 0.022 0.005 -10000 0 -10000 0 0
NF1 0.023 0.003 -10000 0 -10000 0 0
RAS 0.023 0.049 0.25 5 -0.18 11 16
ERBB2 0.024 0.023 0.38 2 -10000 0 2
proliferation/survival/translation -0.061 0.073 0.26 4 -0.25 11 15
PI3K 0.045 0.072 0.22 32 -0.21 6 38
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
KRAS 0.021 0.006 -10000 0 -10000 0 0
FOXO 0.079 0.061 0.23 27 -10000 0 27
AKT2 0.021 0.006 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
IGF1 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
NCK2 0.023 0.002 -10000 0 -10000 0 0
PTK2 0.021 0.006 -10000 0 -10000 0 0
CRKL 0.003 0.048 -10000 0 -0.3 12 12
GRB2/SOS1/SHC 0.042 0.014 -10000 0 -10000 0 0
HRAS 0.022 0.004 -10000 0 -10000 0 0
IRS1/Crk 0.011 0.052 -10000 0 -0.29 13 13
IGF-1R heterotetramer/IGF1/PTP1B 0.033 0.062 -10000 0 -0.34 12 12
AKT1 0.057 0.095 0.25 10 -0.27 4 14
BAD 0.052 0.091 0.24 10 -0.26 4 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.002 0.05 -10000 0 -0.29 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.016 0.054 -10000 0 -0.3 13 13
RAF1 0.056 0.12 0.28 9 -0.43 9 18
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.042 0.057 -10000 0 -0.29 12 12
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.019 0.058 -10000 0 -0.32 13 13
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
RPS6KB1 0.059 0.097 0.25 12 -0.27 4 16
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.054 0.1 0.27 16 -0.33 5 21
PXN 0.023 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.033 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.044 -10000 0 -0.27 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.054 0.055 -10000 0 -0.28 9 9
IGF-1R heterotetramer 0.021 0.02 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.031 0.058 -10000 0 -0.3 13 13
Crk/p130 Cas/Paxillin 0.037 0.056 -10000 0 -0.28 12 12
IGF1R 0.021 0.02 -10000 0 -10000 0 0
IGF1 0.007 0.1 0.27 1 -0.57 15 16
IRS2/Crk 0.009 0.053 -10000 0 -0.29 14 14
PI3K 0.022 0.045 -10000 0 -0.29 4 4
apoptosis -0.056 0.092 -10000 0 -0.26 14 14
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
PRKCD -0.001 0.068 -10000 0 -0.37 14 14
RAF1/14-3-3 E 0.055 0.12 0.28 10 -0.37 11 21
BAD/14-3-3 0.058 0.096 0.27 12 -10000 0 12
PRKCZ 0.056 0.096 0.25 9 -0.27 4 13
Crk/p130 Cas/Paxillin/FAK1 0.054 0.062 -10000 0 -10000 0 0
PTPN1 0.022 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.001 0.073 -10000 0 -0.39 14 14
BCAR1 0.022 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.044 0.055 -10000 0 -0.3 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.023 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.018 0.056 -10000 0 -0.29 13 13
GRB10 0.022 0.005 -10000 0 -10000 0 0
PTPN11 0.002 0.051 -10000 0 -0.3 13 13
IRS1 0.004 0.057 -10000 0 -0.32 13 13
IRS2 0.001 0.053 -10000 0 -0.3 14 14
IGF-1R heterotetramer/IGF1 0.02 0.078 -10000 0 -0.4 15 15
GRB2 0.023 0.004 -10000 0 -10000 0 0
PDPK1 0.058 0.098 0.26 10 -0.28 4 14
YWHAE 0.022 0.006 -10000 0 -10000 0 0
PRKD1 -0.012 0.094 -10000 0 -0.38 25 25
SHC1 0.022 0.005 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP 0.009 0.097 -10000 0 -0.29 40 40
TC10/GTP 0.006 0.09 -10000 0 -0.29 36 36
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.018 -10000 0 -10000 0 0
HRAS 0.022 0.004 -10000 0 -10000 0 0
APS homodimer 0.022 0.005 -10000 0 -10000 0 0
GRB14 -0.013 0.14 0.24 1 -0.56 30 31
FOXO3 0.031 0.06 -10000 0 -0.53 4 4
AKT1 0.045 0.11 0.3 5 -10000 0 5
INSR 0.024 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.044 0.024 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.005 -10000 0 -10000 0 0
SORBS1 -0.039 0.18 -10000 0 -0.56 50 50
CRK 0.022 0.006 -10000 0 -10000 0 0
PTPN1 0.002 0.035 -10000 0 -10000 0 0
CAV1 -0.089 0.13 -10000 0 -0.31 125 125
CBL/APS/CAP/Crk-II/C3G 0.023 0.11 -10000 0 -0.31 39 39
Insulin Receptor/Insulin/IRS1/NCK2 0.054 0.018 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.023 0.024 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.019 0.053 -10000 0 -0.36 3 3
RPS6KB1 0.039 0.11 0.29 5 -10000 0 5
PARD6A 0.022 0.005 -10000 0 -10000 0 0
CBL 0.023 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.017 0.007 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.049 0.088 -10000 0 -10000 0 0
HRAS/GTP -0.019 0.017 -10000 0 -0.28 1 1
Insulin Receptor 0.024 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.059 0.025 -10000 0 -10000 0 0
PRKCI 0.009 0.031 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.001 0.067 -10000 0 -0.29 21 21
SHC1 0.022 0.005 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.032 0.022 -10000 0 -10000 0 0
PI3K 0.028 0.029 -10000 0 -10000 0 0
NCK2 0.023 0.002 -10000 0 -10000 0 0
RHOQ 0.022 0.006 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
AKT2 0.041 0.11 0.3 8 -0.28 19 27
PRKCZ 0.006 0.042 -10000 0 -10000 0 0
SH2B2 0.022 0.005 -10000 0 -10000 0 0
SHC/SHIP 0.021 0.021 -10000 0 -0.3 1 1
F2RL2 0.049 0.098 0.24 77 -0.35 9 86
TRIP10 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.04 0.015 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.059 0.025 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
RASA1 0.021 0.006 -10000 0 -10000 0 0
NCK1 0.019 0.009 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.014 0.11 -10000 0 -0.32 40 40
TC10/GDP 0.016 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.051 0.021 -10000 0 -10000 0 0
INPP5D -0.011 0.022 -10000 0 -0.32 1 1
SOS1 0.023 0.003 -10000 0 -10000 0 0
SGK1 0 0.061 -10000 0 -0.59 5 5
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
IRS1 0.023 0.004 -10000 0 -10000 0 0
p62DOK/RasGAP 0.033 0.022 -10000 0 -10000 0 0
INS 0.019 0.008 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.011 0.022 -10000 0 -0.32 1 1
GRB2 0.023 0.004 -10000 0 -10000 0 0
EIF4EBP1 0.039 0.11 0.31 13 -10000 0 13
PTPRA 0.023 0.006 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.029 0.009 -10000 0 -10000 0 0
PDPK1 0.022 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.018 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.041 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.032 0.011 -10000 0 -10000 0 0
Par3/Par6 0.06 0.057 -10000 0 -0.31 1 1
Signaling events mediated by PRL

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
CCNE1 0.079 0.11 0.28 106 -10000 0 106
mol:Halofuginone 0.002 0 -10000 0 -10000 0 0
ITGA1 0.016 0.053 -10000 0 -0.56 4 4
CDKN1A 0.009 0.039 -10000 0 -0.31 6 6
PRL-3/alpha Tubulin 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.086 -10000 0 -0.42 23 23
AGT -0.006 0.13 0.24 1 -0.56 24 25
CCNA2 -0.014 0.047 0.39 1 -0.33 1 2
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
EGR1 0.004 0.05 -10000 0 -0.4 7 7
CDK2/Cyclin E1 0.065 0.098 0.33 5 -0.34 4 9
MAPK3 -0.009 0.003 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.033 0.007 -10000 0 -10000 0 0
MAPK1 -0.009 0.003 -10000 0 -10000 0 0
PTP4A1 -0.009 0.035 -10000 0 -0.32 6 6
PTP4A3 0.021 0.006 -10000 0 -10000 0 0
PTP4A2 0.023 0.004 -10000 0 -10000 0 0
ITGB1 -0.009 0.003 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.01 0.03 -10000 0 -0.31 3 3
Rab GGTase beta/Rab GGTase alpha 0.032 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 0.021 0.057 0.3 1 -10000 0 1
RABGGTA 0.022 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.006 -10000 0 -10000 0 0
RHOC 0.007 0.044 -10000 0 -0.31 8 8
RHOA 0.005 0.049 -10000 0 -0.31 10 10
cell motility 0.012 0.065 -10000 0 -0.28 10 10
PRL-1/alpha Tubulin 0.02 0.054 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.043 -10000 0 -0.36 5 5
ROCK1 0.019 0.05 -10000 0 -0.33 3 3
RABGGTB 0.022 0.004 -10000 0 -10000 0 0
CDK2 0.023 0.002 -10000 0 -10000 0 0
mitosis -0.009 0.034 -10000 0 -0.31 6 6
ATF5 0.026 0.026 0.24 7 -10000 0 7
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.023 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.005 0.017 -10000 0 -10000 0 0
FRAP1 0.047 0.056 0.27 1 -0.37 2 3
AKT1 0.055 0.079 0.18 14 -10000 0 14
INSR 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0.079 0.074 0.26 15 -10000 0 15
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.013 -10000 0 -10000 0 0
TSC2 0.022 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.009 0.017 -10000 0 -10000 0 0
TSC1 0.023 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.019 0.033 -10000 0 -0.18 11 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.015 0.023 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.004 -10000 0 -10000 0 0
RPS6KB1 0.072 0.075 0.24 20 -0.3 1 21
MAP3K5 0.001 0.027 0.19 3 -0.18 7 10
PIK3R1 0.022 0.007 -10000 0 -10000 0 0
apoptosis 0.001 0.027 0.19 3 -0.18 7 10
mol:LY294002 0 0 -10000 0 -0.001 13 13
EIF4B 0.067 0.072 0.23 22 -0.27 1 23
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.071 0.062 0.23 11 -0.25 1 12
eIF4E/eIF4G1/eIF4A1 0.008 0.017 -10000 0 -0.27 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.027 -10000 0 -0.18 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.055 0.066 0.19 40 -10000 0 40
FKBP1A 0.023 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.063 0.058 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 13 13
FKBP12/Rapamycin 0.019 0.005 -10000 0 -10000 0 0
PDPK1 -0.002 0.032 0.16 14 -10000 0 14
EIF4E 0.022 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.05 0.084 -10000 0 -0.52 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.006 0.063 -10000 0 -0.87 1 1
TSC1/TSC2 0.088 0.081 0.28 17 -10000 0 17
tumor necrosis factor receptor activity 0 0 0.001 13 -10000 0 13
RPS6 0.021 0.007 -10000 0 -10000 0 0
PPP5C 0.023 0.004 -10000 0 -10000 0 0
EIF4G1 0.013 0.012 -10000 0 -10000 0 0
IRS1 0.005 0.033 -10000 0 -0.19 13 13
INS -0.018 0.003 -10000 0 -10000 0 0
PTEN 0.02 0.006 -10000 0 -10000 0 0
PDK2 -0.002 0.032 0.16 14 -10000 0 14
EIF4EBP1 0.007 0.18 -10000 0 -1 12 12
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PPP2R5D 0.046 0.058 0.24 8 -0.34 2 10
peptide biosynthetic process -0.013 0.013 0.18 2 -10000 0 2
RHEB 0.023 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.002 0.004 62 -10000 0 62
EEF2 -0.013 0.013 0.18 2 -10000 0 2
eIF4E/4E-BP1 0.012 0.16 -10000 0 -0.93 12 12
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.043 0.044 -10000 0 -0.3 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.022 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.039 0.046 0.28 1 -10000 0 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.041 0.022 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.002 0.034 -10000 0 -0.23 1 1
CaM/Ca2+ 0.042 0.044 -10000 0 -0.28 4 4
RAP1A 0.022 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.025 0.042 -10000 0 -0.29 3 3
AKT1 0.067 0.097 0.29 19 -0.26 2 21
MAP2K1 -0.008 0.048 0.27 1 -0.28 4 5
MAP3K11 -0.006 0.048 0.27 1 -0.29 4 5
IFNGR1 0.024 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.004 0.12 -10000 0 -0.4 33 33
Rap1/GTP -0.019 0.021 -10000 0 -10000 0 0
CRKL/C3G 0.032 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.054 0.045 -10000 0 -0.31 4 4
CEBPB -0.013 0.14 0.28 1 -0.48 29 30
STAT3 0.023 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.037 0.13 -10000 0 -0.72 12 12
STAT1 -0.003 0.046 0.27 1 -0.29 3 4
CALM1 0.022 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.017 0.056 0.25 2 -0.56 4 6
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.025 0.046 0.27 1 -0.28 3 4
CEBPB/PTGES2/Cbp/p300 0.003 0.093 -10000 0 -0.39 8 8
mol:Ca2+ 0.04 0.043 -10000 0 -0.29 4 4
MAPK3 -0.003 0.11 -10000 0 -0.68 8 8
STAT1 (dimer) 0.006 0.047 -10000 0 -0.31 1 1
MAPK1 -0.004 0.1 -10000 0 -0.6 9 9
JAK2 0.021 0.01 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
JAK1 0.023 0.009 -10000 0 -10000 0 0
CAMK2D 0.022 0.005 -10000 0 -10000 0 0
DAPK1 -0.026 0.17 -10000 0 -0.59 35 35
SMAD7 0.032 0.05 0.16 19 -0.3 1 20
CBL/CRKL/C3G 0.034 0.045 0.27 1 -0.26 3 4
PI3K 0.023 0.039 -10000 0 -0.27 2 2
IFNG 0.017 0.056 0.25 2 -0.56 4 6
apoptosis -0.008 0.13 -10000 0 -0.43 34 34
CAMK2G 0.022 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.003 -10000 0 -10000 0 0
CAMK2A -0.014 0.14 -10000 0 -0.56 29 29
CAMK2B 0.047 0.075 0.25 55 -0.29 1 56
FRAP1 0.062 0.092 0.28 19 -0.25 2 21
PRKCD 0.065 0.099 0.3 19 -10000 0 19
RAP1B 0.022 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.002 0.034 -10000 0 -0.23 1 1
PTPN2 0.022 0.005 -10000 0 -10000 0 0
EP300 0.023 0.004 -10000 0 -10000 0 0
IRF1 0.003 0.049 0.24 2 -0.33 1 3
STAT1 (dimer)/PIASy 0.023 0.045 0.27 1 -0.28 3 4
SOCS1 -0.006 0.17 -10000 0 -1 13 13
mol:GDP 0.03 0.042 0.25 1 -0.26 3 4
CASP1 0.033 0.051 0.16 19 -0.26 2 21
PTGES2 0.023 0.003 -10000 0 -10000 0 0
IRF9 0.01 0.044 -10000 0 -0.19 1 1
mol:PI-3-4-5-P3 0.016 0.032 -10000 0 -0.27 2 2
RAP1/GDP 0.027 0.033 -10000 0 -10000 0 0
CBL -0.005 0.047 0.27 1 -0.29 4 5
MAP3K1 -0.006 0.047 0.27 1 -0.29 4 5
PIAS1 0.023 0.002 -10000 0 -10000 0 0
PIAS4 0.022 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.002 0.034 -10000 0 -0.23 1 1
PTPN11 0.005 0.051 0.29 1 -0.3 4 5
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
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 0.021 0.006 -10000 0 -10000 0 0
NFATC1 0.026 0.074 0.26 2 -0.38 3 5
NFATC2 -0.02 0.097 0.18 3 -0.28 38 41
NFATC3 0.012 0.009 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.024 0.13 -10000 0 -0.46 27 27
Exportin 1/Ran/NUP214 0.041 0.015 -10000 0 -10000 0 0
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.003 0.12 -10000 0 -0.42 24 24
BCL2/BAX 0.033 0.01 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.014 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0.014 -10000 0 -10000 0 0
BAX 0.023 0.004 -10000 0 -10000 0 0
MAPK14 0.022 0.004 -10000 0 -10000 0 0
BAD 0.023 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D -0.012 0.12 -10000 0 -0.44 26 26
Calcineurin A alpha-beta B1/BCL2 0.023 0.011 0.24 1 -10000 0 1
FKBP8 0.022 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.012 0.12 0.43 26 -10000 0 26
KPNB1 0.023 0.003 -10000 0 -10000 0 0
KPNA2 0.023 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
SFN 0.04 0.072 0.24 45 -0.38 3 48
MAP3K8 0.017 0.029 -10000 0 -0.56 1 1
NFAT4/CK1 alpha 0.017 0.022 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.02 0.15 -10000 0 -0.33 63 63
CABIN1 -0.024 0.13 -10000 0 -0.47 26 26
CALM1 0.017 0.015 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
MAP3K1 0.021 0.006 -10000 0 -10000 0 0
CAMK4 0.019 0.038 -10000 0 -0.56 2 2
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.003 -10000 0 -10000 0 0
YWHAH 0.022 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.03 0.03 -10000 0 -0.41 2 2
YWHAB 0.022 0.004 -10000 0 -10000 0 0
MAPK8 0.018 0.013 -10000 0 -10000 0 0
MAPK9 0.021 0.007 -10000 0 -10000 0 0
YWHAG 0.023 0.004 -10000 0 -10000 0 0
FKBP1A 0.022 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.015 0.094 0.28 1 -0.39 6 7
PRKCH 0.022 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.023 0.026 -10000 0 -10000 0 0
CASP3 0.02 0.007 -10000 0 -10000 0 0
PIM1 0.023 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.009 -10000 0 -10000 0 0
apoptosis 0.016 0.007 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.04 -10000 0 -0.26 5 5
PRKCB -0.005 0.12 -10000 0 -0.56 23 23
PRKCE 0.021 0.027 -10000 0 -0.56 1 1
JNK2/NFAT4 0.024 0.025 -10000 0 -10000 0 0
BAD/BCL-XL 0.032 0.009 -10000 0 -10000 0 0
PRKCD 0.021 0.007 -10000 0 -10000 0 0
NUP214 0.023 0.003 -10000 0 -10000 0 0
PRKCZ 0.018 0.013 -10000 0 -10000 0 0
PRKCA 0.02 0.038 -10000 0 -0.56 2 2
PRKCG 0.029 0.064 0.24 33 -0.29 2 35
PRKCQ -0.027 0.16 -10000 0 -0.56 40 40
FKBP38/BCL2 0.032 0.012 -10000 0 -10000 0 0
EP300 0.016 0.017 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.035 0.073 0.26 1 -0.36 3 4
CaM/Ca2+/FKBP38 0.023 0.019 -10000 0 -10000 0 0
FKBP12/FK506 0.016 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.02 0.032 -10000 0 -0.36 2 2
NFATc/ERK1 0.039 0.074 0.26 1 -0.36 3 4
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0 0.12 -10000 0 -0.42 26 26
NR4A1 -0.067 0.21 0.23 1 -0.54 72 73
GSK3B 0.017 0.013 -10000 0 -10000 0 0
positive T cell selection 0.012 0.009 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.011 0.072 0.16 1 -0.29 15 16
RCH1/ KPNB1 0.033 0.006 -10000 0 -10000 0 0
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
AKAP5 0.02 0.038 -10000 0 -0.56 2 2
MEF2D 0.016 0.018 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.038 0.074 0.26 1 -0.36 3 4
CREBBP 0.016 0.017 -10000 0 -10000 0 0
BCL2 0.023 0.011 0.24 1 -10000 0 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.02 0.019 0.38 1 -10000 0 1
Caspase 8 (4 units) 0.029 0.07 -10000 0 -0.29 3 3
NEF -0.005 0.038 -10000 0 -0.2 15 15
NFKBIA 0.022 0.015 -10000 0 -10000 0 0
BIRC3 0.012 0.069 -10000 0 -0.54 6 6
CYCS 0.011 0.066 0.26 2 -0.32 3 5
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CD247 0.003 0.1 -10000 0 -0.63 11 11
MAP2K7 0.008 0.14 -10000 0 -0.63 17 17
protein ubiquitination 0.021 0.071 0.25 3 -0.39 2 5
CRADD 0.023 0.002 -10000 0 -10000 0 0
DAXX 0.023 0.004 -10000 0 -10000 0 0
FAS 0.021 0.027 -10000 0 -0.56 1 1
BID 0.013 0.068 -10000 0 -0.28 13 13
NF-kappa-B/RelA/I kappa B alpha 0.044 0.037 -10000 0 -0.29 5 5
TRADD 0.022 0.005 -10000 0 -10000 0 0
MAP3K5 0.023 0.003 -10000 0 -10000 0 0
CFLAR 0.022 0.004 -10000 0 -10000 0 0
FADD 0.02 0.008 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.037 -10000 0 -0.29 5 5
MAPK8 0.008 0.13 -10000 0 -0.6 16 16
APAF1 0.023 0.002 -10000 0 -10000 0 0
TRAF1 0.023 0.003 -10000 0 -10000 0 0
TRAF2 0.023 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.013 0.07 -10000 0 -0.29 19 19
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.015 0.076 -10000 0 -0.41 5 5
CHUK 0.022 0.074 0.26 3 -0.42 2 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.051 0.035 -10000 0 -0.31 1 1
TCRz/NEF -0.002 0.1 -10000 0 -0.42 24 24
TNF 0.011 0.084 0.24 1 -0.56 10 11
FASLG -0.019 0.15 -10000 0 -0.62 25 25
NFKB1 0.023 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.028 0.057 0.25 1 -0.35 8 9
CASP6 0.018 0.13 -10000 0 -0.52 15 15
CASP7 0.017 0.11 0.34 4 -0.48 11 15
RELA 0.023 0.017 -10000 0 -0.17 1 1
CASP2 0.023 0.004 -10000 0 -10000 0 0
CASP3 0.011 0.11 0.34 4 -0.5 9 13
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.018 0.26 1 -10000 0 1
CASP8 0.022 0.004 -10000 0 -10000 0 0
CASP9 0.022 0.005 -10000 0 -10000 0 0
MAP3K14 0.023 0.08 -10000 0 -0.41 4 4
APAF-1/Caspase 9 0.014 0.07 -10000 0 -0.39 6 6
BCL2 0.007 0.12 0.28 1 -0.55 15 16
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
mol:S1P 0.001 0.001 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.003 0.056 -10000 0 -0.26 13 13
GNAO1 0.022 0.031 0.24 2 -0.56 1 3
S1P/S1P3/G12/G13 0.043 0.012 -10000 0 -10000 0 0
AKT1 0.013 0.08 -10000 0 -0.45 13 13
AKT3 0.018 0.078 -10000 0 -1.2 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
GNAI2 0.022 0.007 -10000 0 -10000 0 0
GNAI3 0.023 0.006 -10000 0 -10000 0 0
GNAI1 0.022 0.027 -10000 0 -0.56 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.023 0.005 -10000 0 -10000 0 0
S1PR2 0.022 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0.039 -10000 0 -0.22 6 6
MAPK3 0.011 0.043 -10000 0 -0.25 1 1
MAPK1 0.009 0.037 -10000 0 -10000 0 0
JAK2 0.013 0.049 -10000 0 -0.27 1 1
CXCR4 0.01 0.042 -10000 0 -0.25 1 1
FLT1 0.023 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
SRC 0.01 0.043 -10000 0 -0.25 1 1
S1P/S1P3/Gi 0.02 0.039 -10000 0 -0.24 2 2
RAC1 0.022 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.021 0.054 -10000 0 -10000 0 0
VEGFA 0.024 0.004 -10000 0 -10000 0 0
S1P/S1P2/Gi 0.02 0.034 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.035 0.011 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.047 0.12 -10000 0 -0.27 109 109
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
G12/G13 0.033 0.008 -10000 0 -10000 0 0
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.022 0.004 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
GNA11 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.058 -10000 0 -10000 0 0
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.003 0.092 0.25 1 -0.38 15 16
PDGFB-D/PDGFRB/SLAP 0.009 0.099 -10000 0 -0.42 23 23
PDGFB-D/PDGFRB/APS/CBL 0.04 0.024 -10000 0 -0.36 1 1
AKT1 0.065 0.1 0.32 23 -10000 0 23
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.007 0.11 -10000 0 -0.42 17 17
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
FGR -0.044 0.19 0.32 1 -0.63 39 40
mol:Ca2+ -0.005 0.12 -10000 0 -0.43 24 24
MYC 0.02 0.1 0.4 1 -0.41 3 4
SHC1 0.022 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.026 0.033 -10000 0 -0.3 1 1
LRP1/PDGFRB/PDGFB 0.042 0.023 -10000 0 -0.36 1 1
GRB10 0.022 0.005 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GO:0007205 -0.005 0.12 -10000 0 -0.44 24 24
PTEN 0.021 0.006 -10000 0 -10000 0 0
GRB2 0.023 0.004 -10000 0 -10000 0 0
GRB7 0.026 0.032 0.38 4 -10000 0 4
PDGFB-D/PDGFRB/SHP2 0.032 0.022 -10000 0 -0.42 1 1
PDGFB-D/PDGFRB/GRB10 0.03 0.023 -10000 0 -0.42 1 1
cell cycle arrest 0.009 0.099 -10000 0 -0.42 23 23
HRAS 0.022 0.004 -10000 0 -10000 0 0
HIF1A 0.058 0.096 0.28 28 -10000 0 28
GAB1 -0.002 0.11 -10000 0 -0.44 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.001 0.097 0.32 1 -0.4 11 12
PDGFB-D/PDGFRB 0.042 0.025 -10000 0 -0.37 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.023 -10000 0 -0.42 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.007 0.074 -10000 0 -0.39 5 5
positive regulation of MAPKKK cascade 0.031 0.022 -10000 0 -0.41 1 1
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 -0.005 0.12 -10000 0 -0.44 24 24
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.022 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.033 0.031 0.27 4 -0.42 1 5
SHB 0.021 0.007 -10000 0 -10000 0 0
BLK -0.048 0.18 -10000 0 -0.48 59 59
PTPN2 0.022 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.031 0.022 -10000 0 -0.42 1 1
BCAR1 0.022 0.006 -10000 0 -10000 0 0
VAV2 -0.002 0.12 -10000 0 -0.45 18 18
CBL 0.023 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.031 -10000 0 -0.42 2 2
LCK -0.007 0.11 0.32 1 -0.59 12 13
PDGFRB 0.021 0.028 -10000 0 -0.57 1 1
ACP1 0.023 0.004 -10000 0 -10000 0 0
HCK 0.003 0.071 0.32 1 -0.54 5 6
ABL1 -0.003 0.1 -10000 0 -0.41 19 19
PDGFB-D/PDGFRB/CBL -0.006 0.13 -10000 0 -0.49 23 23
PTPN1 0.023 0.005 -10000 0 -10000 0 0
SNX15 0.023 0.001 -10000 0 -10000 0 0
STAT3 0.023 0.003 -10000 0 -10000 0 0
STAT1 0.022 0.004 -10000 0 -10000 0 0
cell proliferation 0.021 0.098 0.33 2 -0.38 3 5
SLA -0.007 0.12 -10000 0 -0.56 23 23
actin cytoskeleton reorganization 0.025 0.081 0.33 5 -0.3 1 6
SRC 0.004 0.068 0.31 1 -0.65 3 4
PI3K -0.011 0.018 -10000 0 -0.28 1 1
PDGFB-D/PDGFRB/GRB7/SHC 0.043 0.027 0.25 4 -10000 0 4
SH2B2 0.022 0.005 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.006 0.11 -10000 0 -0.43 17 17
LYN 0 0.083 0.3 1 -0.54 8 9
LRP1 0.023 0.002 -10000 0 -10000 0 0
SOS1 0.023 0.003 -10000 0 -10000 0 0
STAT5B 0.023 0.003 -10000 0 -10000 0 0
STAT5A 0.023 0.003 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.05 0.037 -10000 0 -0.31 1 1
SPHK1 0.023 0.005 -10000 0 -10000 0 0
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG -0.005 0.12 -10000 0 -0.44 24 24
PLCG1 -0.006 0.12 -10000 0 -0.45 24 24
NHERF/PDGFRB 0.041 0.038 0.25 1 -0.35 3 4
YES1 0.001 0.073 -10000 0 -0.54 6 6
cell migration 0.041 0.038 0.25 1 -0.35 3 4
SHC/Grb2/SOS1 0.057 0.03 -10000 0 -10000 0 0
SLC9A3R2 0.02 0.038 -10000 0 -0.56 2 2
SLC9A3R1 0.025 0.024 0.27 4 -10000 0 4
NHERF1-2/PDGFRB/PTEN 0.05 0.038 -10000 0 -0.32 3 3
FYN 0.002 0.075 -10000 0 -0.57 6 6
DOK1 -0.003 0.039 -10000 0 -0.33 1 1
HRAS/GTP 0.017 0.003 -10000 0 -10000 0 0
PDGFB 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.002 0.11 0.29 1 -0.46 11 12
PRKCD -0.002 0.041 -10000 0 -0.34 1 1
FER -0.002 0.042 -10000 0 -0.34 1 1
MAPKKK cascade 0.005 0.067 0.38 5 -10000 0 5
RASA1 -0.002 0.042 -10000 0 -0.34 1 1
NCK1 0.019 0.009 -10000 0 -10000 0 0
NCK2 0.023 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.027 0.033 -10000 0 -0.31 1 1
PDGFB-D/PDGFRB/SHB 0.03 0.023 -10000 0 -0.42 1 1
chemotaxis -0.003 0.1 -10000 0 -0.4 19 19
STAT1-3-5/STAT1-3-5 0.048 0.028 -10000 0 -0.3 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.02 -10000 0 -0.42 1 1
PTPRJ 0.021 0.027 -10000 0 -0.56 1 1
EPO 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
BCL2L1 0.041 0.05 0.34 2 -10000 0 2
CRKL 0.023 0.063 0.3 8 -0.28 2 10
mol:DAG 0.026 0.038 -10000 0 -0.33 1 1
HRAS 0.016 0.076 0.28 15 -10000 0 15
MAPK8 0.003 0.051 0.19 12 -0.33 1 13
RAP1A 0.023 0.062 0.3 8 -0.28 2 10
GAB1 0.023 0.062 0.3 8 -0.27 2 10
MAPK14 0.004 0.054 0.19 16 -0.33 1 17
EPO 0.026 0.028 0.26 6 -10000 0 6
PLCG1 0.026 0.039 -10000 0 -0.33 1 1
EPOR/TRPC2/IP3 Receptors 0.026 0.01 -10000 0 -10000 0 0
RAPGEF1 0.023 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.044 0.037 -10000 0 -0.37 2 2
GAB1/SHC/GRB2/SOS1 0.047 0.049 0.26 6 -10000 0 6
EPO/EPOR (dimer) 0.037 0.024 0.23 1 -10000 0 1
IRS2 0.02 0.066 0.3 8 -0.28 5 13
STAT1 0.031 0.039 -10000 0 -10000 0 0
STAT5B 0.029 0.041 -10000 0 -0.33 1 1
cell proliferation 0.001 0.053 0.19 18 -0.32 1 19
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.038 -10000 0 -10000 0 0
TEC 0.02 0.065 0.3 7 -0.29 5 12
SOCS3 0.02 0.038 -10000 0 -0.56 2 2
STAT1 (dimer) 0.031 0.038 -10000 0 -10000 0 0
JAK2 0.023 0.011 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.061 0.05 0.33 1 -0.29 2 3
EPO/EPOR 0.037 0.024 0.23 1 -10000 0 1
LYN 0.021 0.038 -10000 0 -0.56 2 2
TEC/VAV2 0.033 0.063 0.27 5 -0.35 5 10
elevation of cytosolic calcium ion concentration 0.026 0.01 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.047 0.032 -10000 0 -0.37 1 1
mol:IP3 0.026 0.038 -10000 0 -0.33 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.042 0.062 0.3 7 -0.28 5 12
SH2B3 0.024 0.039 -10000 0 -0.56 2 2
NFKB1 0.005 0.054 0.18 20 -0.33 1 21
EPO/EPOR (dimer)/JAK2/SOCS3 0.009 0.033 0.26 2 -0.2 6 8
PTPN6 0.016 0.046 0.3 2 -0.29 2 4
TEC/VAV2/GRB2 0.042 0.062 0.27 5 -0.36 4 9
EPOR 0.026 0.01 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
mol:GDP 0.047 0.049 0.26 6 -10000 0 6
SOS1 0.023 0.003 -10000 0 -10000 0 0
PLCG2 0.022 0.005 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.045 0.052 0.27 5 -0.27 1 6
VAV2 0.021 0.065 0.3 7 -0.31 4 11
CBL 0.023 0.063 0.3 8 -0.28 2 10
SHC/Grb2/SOS1 0.03 0.03 -10000 0 -0.26 2 2
STAT5A 0.029 0.041 -10000 0 -0.33 1 1
GRB2 0.023 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.044 0.045 -10000 0 -0.31 1 1
LYN/PLCgamma2 0.03 0.03 -10000 0 -0.41 2 2
PTPN11 0.023 0.002 -10000 0 -10000 0 0
BTK -0.001 0.1 0.3 7 -0.31 32 39
BCL2 0.042 0.054 0.34 2 -10000 0 2
TRAIL signaling pathway

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
TNFSF10 0.013 0.012 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0.009 0.055 -10000 0 -0.25 16 16
MAP2K4 0.012 0.031 -10000 0 -10000 0 0
IKBKB 0.022 0.018 0.38 1 -10000 0 1
TNFRSF10B 0.021 0.007 -10000 0 -10000 0 0
TNFRSF10A 0.019 0.027 -10000 0 -0.56 1 1
SMPD1 0.006 0.006 -10000 0 -10000 0 0
IKBKG 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.002 0.1 -10000 0 -0.56 15 15
TRAIL/TRAILR2 0.018 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR3 -0.01 0.094 -10000 0 -0.27 47 47
TRAIL/TRAILR1 0.017 0.026 -10000 0 -0.41 1 1
TRAIL/TRAILR4 0.009 0.055 -10000 0 -0.25 16 16
TRAIL/TRAILR1/DAP3/GTP 0.022 0.027 -10000 0 -0.32 1 1
IKK complex 0.007 0.027 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.016 0.004 -10000 0 -10000 0 0
MAPK3 -0.006 0.005 -10000 0 -10000 0 0
MAP3K1 0.017 0.03 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.002 0.1 -10000 0 -0.56 15 15
TRADD 0.022 0.005 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.019 0.027 -10000 0 -0.56 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.009 0.02 -10000 0 -0.26 1 1
CFLAR 0.022 0.004 -10000 0 -10000 0 0
MAPK1 -0.005 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.029 0.038 -10000 0 -0.31 1 1
mol:ceramide 0.006 0.006 -10000 0 -10000 0 0
FADD 0.02 0.008 -10000 0 -10000 0 0
MAPK8 0.044 0.054 0.28 1 -10000 0 1
TRAF2 0.023 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.035 0.17 -10000 0 -0.56 46 46
CHUK 0.022 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.02 0.029 -10000 0 -0.36 1 1
DAP3 0.022 0.005 -10000 0 -10000 0 0
CASP10 0.06 0.094 0.36 15 -10000 0 15
JNK cascade 0.009 0.055 -10000 0 -0.25 16 16
TRAIL (trimer) 0.013 0.012 -10000 0 -10000 0 0
TNFRSF10C -0.035 0.17 -10000 0 -0.56 46 46
TRAIL/TRAILR1/DAP3/GTP/FADD 0.023 0.031 -10000 0 -0.31 1 1
TRAIL/TRAILR2/FADD 0.021 0.023 -10000 0 -10000 0 0
cell death 0.006 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.01 0.016 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.02 0.007 -10000 0 -10000 0 0
CASP8 -0.005 0.076 -10000 0 -0.47 11 11
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.029 0.034 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.009 0.051 -10000 0 -10000 0 0
DAPP1 -0.011 0.12 0.23 2 -0.4 29 31
Src family/SYK family/BLNK-LAT/BTK-ITK -0.023 0.17 0.31 1 -0.55 34 35
mol:DAG -0.002 0.085 0.2 9 -0.24 24 33
HRAS 0.024 0.008 -10000 0 -10000 0 0
RAP1A 0.023 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.015 0.081 -10000 0 -0.35 12 12
PLCG2 0.022 0.005 -10000 0 -10000 0 0
PLCG1 0.022 0.004 -10000 0 -10000 0 0
ARF5 0.023 0.004 -10000 0 -10000 0 0
mol:GTP -0.007 0.048 -10000 0 -0.27 3 3
ARF1/GTP -0.003 0.043 0.23 1 -10000 0 1
RHOA 0.021 0.007 -10000 0 -10000 0 0
YES1 0.022 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.007 0.049 -10000 0 -0.27 3 3
ADAP1 -0.012 0.057 -10000 0 -0.3 6 6
ARAP3 -0.007 0.048 -10000 0 -0.27 3 3
INPPL1 0.022 0.005 -10000 0 -10000 0 0
PREX1 0.016 0.059 -10000 0 -0.56 5 5
ARHGEF6 0.003 0.1 -10000 0 -0.56 16 16
ARHGEF7 0.022 0.006 -10000 0 -10000 0 0
ARF1 0.022 0.004 -10000 0 -10000 0 0
NRAS 0.023 0.009 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
ARF6 0.022 0.005 -10000 0 -10000 0 0
FGR -0.011 0.13 -10000 0 -0.56 27 27
mol:Ca2+ 0.001 0.05 0.24 3 -10000 0 3
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.023 0.004 -10000 0 -10000 0 0
ZAP70 0.013 0.075 -10000 0 -0.56 8 8
mol:IP3 -0.002 0.065 0.18 17 -0.19 10 27
LYN 0.02 0.038 -10000 0 -0.56 2 2
ARF1/GDP 0.015 0.082 -10000 0 -0.36 12 12
RhoA/GDP 0.023 0.058 -10000 0 -0.33 1 1
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
BLNK 0.021 0.027 -10000 0 -0.56 1 1
actin cytoskeleton reorganization 0.004 0.085 0.26 4 -0.42 5 9
SRC 0.022 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.009 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
PTEN 0.019 0.014 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.01 0.048 -10000 0 -10000 0 0
RhoA/GTP -0.008 0.05 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.009 0.11 -10000 0 -0.42 21 21
BLK 0.013 0.091 0.24 12 -0.56 10 22
PDPK1 0.022 0.005 -10000 0 -10000 0 0
CYTH1 -0.009 0.046 -10000 0 -10000 0 0
HCK 0.018 0.046 -10000 0 -0.56 3 3
CYTH3 -0.009 0.047 -10000 0 -10000 0 0
CYTH2 -0.009 0.046 -10000 0 -10000 0 0
KRAS 0.022 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.015 0.033 -10000 0 -10000 0 0
SGK1 0.019 0.037 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
mol:GDP 0.002 0.082 -10000 0 -0.34 15 15
SOS1 0.023 0.003 -10000 0 -10000 0 0
SYK 0.023 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.004 0.058 0.21 1 -0.34 1 2
mol:PI-3-4-5-P3 -0.009 0.044 -10000 0 -0.27 3 3
ARAP3/RAP1A/GTP -0.007 0.05 -10000 0 -0.27 3 3
VAV1 0.019 0.046 -10000 0 -0.56 3 3
mol:PI-3-4-P2 -0.01 0.019 -10000 0 -0.41 1 1
RAS family/GTP/PI3K Class I 0.034 0.046 -10000 0 -0.27 3 3
PLEKHA1 -0.012 0.016 -10000 0 -0.36 1 1
Rac1/GDP 0.013 0.082 -10000 0 -0.36 11 11
LAT 0.023 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.002 0.086 -10000 0 -0.38 18 18
ITK -0.023 0.075 -10000 0 -0.29 25 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.01 0.11 0.27 5 -0.34 26 31
LCK 0.021 0.027 -10000 0 -0.56 1 1
BTK -0.031 0.084 -10000 0 -0.29 31 31
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.032 0.06 0.33 7 -0.24 1 8
KIRREL 0.016 0.07 -10000 0 -0.56 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.032 0.06 0.24 1 -0.33 7 8
PLCG1 0.022 0.004 -10000 0 -10000 0 0
ARRB2 0.022 0.006 -10000 0 -10000 0 0
WASL 0.023 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.05 0.055 0.32 1 -0.34 4 5
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.013 0.035 -10000 0 -0.3 2 2
FYN 0.009 0.077 0.28 16 -0.37 4 20
mol:Ca2+ 0.047 0.05 0.31 1 -0.32 2 3
mol:DAG 0.048 0.05 0.32 1 -0.32 2 3
NPHS2 -0.004 0.031 0.26 3 -10000 0 3
mol:IP3 0.048 0.05 0.32 1 -0.32 2 3
regulation of endocytosis 0.039 0.052 -10000 0 -0.34 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.037 0.052 0.31 1 -0.34 4 5
establishment of cell polarity 0.032 0.06 0.24 1 -0.33 7 8
Nephrin/NEPH1/podocin/NCK1-2 0.051 0.057 0.32 1 -0.32 4 5
Nephrin/NEPH1/beta Arrestin2 0.043 0.054 -10000 0 -0.35 4 4
NPHS1 0.024 0.059 0.27 23 -10000 0 23
Nephrin/NEPH1/podocin 0.039 0.056 0.31 1 -0.37 4 5
TJP1 0.023 0.003 -10000 0 -10000 0 0
NCK1 0.019 0.009 -10000 0 -10000 0 0
NCK2 0.023 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.05 0.051 0.32 1 -0.32 2 3
CD2AP 0.023 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.05 0.054 0.32 1 -0.35 3 4
GRB2 0.023 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.01 0.097 0.28 13 -0.36 18 31
cytoskeleton organization 0.005 0.042 -10000 0 -0.36 2 2
Nephrin/NEPH1 0.028 0.045 0.19 1 -0.31 4 5
Nephrin/NEPH1/ZO-1 0.042 0.052 -10000 0 -0.35 4 4
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.048 0.044 -10000 0 -0.33 5 5
HDAC3 0.022 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.004 -10000 0 -10000 0 0
GATA1/HDAC4 -0.007 0.13 -10000 0 -0.41 43 43
GATA1/HDAC5 -0.007 0.12 -10000 0 -0.41 42 42
GATA2/HDAC5 -0.011 0.13 -10000 0 -0.41 43 43
HDAC5/BCL6/BCoR 0.027 0.023 -10000 0 -10000 0 0
HDAC9 0.022 0.032 0.24 3 -0.56 1 4
Glucocorticoid receptor/Hsp90/HDAC6 0.042 0.015 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.031 0.01 -10000 0 -10000 0 0
HDAC5/YWHAB 0.033 0.008 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.01 0.003 -10000 0 -10000 0 0
GATA2 -0.034 0.17 -10000 0 -0.56 45 45
HDAC4/RFXANK 0.032 0.009 -10000 0 -10000 0 0
BCOR 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.022 0.005 -10000 0 -10000 0 0
HDAC5 0.023 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.026 0.05 -10000 0 -0.41 6 6
Histones 0.018 0.036 -10000 0 -0.26 3 3
ADRBK1 0.023 0.004 -10000 0 -10000 0 0
HDAC4 0.023 0.004 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.031 0.01 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.008 -10000 0 -10000 0 0
HDAC7 0.023 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.032 0.009 -10000 0 -10000 0 0
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
HDAC6 0.023 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.032 0.008 -10000 0 -10000 0 0
CAMK4 0.019 0.038 -10000 0 -0.56 2 2
Tubulin/HDAC6 0.044 0.011 -10000 0 -10000 0 0
SUMO1 0.023 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.022 0.004 -10000 0 -10000 0 0
GATA1 -0.034 0.16 -10000 0 -0.56 42 42
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
NR3C1 0.022 0.006 -10000 0 -10000 0 0
SUMO1/HDAC4 0.032 0.029 -10000 0 -0.24 1 1
SRF 0.023 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.008 -10000 0 -10000 0 0
Tubulin 0.033 0.007 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.032 0.009 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
RANGAP1 0.023 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.02 0.017 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.042 0.022 -10000 0 -0.34 1 1
HDAC4/SRF 0.04 0.031 -10000 0 -0.36 2 2
HDAC4/ER alpha 0.014 0.089 -10000 0 -0.41 20 20
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.018 0.036 -10000 0 -0.26 3 3
cell motility 0.044 0.011 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
HDAC7/HDAC3 0.032 0.009 -10000 0 -10000 0 0
BCL6 0.014 0.011 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.022 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.032 0.009 -10000 0 -10000 0 0
ESR1 -0.002 0.12 -10000 0 -0.56 20 20
HDAC6/HDAC11 0.031 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.03 -10000 0 -10000 0 0
NPC 0.014 0.001 -10000 0 -10000 0 0
MEF2C 0.014 0.065 -10000 0 -0.56 6 6
RAN 0.023 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.056 0.049 -10000 0 -0.3 7 7
GNG2 0.016 0.059 -10000 0 -0.56 5 5
NCOR2 0.022 0.027 -10000 0 -0.56 1 1
TUBB2A 0.022 0.004 -10000 0 -10000 0 0
HDAC11 0.021 0.006 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
ANKRA2 0.021 0.006 -10000 0 -10000 0 0
RFXANK 0.022 0.005 -10000 0 -10000 0 0
nuclear import -0.026 0.009 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.033 0.007 -10000 0 -10000 0 0
ATM 0.023 0.004 -10000 0 -10000 0 0
UBE2D3 0.022 0.005 -10000 0 -10000 0 0
PRKDC 0.022 0.005 -10000 0 -10000 0 0
ATR 0.018 0.009 -10000 0 -10000 0 0
UBE2L3 0.022 0.005 -10000 0 -10000 0 0
FANCD2 0.012 0.008 -10000 0 -10000 0 0
protein ubiquitination 0.081 0.058 -10000 0 -10000 0 0
XRCC5 0.022 0.004 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.041 0.016 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
DNA-PK 0.043 0.014 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.012 0.1 0.3 1 -0.48 15 16
FANCF 0.023 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.003 -10000 0 -10000 0 0
CCNE1 0.079 0.11 0.28 106 -10000 0 106
CDK2/Cyclin E1 0.07 0.074 0.26 30 -10000 0 30
FANCG 0.022 0.024 0.38 2 -10000 0 2
BRCA1/BACH1/BARD1 0.033 0.007 -10000 0 -10000 0 0
FANCE 0.023 0.003 -10000 0 -10000 0 0
FANCC 0.023 0.003 -10000 0 -10000 0 0
NBN 0.022 0.005 -10000 0 -10000 0 0
FANCA 0.023 0.02 0.31 2 -10000 0 2
DNA repair 0.016 0.08 0.28 8 -0.42 5 13
BRCA1/BARD1/ubiquitin 0.033 0.007 -10000 0 -10000 0 0
BARD1/DNA-PK 0.054 0.017 -10000 0 -10000 0 0
FANCL 0.022 0.017 0.38 1 -10000 0 1
mRNA polyadenylation -0.033 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.02 0.03 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.039 0.018 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.044 0.026 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.045 0.011 -10000 0 -10000 0 0
BRCA1/BACH1 0.023 0.003 -10000 0 -10000 0 0
BARD1 0.023 0.004 -10000 0 -10000 0 0
PCNA 0.022 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.044 0.012 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.043 0.014 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.07 0.047 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.06 0.024 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.033 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.034 0.012 -10000 0 -10000 0 0
FA complex 0.032 0.042 0.41 1 -0.26 2 3
BARD1/EWS 0.032 0.008 -10000 0 -10000 0 0
RBBP8 -0.009 0.003 -10000 0 -10000 0 0
TP53 0.022 0.006 -10000 0 -10000 0 0
TOPBP1 0.02 0.008 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.042 0.026 -10000 0 -10000 0 0
BRCA1/BARD1 0.09 0.062 -10000 0 -10000 0 0
CSTF1 0.023 0.003 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.017 0.003 -10000 0 -10000 0 0
CDK2 0.023 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.052 0.073 0.24 64 -10000 0 64
RAD50 0.021 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.033 0.007 -10000 0 -10000 0 0
EWSR1 0.022 0.004 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.03 0.032 0.23 1 -0.36 1 2
EFNA5 0.02 0.027 -10000 0 -0.56 1 1
FYN 0.001 0.031 0.18 5 -0.32 2 7
neuron projection morphogenesis 0.03 0.032 0.23 1 -0.36 1 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.03 0.032 0.24 1 -0.36 1 2
EPHA5 0.019 0.052 0.25 19 -10000 0 19
Signaling events mediated by HDAC Class III

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
EP300 0.022 0.004 -10000 0 -10000 0 0
HDAC4 0.023 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.01 0.016 -10000 0 -0.3 1 1
CDKN1A -0.009 0.003 -10000 0 -10000 0 0
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
BAX 0.023 0.004 -10000 0 -10000 0 0
FOXO3 -0.004 0.003 -10000 0 -10000 0 0
FOXO1 0.021 0.006 -10000 0 -10000 0 0
FOXO4 0.011 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
TAT 0.017 0.025 0.31 2 -10000 0 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.019 0.03 0.3 1 -0.31 2 3
PPARGC1A -0.077 0.22 -10000 0 -0.56 81 81
FHL2 0.025 0.02 0.24 4 -10000 0 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.031 0.008 -10000 0 -10000 0 0
HIST2H4A -0.01 0.016 0.3 1 -10000 0 1
SIRT1/FOXO3a 0.011 0.029 -10000 0 -0.2 8 8
SIRT1 0.02 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.041 0.014 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.02 0.035 -10000 0 -10000 0 0
apoptosis -0.041 0.013 -10000 0 -10000 0 0
SIRT1/PGC1A -0.042 0.14 -10000 0 -0.35 81 81
p53/SIRT1 0.025 0.008 -10000 0 -10000 0 0
SIRT1/FOXO4 0.019 0.032 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.04 0.018 -10000 0 -10000 0 0
HIST1H1E 0.014 0.015 0.16 2 -10000 0 2
SIRT1/p300 0.03 0.009 -10000 0 -10000 0 0
muscle cell differentiation -0.014 0.039 0.36 1 -10000 0 1
TP53 0.02 0.005 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.042 0.013 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
MEF2D 0.022 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.015 0.26 1 -10000 0 1
ACSS2 -0.01 0.003 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.014 0.039 -10000 0 -0.36 1 1
IL1-mediated signaling events

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
UBC13/UEV1A 0.032 0.007 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.021 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0 0.056 -10000 0 -0.38 3 3
IRAK/TOLLIP 0.023 0.007 -10000 0 -10000 0 0
IKBKB 0.022 0.018 0.38 1 -10000 0 1
IKBKG 0.023 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.029 0.1 0.3 2 -0.42 19 21
IL1A 0.009 0.12 0.24 20 -0.56 19 39
IL1B -0.021 0.065 -10000 0 -0.41 13 13
IRAK/TRAF6/p62/Atypical PKCs 0.03 0.032 -10000 0 -10000 0 0
IL1R2 0.034 0.048 0.24 24 -10000 0 24
IL1R1 0.022 0.027 -10000 0 -0.56 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.026 0.06 0.25 1 -0.28 3 4
TOLLIP 0.022 0.004 -10000 0 -10000 0 0
TICAM2 0.015 0.059 -10000 0 -0.56 5 5
MAP3K3 0.023 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.015 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.035 0.056 0.38 1 -10000 0 1
JUN -0.009 0.039 0.25 2 -10000 0 2
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.022 0.053 -10000 0 -0.3 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88 0.025 0.075 -10000 0 -0.35 12 12
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.031 0.076 -10000 0 -0.33 12 12
IL1 beta fragment/IL1R1/IL1RAP 0.013 0.053 -10000 0 -0.32 9 9
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.007 0.042 0.26 2 -10000 0 2
IRAK1 -0.013 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 0.033 0.044 0.26 1 -0.58 2 3
IRAK4 0.023 0.003 -10000 0 -10000 0 0
PRKCI 0.013 0.011 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0 0.056 -10000 0 -0.33 5 5
CHUK 0.022 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.013 0.053 -10000 0 -0.32 9 9
IL1 beta/IL1R2 0.026 0.073 0.3 2 -0.36 13 15
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.016 0.048 -10000 0 -0.28 9 9
IRAK3 0.008 0.091 -10000 0 -0.56 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.021 0.066 -10000 0 -0.3 14 14
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.063 -10000 0 -0.32 13 13
IL1 alpha/IL1R1/IL1RAP 0.019 0.078 -10000 0 -0.38 12 12
RELA 0.023 0.001 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.021 0.007 -10000 0 -10000 0 0
MYD88 0.021 0.007 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.04 0.024 -10000 0 -10000 0 0
IL1RAP 0.014 0.011 -10000 0 -10000 0 0
UBE2N 0.023 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 0.007 0.052 -10000 0 -0.28 4 4
CASP1 0.02 0.038 -10000 0 -0.56 2 2
IL1RN/IL1R2 0.041 0.048 0.29 3 -0.41 2 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.019 0.054 -10000 0 -0.31 9 9
TMEM189-UBE2V1 0.011 0.019 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.001 0.071 -10000 0 -0.41 6 6
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
IL1RN 0.023 0.044 0.27 4 -0.56 2 6
TRAF6/TAK1/TAB1/TAB2 0.041 0.012 -10000 0 -10000 0 0
MAP2K6 -0.004 0.045 0.27 2 -10000 0 2
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
MAP4K4 0.006 0.08 -10000 0 -0.48 5 5
BAG4 0.02 0.019 0.38 1 -10000 0 1
BAD 0.002 0.032 0.17 1 -0.15 2 3
NFKBIA 0.022 0.005 -10000 0 -10000 0 0
BIRC3 0.015 0.065 -10000 0 -0.56 6 6
BAX 0.003 0.03 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.004 0.022 -10000 0 -0.093 6 6
IKBKB 0.018 0.09 0.28 3 -0.49 4 7
MAP2K2 0.003 0.037 0.18 9 -10000 0 9
MAP2K1 0.002 0.039 0.18 9 -10000 0 9
SMPD1 0.003 0.028 -10000 0 -0.14 6 6
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.033 0.099 0.27 12 -0.49 4 16
MAP2K4 0.003 0.026 0.17 1 -10000 0 1
protein ubiquitination 0.012 0.083 -10000 0 -0.45 5 5
EnzymeConsortium:2.7.1.37 0.001 0.04 0.19 8 -10000 0 8
response to UV 0 0 0.002 9 -10000 0 9
RAF1 0.005 0.037 0.19 9 -10000 0 9
CRADD 0.023 0.002 -10000 0 -10000 0 0
mol:ceramide 0.005 0.033 0.12 1 -0.14 6 7
I-kappa-B-alpha/RELA/p50/ubiquitin 0.03 0.007 -10000 0 -10000 0 0
MADD 0.023 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.029 0.18 1 -10000 0 1
TRADD 0.022 0.005 -10000 0 -10000 0 0
RELA/p50 0.023 0.001 -10000 0 -10000 0 0
MAPK3 0.003 0.042 0.19 8 -0.21 2 10
MAPK1 0.003 0.04 0.19 7 -0.2 1 8
p50/RELA/I-kappa-B-alpha 0.033 0.008 -10000 0 -10000 0 0
FADD 0.028 0.097 0.26 10 -0.55 3 13
KSR1 0.005 0.04 0.18 10 -10000 0 10
MAPK8 0 0.028 0.16 3 -10000 0 3
TRAF2 0.023 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 1 -10000 0 1
CHUK 0.008 0.077 -10000 0 -0.48 4 4
TNF R/SODD 0.027 0.018 0.26 1 -10000 0 1
TNF 0.011 0.084 0.24 1 -0.56 10 11
CYCS 0.001 0.035 0.13 1 -0.22 2 3
IKBKG 0.008 0.079 0.26 1 -0.42 5 6
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.009 0.083 -10000 0 -0.47 6 6
RELA 0.023 0.001 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AIFM1 0.002 0.032 -10000 0 -0.18 1 1
TNF/TNF R/SODD 0.028 0.056 0.25 1 -0.35 8 9
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.018 0.074 -10000 0 -0.52 8 8
NSMAF 0.011 0.079 0.29 2 -0.46 5 7
response to hydrogen peroxide 0 0 0.002 9 -10000 0 9
BCL2 0.023 0.011 0.24 1 -10000 0 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.032 0.074 -10000 0 -0.36 9 9
Ran/GTP/Exportin 1/HDAC1 -0.01 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.016 0.081 -10000 0 -0.34 10 10
SUMO1 0.023 0.004 -10000 0 -10000 0 0
ZFPM1 0.021 0.027 -10000 0 -0.56 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.01 0.003 -10000 0 -10000 0 0
FKBP3 0.022 0.005 -10000 0 -10000 0 0
Histones 0.04 0.065 -10000 0 -10000 0 0
YY1/LSF 0.013 0.063 -10000 0 -0.29 6 6
SMG5 0.022 0.005 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.012 0.041 -10000 0 -0.28 8 8
I kappa B alpha/HDAC1 0.019 0.057 -10000 0 -0.26 1 1
SAP18 0.022 0.006 -10000 0 -10000 0 0
RELA 0.018 0.049 -10000 0 -0.27 8 8
HDAC1/Smad7 0.04 0.024 -10000 0 -0.36 1 1
RANGAP1 0.023 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.017 0.062 -10000 0 -0.26 1 1
NuRD/MBD3 Complex 0.023 0.043 -10000 0 -0.36 3 3
NF kappa B1 p50/RelA 0.016 0.077 -10000 0 -0.3 11 11
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.034 0.17 -10000 0 -0.56 45 45
GATA1 -0.034 0.16 -10000 0 -0.56 42 42
Mad/Max 0.032 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.003 0.094 -10000 0 -0.38 10 10
RBBP7 0.022 0.005 -10000 0 -10000 0 0
NPC 0.014 0.001 -10000 0 -10000 0 0
RBBP4 0.023 0.004 -10000 0 -10000 0 0
MAX 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
NFKBIA 0.011 0.032 -10000 0 -10000 0 0
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.014 0.031 -10000 0 -0.36 1 1
SIN3 complex 0.051 0.021 -10000 0 -10000 0 0
SMURF1 0.022 0.006 -10000 0 -10000 0 0
CHD3 0.022 0.006 -10000 0 -10000 0 0
SAP30 0.021 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.005 -10000 0 -10000 0 0
YY1/HDAC3 0.012 0.059 -10000 0 -0.36 6 6
YY1/HDAC2 0.013 0.063 -10000 0 -0.3 6 6
YY1/HDAC1 0.014 0.062 -10000 0 -0.29 6 6
NuRD/MBD2 Complex (MeCP1) 0.024 0.036 -10000 0 -0.25 1 1
PPARG -0.021 0.13 -10000 0 -0.34 56 56
HDAC8/hEST1B 0.043 0.013 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.017 0.064 -10000 0 -0.36 2 2
MBD3L2 -0.017 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.024 -10000 0 -0.36 1 1
CREBBP 0.022 0.005 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.019 0.063 -10000 0 -0.32 7 7
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.011 0.032 -10000 0 -10000 0 0
HDAC2 0.023 0.002 -10000 0 -10000 0 0
YY1 0.013 0.011 -10000 0 -10000 0 0
HDAC8 0.023 0.003 -10000 0 -10000 0 0
SMAD7 0.021 0.027 -10000 0 -0.56 1 1
NCOR2 0.022 0.027 -10000 0 -0.56 1 1
MXD1 0.022 0.005 -10000 0 -10000 0 0
STAT3 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.026 0.062 -10000 0 -0.26 6 6
YY1/SAP30/HDAC1 0.025 0.059 -10000 0 -0.27 4 4
EP300 0.022 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.015 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.032 -10000 0 -10000 0 0
histone deacetylation 0.024 0.036 -10000 0 -0.25 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.016 0.033 -10000 0 -10000 0 0
nuclear export -0.043 0.013 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GATAD2B 0.022 0.005 -10000 0 -10000 0 0
GATAD2A 0.022 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 -0.016 0.12 -10000 0 -0.35 43 43
GATA1/HDAC1 -0.007 0.13 -10000 0 -0.41 42 42
GATA1/HDAC3 -0.014 0.12 -10000 0 -0.33 41 41
CHD4 0.021 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.022 0.06 -10000 0 -0.41 8 8
SIN3/HDAC complex/Mad/Max 0.009 0.059 -10000 0 -0.35 4 4
NuRD Complex 0.021 0.058 -10000 0 -0.34 3 3
positive regulation of chromatin silencing 0.038 0.064 -10000 0 -10000 0 0
SIN3B 0.022 0.005 -10000 0 -10000 0 0
MTA2 0.023 0.002 -10000 0 -10000 0 0
SIN3A 0.023 0.002 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
SUMO1/HDAC1 0.032 0.03 -10000 0 -0.26 1 1
HDAC complex 0.055 0.016 -10000 0 -10000 0 0
GATA1/Fog1 -0.009 0.13 -10000 0 -0.41 44 44
FKBP25/HDAC1/HDAC2 0.043 0.013 -10000 0 -10000 0 0
TNF 0.011 0.084 0.24 1 -0.56 10 11
negative regulation of cell growth 0.009 0.059 -10000 0 -0.34 4 4
NuRD/MBD2/PRMT5 Complex 0.024 0.036 -10000 0 -0.25 1 1
Ran/GTP/Exportin 1 0.03 0.03 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.005 0.066 -10000 0 -0.34 11 11
SIN3/HDAC complex/NCoR1 -0.001 0.078 -10000 0 -0.31 21 21
TFCP2 0.023 0.002 -10000 0 -10000 0 0
NR2C1 0.023 0.002 -10000 0 -10000 0 0
MBD3 0.021 0.027 -10000 0 -0.56 1 1
MBD2 0.022 0.005 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.001 0.044 -10000 0 -10000 0 0
PLK1 0.066 0.12 -10000 0 -0.96 1 1
CDKN1B 0.071 0.11 0.3 3 -0.37 10 13
FOXO3 0.07 0.11 -10000 0 -0.73 3 3
KAT2B 0.027 0.031 -10000 0 -0.55 1 1
FOXO1/SIRT1 0.019 0.038 -10000 0 -10000 0 0
CAT 0.051 0.14 -10000 0 -1.1 3 3
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.03 0.017 -10000 0 -10000 0 0
FOXO1 0.007 0.045 -10000 0 -10000 0 0
MAPK10 0.018 0.05 0.19 17 -0.3 7 24
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.035 0.06 0.26 3 -10000 0 3
response to oxidative stress 0.01 0.01 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.071 0.1 -10000 0 -0.92 1 1
XPO1 0.021 0.007 -10000 0 -10000 0 0
EP300 0.023 0.004 -10000 0 -10000 0 0
BCL2L11 0.033 0.044 -10000 0 -0.78 1 1
FOXO1/SKP2 0.017 0.04 0.25 2 -10000 0 2
mol:GDP 0.01 0.01 -10000 0 -10000 0 0
RAN 0.024 0.002 -10000 0 -10000 0 0
GADD45A 0.048 0.15 -10000 0 -0.59 21 21
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.014 0.12 -10000 0 -0.46 20 20
MST1 0.028 0.02 0.24 1 -10000 0 1
CSNK1D 0.022 0.004 -10000 0 -10000 0 0
CSNK1E 0.022 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.017 0.088 -10000 0 -0.42 11 11
YWHAB 0.022 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.032 0.19 16 -10000 0 16
MAPK9 0.022 0.033 0.19 17 -10000 0 17
YWHAG 0.023 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
SIRT1 0.021 0.013 -10000 0 -10000 0 0
SOD2 0.062 0.1 -10000 0 -0.62 2 2
RBL2 0.037 0.2 -10000 0 -0.82 22 22
RAL/GDP 0.038 0.014 -10000 0 -10000 0 0
CHUK 0.029 0.016 -10000 0 -10000 0 0
Ran/GTP 0.019 0.002 -10000 0 -10000 0 0
CSNK1G2 0.022 0.005 -10000 0 -10000 0 0
RAL/GTP 0.04 0.012 -10000 0 -10000 0 0
CSNK1G1 0.023 0.002 -10000 0 -10000 0 0
FASLG -0.022 0.28 -10000 0 -1.3 21 21
SKP2 0.02 0.027 0.33 3 -10000 0 3
USP7 0.023 0.005 -10000 0 -10000 0 0
IKBKB 0.028 0.024 0.38 1 -10000 0 1
CCNB1 0.062 0.11 -10000 0 -0.96 1 1
FOXO1-3a-4/beta catenin 0.071 0.09 0.31 1 -0.39 1 2
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.04 0.25 2 -10000 0 2
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
SGK1 0.03 0.016 -10000 0 -10000 0 0
CSNK1G3 0.021 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.01 -10000 0 -10000 0 0
ZFAND5 0.031 0.067 0.39 3 -10000 0 3
SFN 0.04 0.072 0.24 45 -0.38 3 48
CDK2 0.023 0.003 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.027 0.09 -10000 0 -0.41 12 12
CREBBP 0.022 0.005 -10000 0 -10000 0 0
FBXO32 0.065 0.12 -10000 0 -0.76 2 2
BCL6 0.054 0.098 -10000 0 -0.68 1 1
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.023 0.005 -10000 0 -10000 0 0
YWHAH 0.022 0.004 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.01 0.092 -10000 0 -0.34 27 27
KLHL20 0.017 0.059 0.17 2 -0.25 8 10
CYFIP2 0.009 0.083 -10000 0 -0.56 10 10
Rac1/GDP 0.013 0.07 0.25 2 -0.27 1 3
ENAH -0.01 0.097 -10000 0 -0.34 30 30
AP1M1 0.022 0.005 -10000 0 -10000 0 0
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.014 0.029 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.036 -10000 0 -0.19 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.027 -10000 0 -0.33 1 1
RAPGEF1 -0.004 0.081 0.22 2 -0.31 10 12
CTNND1 0.023 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.007 0.1 -10000 0 -0.34 30 30
CRK -0.004 0.073 -10000 0 -0.31 19 19
E-cadherin/gamma catenin/alpha catenin 0.043 0.014 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.031 0.022 -10000 0 -0.41 1 1
IQGAP1 0.023 0.003 -10000 0 -10000 0 0
NCKAP1 0.023 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.014 -10000 0 -10000 0 0
DLG1 -0.001 0.064 -10000 0 -0.34 14 14
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.011 -10000 0 -10000 0 0
MLLT4 0.023 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.041 0.013 -10000 0 -10000 0 0
PI3K -0.009 0.013 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.032 0.008 -10000 0 -10000 0 0
TIAM1 0.023 0.004 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.049 0.018 -10000 0 -10000 0 0
AKT1 0.005 0.031 0.13 1 -10000 0 1
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
CDH1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.066 0.25 2 -10000 0 2
actin cytoskeleton organization 0.016 0.047 0.16 6 -0.18 8 14
CDC42/GDP 0.016 0.068 0.25 2 -10000 0 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.015 0.005 -10000 0 -10000 0 0
ITGB7 0.022 0.027 -10000 0 -0.56 1 1
RAC1 0.022 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.053 0.02 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.037 0.013 -10000 0 -10000 0 0
mol:GDP 0.002 0.075 0.26 2 -0.31 1 3
CDC42/GTP/IQGAP1 0.03 0.007 -10000 0 -10000 0 0
JUP 0.023 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.024 0.065 0.25 2 -10000 0 2
RAC1/GTP/IQGAP1 0.03 0.007 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.033 0.008 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
CTNNA1 0.022 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.01 0.041 0.13 6 -0.24 6 12
NME1 0.023 0.01 0.24 1 -10000 0 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.007 0.093 -10000 0 -0.34 26 26
regulation of cell-cell adhesion 0.009 0.024 -10000 0 -10000 0 0
WASF2 0.008 0.026 -10000 0 -0.12 3 3
Rap1/GTP 0.018 0.04 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.06 0.028 -10000 0 -0.31 1 1
CCND1 0.011 0.049 0.15 5 -0.3 6 11
VAV2 -0.011 0.12 -10000 0 -0.64 9 9
RAP1/GDP 0.02 0.055 0.25 1 -10000 0 1
adherens junction assembly -0.007 0.091 -10000 0 -0.33 26 26
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.022 0.004 -10000 0 -10000 0 0
PIP5K1C 0.022 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.044 0.025 -10000 0 -0.3 1 1
E-cadherin/beta catenin 0.01 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.008 0.093 -10000 0 -0.34 27 27
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
Rac1/GTP -0.013 0.077 -10000 0 -0.4 11 11
E-cadherin/beta catenin/alpha catenin 0.042 0.015 -10000 0 -10000 0 0
ITGAE 0.022 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.1 -10000 0 -0.35 30 30
Arf6 trafficking events

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
SLC2A4 0.018 0.046 -10000 0 -0.56 3 3
CLTC 0.02 0.071 -10000 0 -0.38 12 12
calcium ion-dependent exocytosis 0.006 0.025 -10000 0 -0.24 2 2
Dynamin 2/GTP 0.02 0.007 -10000 0 -10000 0 0
EXOC4 0.023 0.004 -10000 0 -10000 0 0
CD59 0.003 0.043 -10000 0 -0.33 7 7
CPE 0.009 0.017 -10000 0 -0.35 1 1
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
membrane fusion 0.007 0.016 -10000 0 -10000 0 0
CTNND1 -0.006 0.034 0.18 16 -10000 0 16
DNM2 0.022 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.043 0.21 4 -0.28 5 9
TSHR 0.012 0.017 -10000 0 -10000 0 0
INS 0 0.11 -10000 0 -0.54 17 17
BIN1 0.021 0.038 -10000 0 -0.56 2 2
mol:Choline 0.007 0.016 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0.006 -10000 0 -10000 0 0
JUP 0.002 0.046 -10000 0 -0.34 8 8
ASAP2/amphiphysin II 0.039 0.026 -10000 0 -0.32 2 2
ARF6/GTP 0.016 0.004 -10000 0 -10000 0 0
CDH1 0.004 0.039 -10000 0 -0.35 5 5
clathrin-independent pinocytosis 0.016 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.022 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.016 0.004 -10000 0 -10000 0 0
EXOC2 0.022 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.006 0.044 -10000 0 -0.32 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.023 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.054 0.3 8 -10000 0 8
positive regulation of phagocytosis 0.01 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.029 0.008 -10000 0 -10000 0 0
ACAP1 0.009 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.039 0.097 -10000 0 -0.38 11 11
clathrin heavy chain/ACAP1 0.004 0.055 0.24 2 -0.34 8 10
JIP4/KLC1 0.04 0.013 -10000 0 -10000 0 0
EXOC1 0.021 0.006 -10000 0 -10000 0 0
exocyst 0.01 0.038 -10000 0 -0.32 3 3
RALA/GTP 0.017 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.008 -10000 0 -10000 0 0
receptor recycling 0.016 0.004 -10000 0 -10000 0 0
CTNNA1 -0.006 0.032 0.18 14 -10000 0 14
NME1 0.01 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.021 0.071 -10000 0 -0.38 12 12
IL2RA 0.004 0.04 -10000 0 -0.32 6 6
VAMP3 0.01 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.029 0.064 -10000 0 -0.31 11 11
EXOC6 0.022 0.005 -10000 0 -10000 0 0
PLD1 0.007 0.015 0.18 3 -10000 0 3
PLD2 0.009 0.008 -10000 0 -10000 0 0
EXOC5 0.022 0.005 -10000 0 -10000 0 0
PIP5K1C 0.003 0.038 -10000 0 -0.29 5 5
SDC1 0.003 0.048 -10000 0 -0.34 8 8
ARF6/GDP 0.02 0.005 -10000 0 -10000 0 0
EXOC7 0.023 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.056 -10000 0 -0.31 8 8
mol:Phosphatidic acid 0.007 0.016 -10000 0 -10000 0 0
endocytosis -0.038 0.026 0.31 2 -10000 0 2
SCAMP2 0.023 0.002 -10000 0 -10000 0 0
ADRB2 -0.054 0.13 -10000 0 -0.3 59 59
EXOC3 0.018 0.01 -10000 0 -10000 0 0
ASAP2 0.022 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.023 0.008 -10000 0 -10000 0 0
KLC1 0.022 0.005 -10000 0 -10000 0 0
AVPR2 -0.045 0.14 0.23 5 -0.31 58 63
RALA 0.022 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.027 0.052 -10000 0 -0.3 5 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.009 0.003 -10000 0 -10000 0 0
mol:DAG -0.01 0.022 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.022 -10000 0 -10000 0 0
HIF1A 0.026 0.005 -10000 0 -10000 0 0
GAB1 0.022 0.006 -10000 0 -10000 0 0
AKT1 0.055 0.079 0.31 3 -10000 0 3
PLCG1 -0.01 0.022 -10000 0 -10000 0 0
NOS3 0.036 0.052 0.31 1 -0.33 1 2
CBL 0.023 0.004 -10000 0 -10000 0 0
mol:NO 0.041 0.075 0.42 6 -0.36 3 9
FLT1 0.012 0.004 -10000 0 -10000 0 0
PGF 0.034 0.05 0.24 25 -10000 0 25
VEGFR1 homodimer/NRP2/VEGFR121 0.033 0.031 -10000 0 -0.31 3 3
CALM1 0.022 0.005 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
eNOS/Hsp90 0.044 0.072 0.3 1 -0.37 4 5
endothelial cell proliferation 0.007 0.055 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.022 -10000 0 -10000 0 0
MAPK3 -0.011 0.039 0.34 3 -10000 0 3
MAPK1 -0.01 0.041 0.34 4 -10000 0 4
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
PLGF homodimer 0.034 0.05 0.24 25 -10000 0 25
PRKACA 0.022 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.13 0.26 -10000 0 -0.56 125 125
VEGFA homodimer 0.023 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.024 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.011 0.042 0.32 5 -10000 0 5
PI3K 0.028 0.036 -10000 0 -10000 0 0
PRKCA -0.012 0.024 -10000 0 -0.29 1 1
PRKCB -0.023 0.061 -10000 0 -0.31 19 19
VEGFR1 homodimer/PLGF homodimer 0.031 0.033 0.26 1 -10000 0 1
VEGFA 0.023 0.004 -10000 0 -10000 0 0
VEGFB 0.023 0.002 -10000 0 -10000 0 0
mol:IP3 -0.01 0.022 -10000 0 -10000 0 0
RASA1 -0.008 0.02 -10000 0 -10000 0 0
NRP2 0.019 0.046 -10000 0 -0.56 3 3
VEGFR1 homodimer 0.012 0.004 -10000 0 -10000 0 0
VEGFB homodimer 0.023 0.002 -10000 0 -10000 0 0
NCK1 0.019 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.026 0.15 0.43 5 -0.43 14 19
PTPN11 0.023 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.034 -10000 0 -10000 0 0
mol:L-citrulline 0.041 0.075 0.42 6 -0.36 3 9
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.046 0.018 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.03 0.017 -10000 0 -10000 0 0
CD2AP 0.023 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.035 0.041 -10000 0 -10000 0 0
PDPK1 0.057 0.088 0.34 2 -10000 0 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.036 0.013 -10000 0 -10000 0 0
mol:NADP 0.041 0.075 0.42 6 -0.36 3 9
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.022 0.03 -10000 0 -0.34 3 3
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.017 0.018 -10000 0 -10000 0 0
regulation of axonogenesis -0.004 0.024 0.24 3 -0.17 3 6
myoblast fusion -0.027 0.036 0.34 1 -10000 0 1
mol:GTP 0.016 0.028 -10000 0 -0.15 11 11
regulation of calcium-dependent cell-cell adhesion -0.045 0.028 -10000 0 -10000 0 0
ARF1/GTP 0.028 0.027 -10000 0 -10000 0 0
mol:GM1 0.007 0.021 -10000 0 -10000 0 0
mol:Choline 0.004 0.02 0.23 3 -10000 0 3
lamellipodium assembly 0.009 0.046 -10000 0 -0.33 7 7
MAPK3 0.017 0.018 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.046 0.029 -10000 0 -10000 0 0
ARF1 0.022 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.028 0.036 -10000 0 -0.34 1 1
ARF1/GDP 0.026 0.048 -10000 0 -0.27 3 3
ARF6 0.03 0.012 -10000 0 -10000 0 0
RAB11A 0.023 0.002 -10000 0 -10000 0 0
TIAM1 0.024 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.018 -10000 0 -10000 0 0
actin filament bundle formation -0.025 0.044 0.25 3 -10000 0 3
KALRN 0.008 0.027 -10000 0 -0.31 3 3
RAB11FIP3/RAB11A 0.033 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.044 -10000 0 -0.25 3 3
NME1 0.024 0.012 0.24 1 -10000 0 1
Rac1/GDP 0.027 0.045 -10000 0 -0.3 1 1
substrate adhesion-dependent cell spreading 0.016 0.028 -10000 0 -0.15 10 10
cortical actin cytoskeleton organization 0.009 0.046 -10000 0 -0.33 7 7
RAC1 0.022 0.004 -10000 0 -10000 0 0
liver development 0.016 0.028 -10000 0 -0.15 10 10
ARF6/GTP 0.016 0.028 -10000 0 -0.15 10 10
RhoA/GTP 0.027 0.025 -10000 0 -10000 0 0
mol:GDP 0.007 0.029 -10000 0 -0.21 8 8
ARF6/GTP/RAB11FIP3/RAB11A 0.04 0.028 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
PLD1 0.009 0.028 0.28 3 -10000 0 3
RAB11FIP3 0.022 0.005 -10000 0 -10000 0 0
tube morphogenesis 0.009 0.046 -10000 0 -0.33 7 7
ruffle organization 0.004 0.024 0.17 3 -0.24 3 6
regulation of epithelial cell migration 0.016 0.028 -10000 0 -0.15 10 10
PLD2 0.015 0.018 -10000 0 -10000 0 0
PIP5K1A 0.004 0.024 0.17 3 -0.24 3 6
mol:Phosphatidic acid 0.004 0.02 0.23 3 -10000 0 3
Rac1/GTP 0.009 0.046 -10000 0 -0.33 7 7
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.043 0.11 -10000 0 -0.38 13 13
CaM/Ca2+ 0.016 0.004 -10000 0 -10000 0 0
AKT1 0.022 0.006 -10000 0 -10000 0 0
AKT2 0.021 0.006 -10000 0 -10000 0 0
STXBP4 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.029 0.12 0.22 2 -0.4 16 18
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
TBC1D4 -0.009 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.022 0.004 -10000 0 -10000 0 0
YWHAB 0.022 0.004 -10000 0 -10000 0 0
SNARE/Synip 0.043 0.014 -10000 0 -10000 0 0
YWHAG 0.023 0.004 -10000 0 -10000 0 0
ASIP 0.008 0.025 0.24 2 -10000 0 2
PRKCI 0.013 0.011 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.016 0.004 -10000 0 -10000 0 0
RHOQ 0.022 0.006 -10000 0 -10000 0 0
GYS1 0.005 0.003 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
TRIP10 0.022 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.039 -10000 0 -0.3 2 2
VAMP2 0.022 0.006 -10000 0 -10000 0 0
SLC2A4 0.028 0.13 -10000 0 -0.44 17 17
STX4 0.023 0.003 -10000 0 -10000 0 0
GSK3B 0.013 0.007 -10000 0 -10000 0 0
SFN 0.04 0.072 0.24 45 -0.38 3 48
LNPEP 0.021 0.006 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.009 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.032 0.014 -10000 0 -10000 0 0
CDKN1B 0.019 0.064 -10000 0 -0.38 7 7
CDKN1A 0.016 0.049 -10000 0 -0.37 4 4
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.022 0.005 -10000 0 -10000 0 0
FOXO3 0.015 0.057 -10000 0 -0.5 3 3
AKT1 0.005 0.052 -10000 0 -0.39 7 7
BAD 0.023 0.002 -10000 0 -10000 0 0
AKT3 0.01 0.016 -10000 0 -0.34 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.013 0.058 -10000 0 -0.4 6 6
AKT1/ASK1 0.032 0.065 -10000 0 -0.49 3 3
BAD/YWHAZ 0.043 0.014 -10000 0 -10000 0 0
RICTOR 0.018 0.01 -10000 0 -10000 0 0
RAF1 0.021 0.006 -10000 0 -10000 0 0
JNK cascade -0.031 0.062 0.39 5 -10000 0 5
TSC1 0.013 0.057 -10000 0 -0.37 8 8
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.035 0.067 -10000 0 -0.49 3 3
EP300 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0.006 0.055 -10000 0 -0.38 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.017 0.036 -10000 0 -0.29 4 4
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
TBC1D4 0.003 0.001 -10000 0 -10000 0 0
MAP3K5 0.023 0.003 -10000 0 -10000 0 0
MAPKAP1 0.023 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.067 0.37 6 -10000 0 6
YWHAH 0.022 0.004 -10000 0 -10000 0 0
AKT1S1 0.016 0.046 -10000 0 -0.37 4 4
CASP9 0.015 0.045 -10000 0 -0.35 5 5
YWHAB 0.022 0.004 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.037 0.073 0.3 2 -0.57 2 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 0.012 0.055 0.25 1 -0.42 4 5
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.052 -10000 0 -0.34 8 8
CHUK 0.016 0.043 -10000 0 -0.45 2 2
BAD/BCL-XL 0.034 0.065 -10000 0 -0.58 2 2
mTORC2 0.023 0.012 -10000 0 -10000 0 0
AKT2 0.01 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.032 0.087 -10000 0 -0.48 6 6
PDPK1 0.022 0.005 -10000 0 -10000 0 0
MDM2 0.016 0.063 -10000 0 -0.4 6 6
MAPKKK cascade -0.034 0.066 0.48 3 -10000 0 3
MDM2/Cbp/p300 0.049 0.074 0.3 1 -0.54 2 3
TSC1/TSC2 0.012 0.053 -10000 0 -0.57 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.071 0.29 1 -0.51 2 3
glucose import -0.005 0.026 0.2 1 -0.31 3 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.015 0.048 -10000 0 -0.35 4 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.005 0.025 -10000 0 -0.31 3 3
GSK3A 0.017 0.048 -10000 0 -0.35 5 5
FOXO1 0.015 0.048 -10000 0 -0.5 3 3
GSK3B 0.026 0.073 -10000 0 -0.5 3 3
SFN 0.04 0.072 0.24 45 -0.38 3 48
G1/S transition of mitotic cell cycle 0.037 0.076 0.25 17 -0.59 1 18
p27Kip1/14-3-3 family 0.028 0.055 -10000 0 -0.54 2 2
PRKACA 0.022 0.005 -10000 0 -10000 0 0
KPNA1 0.02 0.008 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
YWHAG 0.023 0.004 -10000 0 -10000 0 0
RHEB 0.022 0.004 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.013 0.035 -10000 0 -0.32 5 5
CRKL 0.022 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
DOCK1 0.022 0.005 -10000 0 -10000 0 0
ITGA4 0.018 0.053 -10000 0 -0.56 4 4
alpha4/beta7 Integrin/MAdCAM1 0.048 0.044 -10000 0 -0.31 5 5
EPO 0.017 0.03 0.24 6 -10000 0 6
alpha4/beta7 Integrin 0.029 0.046 -10000 0 -0.41 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.029 0.041 -10000 0 -0.41 4 4
EPO/EPOR (dimer) 0.033 0.019 -10000 0 -10000 0 0
lamellipodium assembly 0.046 0.12 -10000 0 -0.52 12 12
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
JAK2 0.015 0.029 -10000 0 -0.32 3 3
PXN 0.023 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
MADCAM1 0.02 0.021 0.24 3 -10000 0 3
cell adhesion 0.047 0.043 -10000 0 -0.31 5 5
CRKL/CBL 0.032 0.009 -10000 0 -10000 0 0
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC -0.011 0.052 0.18 15 -0.42 4 19
ITGB7 0.022 0.027 -10000 0 -0.56 1 1
RAC1 0.022 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.039 0.057 -10000 0 -0.47 5 5
p130Cas/Crk/Dock1 0.025 0.048 -10000 0 -0.4 3 3
VCAM1 0.02 0.049 0.24 3 -0.56 3 6
RHOA 0.021 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.052 0.038 -10000 0 -0.32 4 4
BCAR1 -0.012 0.05 0.18 15 -0.4 4 19
EPOR 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.023 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.046 0.12 -10000 0 -0.57 11 11
Regulation of Telomerase

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
Telomerase catalytic core complex 0.055 0.11 0.38 2 -0.51 4 6
RAD9A 0.023 0.004 -10000 0 -10000 0 0
AP1 -0.015 0.14 -10000 0 -0.41 53 53
IFNAR2 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.008 0.057 -10000 0 -0.25 19 19
ER alpha/Oestrogen 0 0.086 -10000 0 -0.4 21 21
NFX1/SIN3/HDAC complex 0.013 0.059 -10000 0 -0.33 6 6
EGF 0.016 0.072 0.24 3 -0.56 7 10
SMG5 0.022 0.005 -10000 0 -10000 0 0
SMG6 0.022 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.011 -10000 0 -10000 0 0
TERT/c-Abl 0.06 0.1 0.34 2 -0.5 3 5
SAP18 0.022 0.006 -10000 0 -10000 0 0
MRN complex 0.041 0.016 -10000 0 -10000 0 0
WT1 0.037 0.051 0.24 26 -10000 0 26
WRN 0.021 0.007 -10000 0 -10000 0 0
SP1 0.027 0.008 -10000 0 -10000 0 0
SP3 0.024 0.005 -10000 0 -10000 0 0
TERF2IP 0.022 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.062 0.096 -10000 0 -0.46 3 3
Mad/Max 0.035 0.012 -10000 0 -10000 0 0
TERT 0.055 0.11 0.38 2 -0.52 4 6
CCND1 0.067 0.18 0.43 5 -1.1 6 11
MAX 0.023 0.006 -10000 0 -10000 0 0
RBBP7 0.023 0.005 -10000 0 -10000 0 0
RBBP4 0.023 0.004 -10000 0 -10000 0 0
TERF2 0.019 0.008 -10000 0 -10000 0 0
PTGES3 0.023 0.002 -10000 0 -10000 0 0
SIN3A 0.023 0.002 -10000 0 -10000 0 0
Telomerase/911 0.045 0.074 -10000 0 -0.5 3 3
CDKN1B 0.012 0.034 -10000 0 -0.34 4 4
RAD1 0.018 0.009 -10000 0 -10000 0 0
XRCC5 0.022 0.004 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
SAP30 0.022 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.03 0.011 -10000 0 -10000 0 0
UBE3A 0.024 0.005 -10000 0 -10000 0 0
JUN 0.023 0.006 -10000 0 -10000 0 0
E6 0.001 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.005 -10000 0 -10000 0 0
FOS -0.041 0.18 -10000 0 -0.56 53 53
IFN-gamma/IRF1 0.034 0.044 -10000 0 -0.4 4 4
PARP2 0.022 0.006 -10000 0 -10000 0 0
BLM 0.028 0.036 0.26 10 -10000 0 10
Telomerase 0.025 0.058 -10000 0 -0.28 3 3
IRF1 0.025 0.007 -10000 0 -10000 0 0
ESR1 -0.001 0.12 -10000 0 -0.56 20 20
KU/TER 0.032 0.008 -10000 0 -10000 0 0
ATM/TRF2 0.032 0.009 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.018 0.056 -10000 0 -0.3 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.018 0.057 -10000 0 -0.3 4 4
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.026 0.007 -10000 0 -10000 0 0
ATM 0.012 0.013 -10000 0 -10000 0 0
SMAD3 -0.011 0.004 -10000 0 -10000 0 0
ABL1 0.023 0.003 -10000 0 -10000 0 0
MXD1 0.023 0.006 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
HUS1 0.022 0.005 -10000 0 -10000 0 0
RPS6KB1 0.023 0.003 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.064 0.12 0.35 1 -0.52 7 8
NR2F2 0.019 0.006 -10000 0 -10000 0 0
MAPK3 0 0.013 -10000 0 -10000 0 0
MAPK1 0 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
HNRNPC 0.022 0.006 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.013 -10000 0 -10000 0 0
NBN 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.023 0.083 0.36 11 -0.56 6 17
mol:Oestrogen 0.001 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.026 0.083 0.27 8 -0.44 12 20
MYC 0.022 0.009 -10000 0 -10000 0 0
IL2 0.023 0.009 -10000 0 -10000 0 0
KU 0.032 0.008 -10000 0 -10000 0 0
RAD50 0.021 0.006 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
TGFB1 0.021 0.005 -10000 0 -10000 0 0
TRF2/BLM 0.034 0.024 0.25 2 -10000 0 2
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.068 0.11 0.36 2 -0.5 3 5
SP1/HDAC2 0.042 0.013 -10000 0 -10000 0 0
PINX1 0.02 0.008 -10000 0 -10000 0 0
Telomerase/EST1A 0.061 0.095 -10000 0 -0.46 3 3
Smad3/Myc 0.019 0.008 -10000 0 -10000 0 0
911 complex 0.035 0.021 -10000 0 -10000 0 0
IFNG 0.021 0.055 0.24 2 -0.55 4 6
Telomerase/PinX1 0.056 0.095 -10000 0 -0.46 3 3
Telomerase/AKT1/mTOR/p70S6K 0.023 0.097 0.24 1 -0.5 11 12
SIN3B 0.023 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
Telomerase/EST1B 0.061 0.093 -10000 0 -0.49 2 2
response to DNA damage stimulus 0.004 0.015 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.056 0.024 -10000 0 -10000 0 0
TRF2/WRN 0.029 0.015 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.059 0.096 -10000 0 -0.46 3 3
E2F1 0.025 0.008 -10000 0 -10000 0 0
ZNFX1 0.023 0.004 -10000 0 -10000 0 0
PIF1 0.043 0.064 0.24 45 -10000 0 45
NCL 0.023 0.004 -10000 0 -10000 0 0
DKC1 0.023 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.011 -10000 0 -10000 0 0
TRAF2/ASK1 0.03 0.006 -10000 0 -10000 0 0
ATM 0.023 0.004 -10000 0 -10000 0 0
MAP2K3 -0.001 0.093 -10000 0 -0.35 18 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0 0.077 -10000 0 -0.35 11 11
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.018 0.053 -10000 0 -0.56 4 4
TXN 0.005 0.001 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
GADD45A 0.022 0.004 -10000 0 -10000 0 0
GADD45B 0.008 0.091 -10000 0 -0.56 12 12
MAP3K1 0.021 0.006 -10000 0 -10000 0 0
MAP3K6 0.022 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
MAP3K4 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.033 0.008 -10000 0 -10000 0 0
TAK1/TAB family -0.003 0.018 -10000 0 -0.14 5 5
RAC1/OSM/MEKK3 0.042 0.011 -10000 0 -10000 0 0
TRAF2 0.023 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.017 0.079 -10000 0 -0.36 5 5
TRAF6 0.005 0.001 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.047 0.075 0.25 55 -0.29 1 56
CCM2 0.022 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.044 0.046 0.24 4 -0.16 1 5
MAPK11 0.022 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.054 0.046 0.24 4 -10000 0 4
OSM/MEKK3 0.033 0.008 -10000 0 -10000 0 0
TAOK1 0.01 0.011 -10000 0 -0.22 1 1
TAOK2 0.011 0.002 -10000 0 -10000 0 0
TAOK3 0.011 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.023 0.003 -10000 0 -10000 0 0
MAP3K10 0.022 0.017 0.38 1 -10000 0 1
MAP3K3 0.023 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.013 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.038 0.069 -10000 0 -0.32 15 15
Canonical NF-kappaB pathway

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
FBXW11 0.023 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.091 0.24 2 -0.35 10 12
ERC1 0.021 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.023 -10000 0 -0.41 1 1
NFKBIA -0.006 0.015 0.2 2 -10000 0 2
BIRC2 0.022 0.004 -10000 0 -10000 0 0
IKBKB 0.022 0.018 0.38 1 -10000 0 1
RIPK2 0.022 0.005 -10000 0 -10000 0 0
IKBKG 0.016 0.027 -10000 0 -10000 0 0
IKK complex/A20 0.024 0.1 -10000 0 -0.45 9 9
NEMO/A20/RIP2 0.022 0.005 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
NEMO/ATM 0.016 0.099 -10000 0 -0.38 22 22
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.028 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.021 0.089 -10000 0 -0.42 9 9
BCL10/MALT1/TRAF6 0.043 0.014 -10000 0 -10000 0 0
NOD2 0.021 0.027 -10000 0 -0.56 1 1
NFKB1 0.023 0.005 -10000 0 -10000 0 0
RELA 0.025 0.002 -10000 0 -10000 0 0
MALT1 0.022 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.009 -10000 0 -10000 0 0
ATM 0.023 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.022 0.06 -10000 0 -0.41 8 8
TRAF6 0.023 0.004 -10000 0 -10000 0 0
PRKCA 0.02 0.038 -10000 0 -0.56 2 2
CHUK 0.022 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.005 -10000 0 -10000 0 0
TNF 0.011 0.084 0.24 1 -0.56 10 11
NF kappa B1 p50/RelA 0.046 0.016 -10000 0 -10000 0 0
BCL10 0.022 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.015 0.2 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
IKK complex 0.025 0.097 -10000 0 -0.44 11 11
CYLD 0.022 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.032 0.1 -10000 0 -0.48 10 10
a4b1 and a4b7 Integrin 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
ITGB1 0.022 0.004 -9999 0 -10000 0 0
ITGB7 0.022 0.027 -9999 0 -0.56 1 1
ITGA4 0.018 0.053 -9999 0 -0.56 4 4
alpha4/beta7 Integrin 0.029 0.046 -9999 0 -0.41 5 5
alpha4/beta1 Integrin 0.029 0.041 -9999 0 -0.41 4 4
Paxillin-dependent events mediated by a4b1

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
CRKL 0.022 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.01 -10000 0 -10000 0 0
DOCK1 0.022 0.005 -10000 0 -10000 0 0
ITGA4 0.018 0.053 -10000 0 -0.56 4 4
RAC1 0.022 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.046 -10000 0 -0.41 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.04 0.035 -10000 0 -0.36 3 3
alpha4/beta7 Integrin/Paxillin 0.031 0.035 -10000 0 -0.33 4 4
lamellipodium assembly -0.013 0.1 -10000 0 -0.39 28 28
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
TLN1 0.021 0.007 -10000 0 -10000 0 0
PXN -0.01 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.04 0.032 -10000 0 -0.29 3 3
cell adhesion 0.038 0.031 -10000 0 -0.31 2 2
CRKL/CBL 0.032 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.032 0.032 -10000 0 -0.33 3 3
ITGB1 0.022 0.004 -10000 0 -10000 0 0
ITGB7 0.022 0.027 -10000 0 -0.56 1 1
ARF6/GDP 0.022 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.041 0.049 -10000 0 -0.39 5 5
p130Cas/Crk/Dock1 0.042 0.015 -10000 0 -10000 0 0
VCAM1 0.02 0.049 0.24 3 -0.56 3 6
alpha4/beta1 Integrin/Paxillin/Talin 0.04 0.032 -10000 0 -0.31 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.043 0.033 -10000 0 -0.31 3 3
BCAR1 0.022 0.006 -10000 0 -10000 0 0
mol:GDP -0.041 0.033 0.31 3 -10000 0 3
CBL 0.023 0.004 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.04 0.032 -10000 0 -0.31 2 2
Rac1/GTP -0.015 0.11 -10000 0 -0.44 28 28
Circadian rhythm 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
chromatin modification 0.036 0.024 -10000 0 -10000 0 0
CLOCK 0.022 0.007 -10000 0 -10000 0 0
TIMELESS/CRY2 0.033 0.018 -10000 0 -10000 0 0
DEC1/BMAL1 0.039 0.035 -10000 0 -10000 0 0
ATR 0.018 0.009 -10000 0 -10000 0 0
NR1D1 0.014 0.006 -10000 0 -10000 0 0
ARNTL 0.024 0.005 -10000 0 -10000 0 0
TIMELESS 0.014 0.006 -10000 0 -10000 0 0
NPAS2 0.024 0.002 -10000 0 -10000 0 0
CRY2 0.022 0.004 -10000 0 -10000 0 0
mol:CO -0.006 0 -10000 0 -10000 0 0
CHEK1 0.023 0.011 0.24 1 -10000 0 1
mol:HEME 0.006 0 -10000 0 -10000 0 0
PER1 0.019 0.038 -10000 0 -0.56 2 2
BMAL/CLOCK/NPAS2 0.048 0.018 -10000 0 -10000 0 0
BMAL1/CLOCK 0.022 0.051 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.036 0.024 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.037 0.024 -10000 0 -10000 0 0
mol:NADPH 0.006 0 -10000 0 -10000 0 0
PER1/TIMELESS 0.031 0.026 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.015 0.057 0.24 26 -10000 0 26
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.015 0.054 0.24 2 -10000 0 2
GNAI2 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0.03 0.024 -10000 0 -0.35 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.03 0.24 2 -0.56 1 3
RhoA/GTP 0.016 0.055 -10000 0 -0.25 2 2
negative regulation of cAMP metabolic process 0.017 0.036 -10000 0 -0.23 5 5
GNAZ 0.016 0.059 -10000 0 -0.56 5 5
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
S1PR5 0.024 0.036 0.24 6 -0.56 1 7
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.017 0.037 -10000 0 -0.23 5 5
RhoA/GDP 0.016 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.004 -10000 0 -10000 0 0
SNTA1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.004 -10000 0 -10000 0 0
MAPK12 -0.003 0.002 -10000 0 -10000 0 0
CCND1 0.004 0.05 -10000 0 -0.42 6 6
p38 gamma/SNTA1 0.019 0.034 -10000 0 -10000 0 0
MAP2K3 0.022 0.005 -10000 0 -10000 0 0
PKN1 0.022 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint 0.001 0.031 0.2 11 -10000 0 11
MAP2K6 0.003 0.002 -10000 0 -10000 0 0
MAPT 0.001 0.051 0.18 3 -0.33 6 9
MAPK13 -0.009 0.003 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.011 0.003 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.006 -10000 0 -10000 0 0
MDM2/SUMO1 0.03 0.033 0.24 1 -0.26 1 2
HDAC4 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.009 0.006 -10000 0 -10000 0 0
SUMO1 0.023 0.004 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.005 0.002 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.032 0.029 -10000 0 -0.24 1 1
SUMO1/HDAC1 0.032 0.03 -10000 0 -0.26 1 1
RANGAP1 0.023 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.053 0.022 0.25 1 -10000 0 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.01 0.003 -10000 0 -10000 0 0
Ran/GTP 0.022 0.029 -10000 0 -0.24 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.017 0.38 1 -10000 0 1
UBE2I 0.022 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.055 0.19 43 -10000 0 43
NPC 0.014 0.001 -10000 0 -10000 0 0
PIAS2 0.022 0.005 -10000 0 -10000 0 0
PIAS1 0.023 0.002 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.031 0.049 -10000 0 -0.34 7 7
MAPK9 0.005 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.024 0.043 -10000 0 -0.35 6 6
GNB1 0.021 0.027 -10000 0 -0.56 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 0.005 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.012 0.027 -10000 0 -0.27 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 0.002 0.007 0.07 4 -10000 0 4
GNAL 0.019 0.046 -10000 0 -0.56 3 3
GNG2 0.016 0.059 -10000 0 -0.56 5 5
CRH -0.011 0.019 0.24 1 -10000 0 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.001 -10000 0 -10000 0 0
MAPK11 0.005 0.001 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.021 0.027 0.56 1 -10000 0 1
PI3K Class IB/PDE3B 0.021 0.027 -10000 0 -0.56 1 1
PDE3B 0.021 0.027 -10000 0 -0.56 1 1
Arf1 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
coatomer protein complex 0.004 0.018 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.012 0.03 -10000 0 -0.18 1 1
AP2 0.019 0.021 0.26 1 -10000 0 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.009 -10000 0 -10000 0 0
CLTB 0.021 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.012 0.006 -10000 0 -10000 0 0
CD4 0.006 0.095 -10000 0 -0.56 13 13
CLTA 0.021 0.007 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.005 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.008 -10000 0 -10000 0 0
ARF1/GTP 0.026 0.011 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.006 0.003 -10000 0 -10000 0 0
mol:Choline 0.004 0.008 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.023 0.007 -10000 0 -10000 0 0
DDEF1 0.003 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.003 0.015 -10000 0 -10000 0 0
AP2M1 0.013 0.02 0.38 1 -10000 0 1
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.009 0.005 -10000 0 -10000 0 0
Rac/GTP 0.017 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.031 0.011 -10000 0 -10000 0 0
ARFIP2 0.018 0.013 -10000 0 -10000 0 0
COPA 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.035 -10000 0 -0.21 4 4
ARF1/GTP/ARHGAP10 0.015 0.006 -10000 0 -10000 0 0
GGA3 0.023 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.02 0.017 -10000 0 -0.25 1 1
AP2A1 0.023 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.001 0.041 -10000 0 -0.21 9 9
ARF1/GDP/Membrin 0.021 0.021 -10000 0 -0.24 2 2
Arfaptin 2/Rac/GDP 0.029 0.009 -10000 0 -10000 0 0
CYTH2 0.024 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.03 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.007 0.028 -10000 0 -0.24 4 4
PLD2 0.004 0.008 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.005 0.001 -10000 0 -10000 0 0
PIP5K1A 0.004 0.008 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.014 0.019 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.008 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.005 0.001 -10000 0 -10000 0 0
GOSR2 0.009 0.017 -10000 0 -0.33 1 1
USO1 0.006 0.037 -10000 0 -0.32 6 6
GBF1 0.002 0.051 -10000 0 -0.32 12 12
ARF1/GTP/Arfaptin 2 0.03 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.018 0.046 0.25 1 -0.36 3 4
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.022 0.005 -9999 0 -10000 0 0
SMAD2 0.003 0.043 -9999 0 -0.23 6 6
SMAD3 0.02 0.028 -9999 0 -10000 0 0
SMAD3/SMAD4 0.024 0.058 -9999 0 -0.45 4 4
SMAD4/Ubc9/PIASy 0.042 0.014 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.04 0.053 -9999 0 -10000 0 0
PPM1A 0.022 0.004 -9999 0 -10000 0 0
CALM1 0.022 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 0.011 0.051 -9999 0 -0.24 5 5
MAP3K1 0.021 0.006 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.033 0.008 -9999 0 -10000 0 0
MAPK3 0.023 0.003 -9999 0 -10000 0 0
MAPK1 0.022 0.006 -9999 0 -10000 0 0
NUP214 0.023 0.003 -9999 0 -10000 0 0
CTDSP1 0.022 0.004 -9999 0 -10000 0 0
CTDSP2 0.023 0.003 -9999 0 -10000 0 0
CTDSPL 0.021 0.007 -9999 0 -10000 0 0
KPNB1 0.023 0.003 -9999 0 -10000 0 0
TGFBRAP1 0.023 0.002 -9999 0 -10000 0 0
UBE2I 0.022 0.005 -9999 0 -10000 0 0
NUP153 0.023 0.004 -9999 0 -10000 0 0
KPNA2 0.023 0.003 -9999 0 -10000 0 0
PIAS4 0.022 0.004 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.021 0.006 -10000 0 -9999 0 0
PLK4 0.022 0.011 0.24 1 -9999 0 1
regulation of centriole replication -0.009 0.004 -10000 0 -9999 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.033 0.007 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.019 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.039 -10000 0 -10000 0 0
NFKBIA 0.011 0.022 -10000 0 -0.22 1 1
MAPK14 0.023 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.02 0.009 -10000 0 -10000 0 0
ARRB2 0.01 0.003 -10000 0 -10000 0 0
REL 0.021 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.008 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.017 0.029 0.42 2 -10000 0 2
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
NFKB1 -0.008 0.027 0.58 1 -10000 0 1
RELA 0.023 0.001 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.019 0.034 0.24 1 -0.23 1 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.022 0.043 -10000 0 -0.26 1 1
SRC 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.019 0.034 0.25 1 -0.23 1 2
IKBKB 0.022 0.018 0.38 1 -10000 0 1
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -10000 0 0
SYK 0.023 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.034 -10000 0 -0.23 2 2
cell death 0.021 0.042 -10000 0 -0.26 1 1
NF kappa B1 p105/c-Rel 0.019 0.01 -10000 0 -10000 0 0
LCK 0.021 0.027 -10000 0 -0.56 1 1
BCL3 0.022 0.004 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.042 0.015 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.031 0.011 -9999 0 -9999 0 0
CTNNB1 0.021 0.007 -9999 0 -9999 0 0
JUP 0.023 0.003 -9999 0 -9999 0 0
CDH1 0.022 0.005 -9999 0 -9999 0 0
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 0.032 0.009 -10000 0 -9999 0 0
FBXW11 0.021 0.006 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -9999 0 0
CHUK 0.022 0.005 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.061 0.025 -10000 0 -9999 0 0
NFKB1 0.022 0.005 -10000 0 -9999 0 0
MAP3K14 0.023 0.003 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.033 0.014 0.26 1 -9999 0 1
RELB 0.023 0.017 0.38 1 -9999 0 1
NFKB2 0.022 0.005 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.03 0.013 0.24 1 -9999 0 1
regulation of B cell activation 0.029 0.012 0.23 1 -9999 0 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 479 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.O2.A5IB TCGA.O2.A52W TCGA.O2.A52V TCGA.O2.A52S
109_MAP3K5 -0.17 0.021 0.021 -0.18
47_PPARGC1A 0 0.023 0.023 -0.56
105_BMP4 0.023 0.023 0.023 0.023
105_BMP6 0.023 0.023 0.023 0.023
105_BMP7 0.023 0.24 0.24 0.023
105_BMP2 -0.56 0.023 0.023 0.023
131_RELN/VLDLR 0.06 0.06 0.06 -0.33
30_TGFB1/TGF beta receptor Type II 0.028 0.021 0.022 0.022
84_STAT5B -0.34 0.025 0.025 -0.074
84_STAT5A -0.34 0.025 0.025 -0.074
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 = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LUSC-TP/6154696/Gistic2_Analysis_6154866/all_data_by_genes.txt

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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