PARADIGM pathway analysis of mRNASeq expression data
Lung Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1W37VR1
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 36 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Signaling events mediated by the Hedgehog family 165
Angiopoietin receptor Tie2-mediated signaling 158
Aurora B signaling 139
FOXM1 transcription factor network 129
Endothelins 81
TCGA08_p53 67
TCGA08_retinoblastoma 64
Glypican 2 network 61
amb2 Integrin signaling 60
Thromboxane A2 receptor signaling 58
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 501 . 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 ( 501 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events mediated by the Hedgehog family 0.3293 165 8614 52 -0.64 0.34 1000 -1000 -0.097 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3154 158 13905 88 -0.75 0.06 1000 -1000 -0.13 -1000
Aurora B signaling 0.2774 139 9321 67 -0.62 0.005 1000 -1000 -0.085 -1000
FOXM1 transcription factor network 0.2575 129 6583 51 -0.71 0.002 1000 -1000 -0.21 -1000
Endothelins 0.1617 81 7816 96 -0.44 0.036 1000 -1000 -0.089 -1000
TCGA08_p53 0.1337 67 470 7 -0.19 0.097 1000 -1000 -0.037 -1000
TCGA08_retinoblastoma 0.1277 64 516 8 -0.28 0.087 1000 -1000 -0.03 -1000
Glypican 2 network 0.1218 61 247 4 -0.085 -0.068 1000 -1000 -0.044 -1000
amb2 Integrin signaling 0.1198 60 4929 82 -0.68 0 1000 -1000 -0.097 -1000
Thromboxane A2 receptor signaling 0.1158 58 6091 105 -0.18 0.041 1000 -1000 -0.08 -1000
Visual signal transduction: Cones 0.1058 53 2031 38 -0.29 0.009 1000 -1000 -0.079 -1000
Fc-epsilon receptor I signaling in mast cells 0.1058 53 5224 97 -0.26 0.033 1000 -1000 -0.11 -1000
Aurora C signaling 0.1018 51 363 7 -0.41 0 1000 -1000 -0.051 -1000
IL4-mediated signaling events 0.0998 50 4603 91 -0.81 0.45 1000 -1000 -0.18 -1000
Glucocorticoid receptor regulatory network 0.0998 50 5731 114 -0.56 0.36 1000 -1000 -0.088 -1000
Signaling events regulated by Ret tyrosine kinase 0.0998 50 4171 82 -0.2 0 1000 -1000 -0.1 -1000
PLK1 signaling events 0.0898 45 3828 85 -0.38 0.072 1000 -1000 -0.063 -1000
BMP receptor signaling 0.0858 43 3557 81 -0.39 0.037 1000 -1000 -0.1 -1000
Arf6 signaling events 0.0838 42 2638 62 -0.3 0.015 1000 -1000 -0.069 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0838 42 2188 52 -0.38 0.057 1000 -1000 -0.078 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0778 39 3060 78 -0.13 0.036 1000 -1000 -0.091 -1000
Nectin adhesion pathway 0.0758 38 2435 63 -0.27 0 1000 -1000 -0.084 -1000
Glypican 1 network 0.0739 37 1779 48 -0.22 0.032 1000 -1000 -0.059 -1000
Signaling mediated by p38-alpha and p38-beta 0.0719 36 1620 44 -0.13 0 1000 -1000 -0.059 -1000
Nongenotropic Androgen signaling 0.0699 35 1835 52 -0.15 0.048 1000 -1000 -0.07 -1000
HIF-1-alpha transcription factor network 0.0639 32 2455 76 -0.44 0.017 1000 -1000 -0.21 -1000
Integrins in angiogenesis 0.0639 32 2711 84 -0.46 0.031 1000 -1000 -0.12 -1000
FOXA2 and FOXA3 transcription factor networks 0.0619 31 1448 46 -0.77 0.072 1000 -1000 -0.12 -1000
Calcium signaling in the CD4+ TCR pathway 0.0599 30 935 31 -0.21 0.012 1000 -1000 -0.13 -1000
Syndecan-3-mediated signaling events 0.0559 28 990 35 -0.34 0 1000 -1000 -0.078 -1000
IL23-mediated signaling events 0.0559 28 1713 60 -0.24 0.018 1000 -1000 -0.18 -1000
Coregulation of Androgen receptor activity 0.0539 27 2092 76 -0.4 0.031 1000 -1000 -0.073 -1000
Aurora A signaling 0.0539 27 1660 60 -0.49 0.028 1000 -1000 -0.069 -1000
Canonical Wnt signaling pathway 0.0539 27 1421 51 -0.47 0.16 1000 -1000 -0.079 -1000
LPA4-mediated signaling events 0.0519 26 323 12 -0.14 0.017 1000 -1000 -0.034 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0519 26 1795 68 -0.23 0.015 1000 -1000 -0.16 -1000
Presenilin action in Notch and Wnt signaling 0.0499 25 1573 61 -0.47 0.016 1000 -1000 -0.076 -1000
Reelin signaling pathway 0.0479 24 1392 56 -0.13 0.003 1000 -1000 -0.12 -1000
IL6-mediated signaling events 0.0479 24 1813 75 -0.48 0.05 1000 -1000 -0.12 -1000
Regulation of Androgen receptor activity 0.0439 22 1600 70 -0.42 0.018 1000 -1000 -0.083 -1000
Syndecan-1-mediated signaling events 0.0419 21 725 34 -0.36 0 1000 -1000 -0.083 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0419 21 2703 125 -0.2 0 1000 -1000 -0.13 -1000
Visual signal transduction: Rods 0.0419 21 1135 52 -0.18 0 1000 -1000 -0.092 -1000
ErbB4 signaling events 0.0399 20 1439 69 -0.38 0.2 1000 -1000 -0.11 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0399 20 686 33 -0.27 0 1000 -1000 -0.076 -1000
IL12-mediated signaling events 0.0379 19 1723 87 -0.16 0.019 1000 -1000 -0.15 -1000
Osteopontin-mediated events 0.0379 19 739 38 -0.29 0 1000 -1000 -0.12 -1000
Plasma membrane estrogen receptor signaling 0.0379 19 1644 86 -0.18 0.031 1000 -1000 -0.1 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0379 19 2369 120 -0.27 0.13 1000 -1000 -0.086 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0359 18 975 54 -0.15 0.02 1000 -1000 -0.11 -1000
HIF-2-alpha transcription factor network 0.0359 18 791 43 -0.38 0.21 1000 -1000 -0.12 -1000
Wnt signaling 0.0359 18 132 7 -0.094 0 1000 -1000 -0.063 -1000
Ephrin A reverse signaling 0.0339 17 121 7 -0.024 0.002 1000 -1000 -0.037 -1000
TCR signaling in naïve CD8+ T cells 0.0339 17 1602 93 -0.066 0.035 1000 -1000 -0.1 -1000
PDGFR-alpha signaling pathway 0.0319 16 720 44 -0.2 0.021 1000 -1000 -0.073 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0299 15 1275 85 -0.16 0.011 1000 -1000 -0.092 -1000
p75(NTR)-mediated signaling 0.0299 15 1936 125 -0.34 0 1000 -1000 -0.12 -1000
Regulation of nuclear SMAD2/3 signaling 0.0240 12 1647 136 -0.34 0.094 1000 -1000 -0.097 -1000
Caspase cascade in apoptosis 0.0220 11 864 74 -0.071 0.035 1000 -1000 -0.064 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0220 11 314 28 -0.18 0.02 1000 -1000 -0.063 -1000
Noncanonical Wnt signaling pathway 0.0220 11 299 26 -0.1 0 1000 -1000 -0.099 -1000
Syndecan-2-mediated signaling events 0.0220 11 775 69 -0.17 0.031 1000 -1000 -0.072 -1000
Signaling events mediated by HDAC Class III 0.0220 11 443 40 -0.15 0.05 1000 -1000 -0.048 -1000
FAS signaling pathway (CD95) 0.0220 11 536 47 -0.19 0.009 1000 -1000 -0.058 -1000
Ras signaling in the CD4+ TCR pathway 0.0220 11 194 17 -0.057 0.008 1000 -1000 -0.074 -1000
JNK signaling in the CD4+ TCR pathway 0.0200 10 175 17 -0.044 0.022 1000 -1000 -0.079 -1000
Effects of Botulinum toxin 0.0200 10 275 26 -0.071 0.005 1000 -1000 -0.07 -1000
BCR signaling pathway 0.0200 10 1072 99 -0.11 0.04 1000 -1000 -0.12 -1000
EGFR-dependent Endothelin signaling events 0.0200 10 228 21 -0.065 0 1000 -1000 -0.091 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0180 9 313 34 -0.029 0 1000 -1000 -0.077 -1000
S1P1 pathway 0.0180 9 329 36 -0.061 0.01 1000 -1000 -0.09 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0180 9 734 74 -0.17 0.068 1000 -1000 -0.11 -1000
Syndecan-4-mediated signaling events 0.0180 9 625 67 -0.17 0.01 1000 -1000 -0.11 -1000
Hedgehog signaling events mediated by Gli proteins 0.0160 8 582 65 -0.6 0.044 1000 -1000 -0.092 -1000
IL2 signaling events mediated by STAT5 0.0160 8 183 22 -0.15 0.06 1000 -1000 -0.073 -1000
S1P4 pathway 0.0160 8 218 25 -0.065 0.003 1000 -1000 -0.064 -1000
Signaling events mediated by PTP1B 0.0140 7 546 76 -0.1 0.033 1000 -1000 -0.093 -1000
TRAIL signaling pathway 0.0140 7 368 48 -0.096 0.046 1000 -1000 -0.075 -1000
Cellular roles of Anthrax toxin 0.0120 6 265 39 -0.092 0.017 1000 -1000 -0.037 -1000
Retinoic acid receptors-mediated signaling 0.0120 6 384 58 -0.22 0.034 1000 -1000 -0.086 -1000
Regulation of p38-alpha and p38-beta 0.0120 6 339 54 -0.087 0.036 1000 -1000 -0.09 -1000
IL27-mediated signaling events 0.0120 6 310 51 -0.12 0.011 1000 -1000 -0.11 -1000
LPA receptor mediated events 0.0120 6 703 102 -0.1 0.035 1000 -1000 -0.1 -1000
IGF1 pathway 0.0120 6 344 57 -0.021 0.04 1000 -1000 -0.12 -1000
S1P3 pathway 0.0120 6 272 42 -0.18 0.041 1000 -1000 -0.072 -1000
Signaling events mediated by PRL 0.0120 6 220 34 -0.13 0.028 1000 -1000 -0.068 -1000
BARD1 signaling events 0.0100 5 303 57 -0.13 0.022 1000 -1000 -0.077 -1000
Ephrin B reverse signaling 0.0100 5 275 48 -0.071 0.04 1000 -1000 -0.079 -1000
IL2 signaling events mediated by PI3K 0.0100 5 305 58 -0.23 0.074 1000 -1000 -0.1 -1000
Arf6 trafficking events 0.0100 5 409 71 -0.085 0.032 1000 -1000 -0.082 -1000
Insulin Pathway 0.0100 5 382 74 -0.1 0.032 1000 -1000 -0.11 -1000
ErbB2/ErbB3 signaling events 0.0080 4 277 65 -0.078 0.054 1000 -1000 -0.087 -1000
Signaling events mediated by HDAC Class II 0.0080 4 350 75 -0.081 0 1000 -1000 -0.074 -1000
a4b1 and a4b7 Integrin signaling 0.0080 4 20 5 -0.009 -0.001 1000 -1000 -0.042 -1000
IL1-mediated signaling events 0.0080 4 298 62 -0.061 0.042 1000 -1000 -0.12 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0080 4 385 83 -0.069 0.05 1000 -1000 -0.095 -1000
Signaling events mediated by HDAC Class I 0.0080 4 416 104 -0.081 0.041 1000 -1000 -0.093 -1000
EPHB forward signaling 0.0080 4 413 85 -0.072 0.033 1000 -1000 -0.1 -1000
Regulation of Telomerase 0.0080 4 408 102 -0.12 0.025 1000 -1000 -0.13 -1000
p38 MAPK signaling pathway 0.0080 4 219 44 -0.069 0.034 1000 -1000 -0.074 -1000
IFN-gamma pathway 0.0060 3 242 68 -0.069 0.065 1000 -1000 -0.12 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0060 3 137 45 -0.027 0.061 1000 -1000 -0.1 -1000
TCGA08_rtk_signaling 0.0060 3 90 26 -0.065 0.038 1000 -1000 -0.035 -1000
Class I PI3K signaling events 0.0060 3 253 73 -0.054 0.026 1000 -1000 -0.092 -1000
VEGFR1 specific signals 0.0060 3 212 56 -0.2 0.043 1000 -1000 -0.093 -1000
Circadian rhythm pathway 0.0040 2 59 22 -0.032 0.038 1000 -1000 -0.072 -1000
EPO signaling pathway 0.0040 2 117 55 -0.007 0.066 1000 -1000 -0.11 -1000
Ceramide signaling pathway 0.0040 2 171 76 -0.028 0.041 1000 -1000 -0.07 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0040 2 107 37 -0.012 0.025 1000 -1000 -0.092 -1000
Paxillin-dependent events mediated by a4b1 0.0040 2 79 36 -0.01 0.02 1000 -1000 -0.083 -1000
PDGFR-beta signaling pathway 0.0040 2 231 97 -0.044 0.054 1000 -1000 -0.1 -1000
Class IB PI3K non-lipid kinase events 0.0040 2 6 3 -0.003 -1000 1000 -1000 -0.033 -1000
Insulin-mediated glucose transport 0.0020 1 53 32 -0.057 0.034 1000 -1000 -0.074 -1000
S1P5 pathway 0.0020 1 26 17 -0.01 0.006 1000 -1000 -0.07 -1000
FoxO family signaling 0.0020 1 98 64 -0.089 0.081 1000 -1000 -0.097 -1000
Signaling mediated by p38-gamma and p38-delta 0.0020 1 15 15 -0.001 0.027 1000 -1000 -0.07 -1000
Rapid glucocorticoid signaling 0.0020 1 31 20 -0.007 0.007 1000 -1000 -0.044 -1000
E-cadherin signaling in keratinocytes 0.0020 1 62 43 -0.023 0.043 1000 -1000 -0.09 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 2 23 -0.001 0.036 1000 -1000 -0.085 -1000
Canonical NF-kappaB pathway 0.0000 0 33 39 -0.019 0.072 1000 -1000 -0.1 -1000
PLK2 and PLK4 events 0.0000 0 2 3 -0.001 0.019 1000 -1000 -0.029 -1000
Arf6 downstream pathway 0.0000 0 21 43 -0.024 0.025 1000 -1000 -0.052 -1000
mTOR signaling pathway 0.0000 0 14 53 -0.004 0.03 1000 -1000 -0.07 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 60 68 -0.057 0.043 1000 -1000 -0.076 -1000
ceramide signaling pathway 0.0000 0 45 49 -0.013 0.044 1000 -1000 -0.059 -1000
Atypical NF-kappaB pathway 0.0000 0 9 31 -0.001 0.03 1000 -1000 -0.08 -1000
E-cadherin signaling in the nascent adherens junction 0.0000 0 52 76 -0.026 0.053 1000 -1000 -0.1 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 2 27 -0.001 0.025 1000 -1000 -0.058 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0 1000 -1000 -0.051 -1000
Arf1 pathway 0.0000 0 32 54 -0.022 0.022 1000 -1000 -0.058 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 -0.001 0 1000 -1000 -0.078 -1000
Total NA 2715 168473 7203 -25 -990 131000 -131000 -12 -131000
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.43 0.29 -10000 0 -0.69 233 233
IHH -0.47 0.38 -10000 0 -0.81 278 278
SHH Np/Cholesterol/GAS1 -0.069 0.16 -10000 0 -0.44 78 78
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.068 0.16 0.44 78 -10000 0 78
SMO/beta Arrestin2 -0.36 0.25 -10000 0 -0.59 239 239
SMO -0.38 0.27 -10000 0 -0.63 240 240
AKT1 -0.15 0.11 -10000 0 -0.34 1 1
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.004 0.049 -10000 0 -0.63 3 3
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.37 0.26 -10000 0 -0.62 240 240
STIL -0.32 0.24 -10000 0 -0.52 258 258
DHH N/PTCH2 -0.046 0.16 -10000 0 -0.56 41 41
DHH N/PTCH1 -0.36 0.24 -10000 0 -0.57 246 246
PIK3CA 0 0 -10000 0 -10000 0 0
DHH -0.053 0.19 -10000 0 -0.74 36 36
PTHLH -0.58 0.36 -10000 0 -0.92 233 233
determination of left/right symmetry -0.37 0.26 -10000 0 -0.62 240 240
PIK3R1 0 0 -10000 0 -10000 0 0
skeletal system development -0.58 0.35 -10000 0 -0.91 233 233
IHH N/Hhip -0.64 0.38 -10000 0 -0.81 396 396
DHH N/Hhip -0.4 0.3 -10000 0 -0.59 339 339
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.37 0.26 -10000 0 -0.62 240 240
pancreas development -0.48 0.35 -10000 0 -0.74 330 330
HHAT 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.013 0.098 -10000 0 -0.74 9 9
somite specification -0.37 0.26 -10000 0 -0.62 240 240
SHH Np/Cholesterol/PTCH1 -0.35 0.25 -10000 0 -0.55 256 256
SHH Np/Cholesterol/PTCH2 -0.066 0.16 -10000 0 -0.43 77 77
SHH Np/Cholesterol/Megalin -0.28 0.26 -10000 0 -0.49 281 281
SHH -0.062 0.2 -10000 0 -0.54 72 72
catabolic process -0.37 0.25 -10000 0 -0.57 288 288
SMO/Vitamin D3 -0.37 0.26 -10000 0 -0.59 255 255
SHH Np/Cholesterol/Hhip -0.35 0.26 -10000 0 -0.5 349 349
LRP2 -0.37 0.37 -10000 0 -0.74 250 250
receptor-mediated endocytosis -0.49 0.31 -10000 0 -0.71 289 289
SHH Np/Cholesterol/BOC -0.063 0.15 -10000 0 -0.43 74 74
SHH Np/Cholesterol/CDO -0.066 0.16 -10000 0 -0.44 70 70
mesenchymal cell differentiation 0.34 0.26 0.49 349 -10000 0 349
mol:Vitamin D3 -0.35 0.26 -10000 0 -0.56 256 256
IHH N/PTCH2 -0.3 0.27 -10000 0 -0.54 278 278
CDON -0.007 0.073 -10000 0 -0.74 5 5
IHH N/PTCH1 -0.38 0.26 -10000 0 -0.58 288 288
Megalin/LRPAP1 -0.28 0.28 -10000 0 -0.56 250 250
PTCH2 -0.008 0.075 -10000 0 -0.68 6 6
SHH Np/Cholesterol -0.062 0.15 -10000 0 -0.43 72 72
PTCH1 -0.37 0.25 -10000 0 -0.57 288 288
HHIP -0.49 0.35 -10000 0 -0.74 330 330
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.51 0.54 -10000 0 -1 263 263
NCK1/PAK1/Dok-R -0.24 0.23 -10000 0 -0.46 263 263
NCK1/Dok-R -0.67 0.67 -10000 0 -1.3 263 263
PIK3CA 0.007 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.06 0.1 0.25 108 -10000 0 108
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.003 0.005 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.05 0.14 -10000 0 -0.57 10 10
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.59 0.58 -10000 0 -1.1 263 263
FN1 -0.019 0.12 -10000 0 -0.74 13 13
PLD2 -0.66 0.72 -10000 0 -1.3 263 263
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.044 0.17 -10000 0 -0.73 30 30
ELK1 -0.56 0.61 -10000 0 -1.1 263 263
GRB7 -0.005 0.051 -10000 0 -0.57 4 4
PAK1 -0.001 0.026 -10000 0 -0.57 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.64 0.63 -10000 0 -1.2 263 263
CDKN1A -0.34 0.36 -10000 0 -0.68 252 252
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.67 0.67 -10000 0 -1.3 263 263
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.35 0.38 -10000 0 -0.71 263 263
PLG -0.66 0.72 -10000 0 -1.3 263 263
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.49 0.49 -10000 0 -0.95 263 263
GRB2 0 0 -10000 0 -10000 0 0
PIK3R1 0.003 0.005 -10000 0 -10000 0 0
ANGPT2 -0.33 0.34 -10000 0 -0.74 173 173
BMX -0.73 0.76 -10000 0 -1.4 263 263
ANGPT1 -0.37 0.62 -10000 0 -1.5 118 118
tube development -0.4 0.41 -10000 0 -0.78 262 262
ANGPT4 -0.33 0.37 -10000 0 -0.74 222 222
response to hypoxia -0.034 0.037 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.73 0.72 -10000 0 -1.4 263 263
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.015 0.12 -10000 0 -0.74 14 14
STAT5A (dimer) -0.47 0.48 -10000 0 -0.91 260 260
mol:L-citrulline -0.35 0.38 -10000 0 -0.71 263 263
AGTR1 -0.3 0.37 -10000 0 -0.74 205 205
MAPK14 -0.68 0.71 -10000 0 -1.3 263 263
Tie2/SHP2 -0.59 0.62 -10000 0 -1.2 229 229
TEK -0.66 0.69 -10000 0 -1.4 229 229
RPS6KB1 -0.48 0.51 -10000 0 -0.96 263 263
Angiotensin II/AT1 -0.23 0.28 -10000 0 -0.56 205 205
Tie2/Ang1/GRB2 -0.71 0.72 -10000 0 -1.4 263 263
MAPK3 -0.58 0.63 -10000 0 -1.2 263 263
MAPK1 -0.58 0.63 -10000 0 -1.2 263 263
Tie2/Ang1/GRB7 -0.71 0.72 -10000 0 -1.4 263 263
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.66 0.72 -10000 0 -1.3 263 263
PI3K -0.61 0.64 -10000 0 -1.2 263 263
FES -0.67 0.71 -10000 0 -1.3 263 263
Crk/Dok-R -0.67 0.67 -10000 0 -1.3 263 263
Tie2/Ang1/ABIN2 -0.71 0.72 -10000 0 -1.4 263 263
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.44 0.47 -10000 0 -0.88 263 263
STAT5A 0.004 0.005 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.48 0.51 -10000 0 -0.96 263 263
Tie2/Ang2 -0.6 0.6 -10000 0 -1.2 262 262
Tie2/Ang1 -0.75 0.83 -10000 0 -1.5 263 263
FOXO1 -0.44 0.47 -10000 0 -0.89 263 263
ELF1 -0.032 0.052 -10000 0 -10000 0 0
ELF2 -0.67 0.73 -10000 0 -1.3 263 263
mol:Choline -0.61 0.66 -10000 0 -1.2 263 263
cell migration -0.13 0.12 -10000 0 -0.25 203 203
FYN -0.47 0.48 -10000 0 -0.92 262 262
DOK2 -0.068 0.21 -10000 0 -0.74 46 46
negative regulation of cell cycle -0.31 0.32 -10000 0 -0.62 252 252
ETS1 -0.061 0.15 -10000 0 -0.82 12 12
PXN -0.38 0.41 -10000 0 -0.77 263 263
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.41 0.44 -10000 0 -0.83 263 263
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.062 0.16 -10000 0 -0.81 13 13
MAPKKK cascade -0.61 0.66 -10000 0 -1.2 263 263
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.7 0.74 -10000 0 -1.4 263 263
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.31 0.34 -10000 0 -0.63 263 263
mol:Phosphatidic acid -0.61 0.66 -10000 0 -1.2 263 263
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.35 0.38 -10000 0 -0.71 263 263
Rac1/GTP -0.47 0.44 -10000 0 -0.88 263 263
MMP2 -0.66 0.72 -10000 0 -1.3 263 263
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.18 0.15 -9999 0 -0.32 242 242
STMN1 -0.29 0.19 -9999 0 -0.41 359 359
Aurora B/RasGAP/Survivin -0.51 0.22 -9999 0 -0.62 365 365
Chromosomal passenger complex/Cul3 protein complex -0.2 0.1 -9999 0 -0.33 124 124
BIRC5 -0.49 0.21 -9999 0 -0.58 426 426
DES -0.56 0.38 -9999 0 -0.83 322 322
Aurora C/Aurora B/INCENP -0.22 0.15 -9999 0 -0.4 9 9
Aurora B/TACC1 -0.25 0.16 -9999 0 -0.35 359 359
Aurora B/PP2A -0.29 0.19 -9999 0 -0.41 359 359
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.059 0.044 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.005 0.003 -9999 0 -10000 0 0
NDC80 -0.41 0.29 -9999 0 -0.56 374 374
Cul3 protein complex -0.01 0.062 -9999 0 -0.37 14 14
KIF2C -0.17 0.087 -9999 0 -0.24 258 258
PEBP1 -0.002 0.048 -9999 0 -0.75 2 2
KIF20A -0.3 0.29 -9999 0 -0.58 259 259
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.29 0.19 -9999 0 -0.41 359 359
SEPT1 -0.001 0.026 -9999 0 -0.57 1 1
SMC2 0 0 -9999 0 -10000 0 0
SMC4 0 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.11 0.067 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B -0.15 0.1 -9999 0 -0.21 359 359
AURKB -0.41 0.26 -9999 0 -0.58 359 359
AURKC -0.003 0.042 -9999 0 -0.66 2 2
CDCA8 -0.15 0.26 -9999 0 -0.59 130 130
cytokinesis -0.32 0.16 -9999 0 -0.49 175 175
Aurora B/Septin1 -0.3 0.16 -9999 0 -0.47 166 166
AURKA -0.018 0.13 -9999 0 -0.58 24 24
INCENP 0.001 0.003 -9999 0 -10000 0 0
KLHL13 -0.013 0.084 -9999 0 -0.57 11 11
BUB1 -0.05 0.17 -9999 0 -0.58 47 47
hSgo1/Aurora B/Survivin -0.62 0.31 -9999 0 -0.78 372 372
EVI5 0.005 0.004 -9999 0 -10000 0 0
RhoA/GTP -0.27 0.18 -9999 0 -0.53 123 123
SGOL1 -0.3 0.29 -9999 0 -0.57 261 261
CENPA -0.24 0.12 -9999 0 -0.31 352 352
NCAPG -0.11 0.23 -9999 0 -0.57 98 98
Aurora B/HC8 Proteasome -0.29 0.19 -9999 0 -0.41 359 359
NCAPD2 -0.001 0.026 -9999 0 -0.57 1 1
Aurora B/PP1-gamma -0.29 0.19 -9999 0 -0.41 359 359
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.3 0.29 -9999 0 -0.57 257 257
NPM1 -0.14 0.084 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.004 0.057 -9999 0 -0.74 3 3
mitotic prometaphase -0.012 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.29 0.19 -9999 0 -0.4 359 359
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.3 0.2 -9999 0 -0.53 167 167
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.14 0.084 -9999 0 -10000 0 0
MYLK -0.15 0.11 -9999 0 -0.21 350 350
KIF23 -0.11 0.23 -9999 0 -0.58 99 99
VIM -0.3 0.21 -9999 0 -0.42 360 360
RACGAP1 0.001 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.14 0.084 -9999 0 -10000 0 0
Chromosomal passenger complex -0.27 0.15 -9999 0 -0.35 344 344
Chromosomal passenger complex/EVI5 -0.49 0.25 -9999 0 -0.63 350 350
TACC1 -0.003 0.046 -9999 0 -0.74 2 2
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.58 0.44 -9999 0 -1 147 147
PLK1 -0.18 0.2 -9999 0 -0.41 121 121
BIRC5 -0.33 0.16 -9999 0 -10000 0 0
HSPA1B -0.58 0.44 -9999 0 -1 139 139
MAP2K1 -0.012 0.024 -9999 0 -10000 0 0
BRCA2 -0.58 0.44 -9999 0 -1 160 160
FOXM1 -0.71 0.56 -9999 0 -1.2 219 219
XRCC1 -0.58 0.44 -9999 0 -1 146 146
FOXM1B/p19 -0.6 0.44 -9999 0 -1 189 189
Cyclin D1/CDK4 -0.54 0.41 -9999 0 -0.98 133 133
CDC2 -0.61 0.46 -9999 0 -1 215 215
TGFA -0.52 0.39 -9999 0 -0.94 128 128
SKP2 -0.58 0.44 -9999 0 -1 168 168
CCNE1 -0.13 0.24 -9999 0 -0.59 111 111
CKS1B -0.58 0.44 -9999 0 -1 149 149
RB1 -0.26 0.16 -9999 0 -0.5 34 34
FOXM1C/SP1 -0.64 0.49 -9999 0 -1.1 202 202
AURKB -0.28 0.19 -9999 0 -0.41 101 101
CENPF -0.64 0.48 -9999 0 -1.1 222 222
CDK4 0.002 0.028 -9999 0 -0.6 1 1
MYC -0.51 0.39 -9999 0 -0.9 146 146
CHEK2 -0.012 0.024 -9999 0 -10000 0 0
ONECUT1 -0.57 0.44 -9999 0 -1 158 158
CDKN2A -0.26 0.29 -9999 0 -0.57 233 233
LAMA4 -0.58 0.44 -9999 0 -1.1 146 146
FOXM1B/HNF6 -0.66 0.51 -9999 0 -1.2 175 175
FOS -0.64 0.51 -9999 0 -1.2 162 162
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.58 0.44 -9999 0 -1 140 140
response to radiation -0.024 0.023 -9999 0 -10000 0 0
CENPB -0.58 0.44 -9999 0 -1.1 138 138
CENPA -0.7 0.47 -9999 0 -1.1 271 271
NEK2 -0.68 0.49 -9999 0 -1.1 243 243
HIST1H2BA -0.58 0.44 -9999 0 -1 147 147
CCNA2 -0.15 0.26 -9999 0 -0.59 129 129
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.66 0.51 -9999 0 -1.2 179 179
CCNB2 -0.66 0.49 -9999 0 -1.1 218 218
CCNB1 -0.62 0.47 -9999 0 -1.1 179 179
ETV5 -0.58 0.44 -9999 0 -1 152 152
ESR1 -0.6 0.46 -9999 0 -1.1 144 144
CCND1 -0.55 0.42 -9999 0 -1 138 138
GSK3A -0.004 0.019 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.17 0.24 -9999 0 -0.44 197 197
CDK2 0.002 0.006 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.03 0.028 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.64 0.42 -9999 0 -1 225 225
GAS1 -0.58 0.45 -9999 0 -1.1 152 152
MMP2 -0.58 0.44 -9999 0 -1 153 153
RB1/FOXM1C -0.58 0.45 -9999 0 -1 173 173
CREBBP 0 0 -9999 0 -10000 0 0
Endothelins

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
AKT1 -0.032 0.24 -9999 0 -0.68 38 38
PTK2B 0.003 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.086 0.3 -9999 0 -0.84 47 47
EDN1 -0.043 0.26 -9999 0 -0.79 44 44
EDN3 -0.086 0.23 -9999 0 -0.7 62 62
EDN2 -0.088 0.21 -9999 0 -0.59 74 74
HRAS/GDP -0.19 0.31 -9999 0 -0.63 134 134
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.057 0.21 -9999 0 -0.49 65 65
ADCY4 -0.08 0.23 -9999 0 -0.69 43 43
ADCY5 -0.091 0.24 -9999 0 -0.67 49 49
ADCY6 -0.056 0.2 -9999 0 -0.62 35 35
ADCY7 -0.054 0.19 -9999 0 -0.62 34 34
ADCY1 -0.055 0.2 -9999 0 -0.62 34 34
ADCY2 -0.087 0.22 -9999 0 -0.65 41 41
ADCY3 -0.054 0.19 -9999 0 -0.61 35 35
ADCY8 -0.18 0.25 -9999 0 -0.66 60 60
ADCY9 -0.055 0.2 -9999 0 -0.69 26 26
arachidonic acid secretion -0.15 0.28 -9999 0 -0.55 123 123
ETB receptor/Endothelin-1/Gq/GTP -0.32 0.36 -9999 0 -0.62 233 233
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
HRAS 0.006 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.035 0.27 -9999 0 -0.64 38 38
ETA receptor/Endothelin-1/Gs/GTP 0.029 0.26 -9999 0 -0.64 37 37
mol:GTP 0 0.004 -9999 0 -10000 0 0
COL3A1 -0.047 0.26 -9999 0 -0.78 28 28
EDNRB -0.44 0.36 -9999 0 -0.73 302 302
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.048 0.29 -9999 0 -0.84 38 38
CYSLTR1 -0.094 0.37 -9999 0 -0.9 73 73
SLC9A1 -0.008 0.13 -9999 0 -0.36 23 23
mol:GDP -0.21 0.34 -9999 0 -0.69 136 136
SLC9A3 -0.37 0.4 -9999 0 -0.69 254 254
RAF1 -0.21 0.33 -9999 0 -0.66 148 148
JUN -0.061 0.24 -9999 0 -0.66 37 37
JAK2 -0.032 0.24 -9999 0 -0.7 35 35
mol:IP3 -0.22 0.31 -9999 0 -0.66 138 138
ETA receptor/Endothelin-1 0.015 0.33 -9999 0 -0.69 56 56
PLCB1 0.002 0.033 -9999 0 -0.74 1 1
PLCB2 -0.005 0.094 -9999 0 -0.74 8 8
ETA receptor/Endothelin-3 -0.054 0.21 -9999 0 -0.54 68 68
FOS -0.21 0.36 -9999 0 -0.87 90 90
Gai/GDP -0.005 0.067 -9999 0 -0.95 1 1
CRK 0.003 0.005 -9999 0 -10000 0 0
mol:Ca ++ -0.26 0.38 -9999 0 -0.76 146 146
BCAR1 0.007 0.005 -9999 0 -10000 0 0
PRKCB1 -0.2 0.3 -9999 0 -0.63 140 140
GNAQ 0.008 0.034 -9999 0 -0.74 1 1
GNAZ -0.009 0.08 -9999 0 -0.74 6 6
GNAL -0.004 0.057 -9999 0 -0.74 3 3
Gs family/GDP -0.21 0.27 -9999 0 -0.61 134 134
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.24 -9999 0 -0.54 71 71
MAPK14 -0.24 0.29 -9999 0 -0.65 139 139
TRPC6 -0.094 0.32 -9999 0 -0.95 44 44
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.001 0.033 -9999 0 -0.74 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.26 0.31 -9999 0 -0.62 171 171
ETB receptor/Endothelin-2 -0.39 0.3 -9999 0 -0.59 333 333
ETB receptor/Endothelin-3 -0.39 0.31 -9999 0 -0.6 328 328
ETB receptor/Endothelin-1 -0.37 0.34 -9999 0 -0.61 315 315
MAPK3 -0.22 0.37 -9999 0 -0.78 123 123
MAPK1 -0.22 0.37 -9999 0 -0.8 113 113
Rac1/GDP -0.18 0.31 -9999 0 -0.63 133 133
cAMP biosynthetic process -0.079 0.21 -9999 0 -0.6 48 48
MAPK8 -0.085 0.28 -9999 0 -0.65 70 70
SRC 0 0 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.17 0.17 -9999 0 -0.44 68 68
p130Cas/CRK/Src/PYK2 -0.19 0.33 -9999 0 -0.67 135 135
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.18 0.31 -9999 0 -0.63 133 133
COL1A2 -0.26 0.32 -9999 0 -0.79 92 92
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.051 0.2 -9999 0 -0.46 78 78
mol:DAG -0.22 0.31 -9999 0 -0.66 138 138
MAP2K2 -0.21 0.33 -9999 0 -0.65 150 150
MAP2K1 -0.21 0.33 -9999 0 -0.65 151 151
EDNRA 0.015 0.15 -9999 0 -0.93 6 6
positive regulation of muscle contraction -0.033 0.21 -9999 0 -0.7 25 25
Gq family/GDP -0.21 0.31 -9999 0 -0.68 129 129
HRAS/GTP -0.22 0.33 -9999 0 -0.68 142 142
PRKCH -0.2 0.3 -9999 0 -0.65 127 127
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.2 0.3 -9999 0 -0.66 128 128
PRKCB -0.22 0.33 -9999 0 -0.7 136 136
PRKCE -0.2 0.3 -9999 0 -0.65 127 127
PRKCD -0.2 0.3 -9999 0 -0.65 127 127
PRKCG -0.22 0.31 -9999 0 -0.66 139 139
regulation of vascular smooth muscle contraction -0.25 0.43 -9999 0 -1 90 90
PRKCQ -0.24 0.34 -9999 0 -0.71 145 145
PLA2G4A -0.17 0.3 -9999 0 -0.61 123 123
GNA14 -0.17 0.32 -9999 0 -0.74 123 123
GNA15 0.008 0.006 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.008 0.006 -9999 0 -10000 0 0
Rac1/GTP 0.036 0.27 -9999 0 -0.66 34 34
MMP1 -0.23 0.24 -9999 0 -0.44 260 260
TCGA08_p53

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
CDKN2A -0.19 0.22 -10000 0 -0.43 233 233
TP53 -0.052 0.058 -10000 0 -0.38 1 1
Senescence -0.051 0.058 -10000 0 -0.38 1 1
Apoptosis -0.051 0.058 -10000 0 -0.38 1 1
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.097 0.11 0.21 233 -0.43 1 234
MDM4 0 0 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.065 0.2 -10000 0 -0.71 46 46
CDKN2C 0.03 0.033 -10000 0 -10000 0 0
CDKN2A -0.28 0.3 -10000 0 -0.6 233 233
CCND2 0.075 0.084 0.27 47 -10000 0 47
RB1 -0.082 0.087 -10000 0 -0.27 48 48
CDK4 0.087 0.09 0.27 47 -10000 0 47
CDK6 0.084 0.092 0.29 47 -10000 0 47
G1/S progression 0.075 0.094 0.27 48 -10000 0 48
Glypican 2 network

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
MDK -0.01 0.076 -9999 0 -0.57 9 9
GPC2 -0.085 0.2 -9999 0 -0.57 74 74
GPC2/Midkine -0.069 0.16 -9999 0 -0.42 82 82
neuron projection morphogenesis -0.068 0.16 -9999 0 -0.42 82 82
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.063 0.22 -9999 0 -0.71 44 44
alphaM/beta2 Integrin/GPIbA -0.064 0.21 -9999 0 -0.7 45 45
alphaM/beta2 Integrin/proMMP-9 -0.079 0.21 -9999 0 -0.66 47 47
PLAUR 0 0 -9999 0 -10000 0 0
HMGB1 0 0.002 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.059 0.2 -9999 0 -0.69 43 43
AGER -0.68 0.21 -9999 0 -0.74 459 459
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG -0.05 0.18 -9999 0 -0.74 34 34
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.47 0.26 -9999 0 -0.52 459 459
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.032 0.13 -9999 0 -0.57 28 28
CYR61 -0.04 0.17 -9999 0 -0.74 27 27
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.2 0.29 -9999 0 -0.63 116 116
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.32 -9999 0 -0.74 131 131
MYH2 -0.31 0.35 -9999 0 -0.7 174 174
MST1R -0.047 0.18 -9999 0 -0.74 32 32
leukocyte activation during inflammatory response -0.088 0.22 -9999 0 -0.58 67 67
APOB -0.047 0.18 -9999 0 -0.72 33 33
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.006 0.066 -9999 0 -0.74 4 4
JAM3 -0.001 0.033 -9999 0 -0.74 1 1
GP1BA -0.007 0.07 -9999 0 -0.7 5 5
alphaM/beta2 Integrin/CTGF -0.077 0.25 -9999 0 -0.74 52 52
alphaM/beta2 Integrin -0.26 0.37 -9999 0 -0.76 120 120
JAM3 homodimer -0.001 0.033 -9999 0 -0.74 1 1
ICAM2 -0.051 0.19 -9999 0 -0.74 35 35
ICAM1 -0.06 0.2 -9999 0 -0.74 41 41
phagocytosis triggered by activation of immune response cell surface activating receptor -0.24 0.36 -9999 0 -0.74 120 120
cell adhesion -0.063 0.21 -9999 0 -0.7 45 45
NFKB1 -0.46 0.31 -9999 0 -0.94 111 111
THY1 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.043 0.14 -9999 0 -0.45 48 48
alphaM/beta2 Integrin/LRP/tPA -0.059 0.19 -9999 0 -0.64 43 43
IL6 -0.48 0.38 -9999 0 -1.1 112 112
ITGB2 -0.031 0.15 -9999 0 -0.74 21 21
elevation of cytosolic calcium ion concentration -0.074 0.2 -9999 0 -0.64 43 43
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.28 -9999 0 -0.64 97 97
JAM2 -0.12 0.27 -9999 0 -0.74 80 80
alphaM/beta2 Integrin/ICAM1 -0.11 0.28 -9999 0 -0.82 49 49
alphaM/beta2 Integrin/uPA/Plg -0.078 0.2 -9999 0 -0.66 43 43
RhoA/GTP -0.29 0.36 -9999 0 -0.86 117 117
positive regulation of phagocytosis -0.18 0.27 -9999 0 -0.75 72 72
Ron/MSP -0.036 0.14 -9999 0 -0.55 33 33
alphaM/beta2 Integrin/uPAR/uPA -0.074 0.2 -9999 0 -0.65 43 43
alphaM/beta2 Integrin/uPAR -0.059 0.2 -9999 0 -0.69 43 43
PLAU -0.037 0.14 -9999 0 -0.57 32 32
PLAT -0.007 0.063 -9999 0 -0.57 6 6
actin filament polymerization -0.29 0.32 -9999 0 -0.65 174 174
MST1 -0.001 0.026 -9999 0 -0.57 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.089 0.22 -9999 0 -0.59 67 67
TNF -0.42 0.28 -9999 0 -0.85 111 111
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.081 0.22 -9999 0 -0.68 46 46
fibrinolysis -0.078 0.2 -9999 0 -0.66 43 43
HCK -0.009 0.08 -9999 0 -0.74 6 6
dendritic cell antigen processing and presentation -0.24 0.36 -9999 0 -0.74 120 120
VTN -0.28 0.36 -9999 0 -0.74 191 191
alphaM/beta2 Integrin/CYR61 -0.084 0.25 -9999 0 -0.74 57 57
LPA -0.021 0.11 -9999 0 -0.57 18 18
LRP1 0 0 -9999 0 -10000 0 0
cell migration -0.075 0.21 -9999 0 -0.66 44 44
FN1 -0.019 0.12 -9999 0 -0.74 13 13
alphaM/beta2 Integrin/Thy1 -0.059 0.2 -9999 0 -0.69 43 43
MPO -0.035 0.16 -9999 0 -0.74 24 24
KNG1 -0.015 0.091 -9999 0 -0.57 13 13
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.25 0.34 -9999 0 -0.78 112 112
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.006 0.057 -9999 0 -0.57 5 5
CTGF -0.029 0.14 -9999 0 -0.74 20 20
alphaM/beta2 Integrin/Hck -0.065 0.22 -9999 0 -0.72 45 45
ITGAM -0.063 0.21 -9999 0 -0.74 42 42
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.19 0.36 -9999 0 -0.66 146 146
HP -0.22 0.34 -9999 0 -0.74 151 151
leukocyte adhesion -0.44 0.31 -9999 0 -0.82 150 150
SELP -0.19 0.32 -9999 0 -0.74 131 131
Thromboxane A2 receptor signaling

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
TGM2 -0.061 0.21 -10000 0 -0.74 45 45
GNB1/GNG2 -0.071 0.09 -10000 0 -0.2 97 97
AKT1 -0.038 0.13 -10000 0 -0.22 59 59
EGF -0.014 0.097 -10000 0 -0.69 10 10
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.039 0.13 -10000 0 -0.6 18 18
mol:Ca2+ -0.078 0.18 -10000 0 -0.31 182 182
LYN -0.016 0.076 -10000 0 -0.52 7 7
RhoA/GTP -0.048 0.059 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.086 0.2 -10000 0 -0.35 174 174
GNG2 -0.007 0.073 -10000 0 -0.74 5 5
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.019 0.099 -10000 0 -0.54 5 5
G beta5/gamma2 -0.094 0.12 -10000 0 -0.28 97 97
PRKCH -0.092 0.21 -10000 0 -0.36 174 174
DNM1 -0.002 0.036 -10000 0 -0.57 2 2
TXA2/TP beta/beta Arrestin3 -0.002 0.013 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.024 0.13 -10000 0 -0.74 16 16
G12 family/GTP -0.12 0.14 -10000 0 -0.31 175 175
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.001 0.033 -10000 0 -0.74 1 1
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.13 0.4 22 -10000 0 22
mol:NADP -0.007 0.073 -10000 0 -0.74 5 5
RAB11A 0 0 -10000 0 -10000 0 0
PRKG1 -0.068 0.21 -10000 0 -0.74 46 46
mol:IP3 -0.1 0.22 -10000 0 -0.39 182 182
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.16 0.3 -10000 0 -0.53 182 182
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.03 0.1 -10000 0 -0.64 7 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.019 0.088 -10000 0 -0.54 10 10
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.016 0.11 -10000 0 -0.74 11 11
PRKCB1 -0.1 0.22 -10000 0 -0.39 178 178
GNAQ -0.001 0.033 -10000 0 -0.74 1 1
mol:L-citrulline -0.007 0.073 -10000 0 -0.74 5 5
TXA2/TXA2-R family -0.15 0.3 -10000 0 -0.55 177 177
LCK -0.016 0.075 -10000 0 -0.52 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.018 0.089 -10000 0 -0.61 7 7
TXA2-R family/G12 family/GDP/G beta/gamma 0.019 0.042 -10000 0 -0.5 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.018 0.088 -10000 0 -0.61 7 7
MAPK14 -0.046 0.14 -10000 0 -0.24 84 84
TGM2/GTP -0.13 0.26 -10000 0 -0.46 186 186
MAPK11 -0.046 0.14 -10000 0 -0.24 72 72
ARHGEF1 -0.037 0.11 -10000 0 -0.2 42 42
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade -0.1 0.23 -10000 0 -0.4 177 177
RAB11/GDP 0 0 -10000 0 -10000 0 0
ICAM1 -0.078 0.19 -10000 0 -0.32 173 173
cAMP biosynthetic process -0.099 0.21 -10000 0 -0.36 186 186
Gq family/GTP/EBP50 -0.037 0.11 -10000 0 -0.23 123 123
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.015 0.071 -10000 0 -0.52 6 6
GNB5 0 0 -10000 0 -10000 0 0
GNB1 -0.001 0.033 -10000 0 -0.74 1 1
EGF/EGFR 0.023 0.097 -10000 0 -0.39 14 14
VCAM1 -0.072 0.17 -10000 0 -0.3 174 174
TP beta/Gq family/GDP/G beta5/gamma2 -0.019 0.099 -10000 0 -0.54 5 5
platelet activation -0.064 0.19 -10000 0 -0.31 175 175
PGI2/IP -0.012 0.083 -10000 0 -0.56 11 11
PRKACA -0.02 0.1 -10000 0 -0.44 23 23
Gq family/GDP/G beta5/gamma2 -0.021 0.1 -10000 0 -0.52 6 6
TXA2/TP beta/beta Arrestin2 -0.002 0.011 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.006 0.11 -10000 0 -0.43 25 25
mol:DAG -0.12 0.25 -10000 0 -0.44 178 178
EGFR -0.023 0.12 -10000 0 -0.63 18 18
TXA2/TP alpha -0.14 0.29 -10000 0 -0.5 186 186
Gq family/GTP -0.068 0.12 -10000 0 -0.28 123 123
YES1 -0.015 0.071 -10000 0 -0.52 6 6
GNAI2/GTP -0.017 0.084 -10000 0 -0.62 6 6
PGD2/DP -0.018 0.099 -10000 0 -0.56 16 16
SLC9A3R1 -0.005 0.051 -10000 0 -0.57 4 4
FYN -0.016 0.076 -10000 0 -0.56 6 6
mol:NO -0.007 0.073 -10000 0 -0.74 5 5
GNA15 0 0 -10000 0 -10000 0 0
PGK/cGMP -0.049 0.15 -10000 0 -0.51 48 48
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.054 0.16 -10000 0 -0.73 19 19
NOS3 -0.007 0.073 -10000 0 -0.74 5 5
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.093 0.21 -10000 0 -0.36 175 175
PRKCB -0.1 0.22 -10000 0 -0.39 177 177
PRKCE -0.092 0.21 -10000 0 -0.36 173 173
PRKCD -0.1 0.22 -10000 0 -0.39 173 173
PRKCG -0.11 0.23 -10000 0 -0.41 177 177
muscle contraction -0.14 0.28 -10000 0 -0.5 177 177
PRKCZ -0.085 0.2 -10000 0 -0.35 175 175
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta -0.02 0.095 -10000 0 -0.63 8 8
PRKCQ -0.11 0.23 -10000 0 -0.4 181 181
MAPKKK cascade -0.13 0.27 -10000 0 -0.48 178 178
SELE -0.11 0.23 -10000 0 -0.42 174 174
TP beta/GNAI2/GDP/G beta/gamma -0.022 0.099 -10000 0 -0.69 7 7
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.74 123 123
chemotaxis -0.18 0.34 -10000 0 -0.62 175 175
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 0 0 -10000 0 -10000 0 0
Rac1/GTP 0 0 -10000 0 -10000 0 0
Visual signal transduction: Cones

Figure 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
Cone Metarhodopsin II/Cone Transducin -0.019 0.082 -9999 0 -0.41 17 17
RGS9BP -0.013 0.098 -9999 0 -0.74 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.002 0.036 -9999 0 -0.57 2 2
mol:Na + -0.18 0.18 -9999 0 -0.36 253 253
mol:ADP -0.012 0.099 -9999 0 -0.42 28 28
GNAT2 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.059 0.16 -9999 0 -0.49 60 60
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 -0.03 0.13 -9999 0 -0.57 26 26
CNGB3 -0.29 0.29 -9999 0 -0.57 251 251
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.21 0.21 -9999 0 -0.36 304 304
Cone PDE6 -0.051 0.14 -9999 0 -0.42 60 60
Cone Metarhodopsin II -0.018 0.075 -9999 0 -0.33 28 28
Na + (4 Units) -0.22 0.2 -9999 0 -0.36 304 304
GNAT2/GDP -0.05 0.14 -9999 0 -0.42 60 60
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.009 0.005 -9999 0 -10000 0 0
Cone Transducin -0.02 0.087 -9999 0 -0.43 17 17
SLC24A2 -0.11 0.23 -9999 0 -0.57 97 97
GNB3/GNGT2 -0.025 0.11 -9999 0 -0.5 25 25
GNB3 -0.01 0.076 -9999 0 -0.57 9 9
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 -0.002 0.036 -9999 0 -0.57 2 2
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.18 0.18 -9999 0 -0.36 253 253
mol:Pi -0.058 0.16 -9999 0 -0.49 60 60
Cone CNG Channel -0.14 0.14 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.11 0.23 -9999 0 -0.57 97 97
RGS9 -0.078 0.23 -9999 0 -0.74 53 53
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.024 0.13 -9999 0 -0.74 16 16
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0 0 -9999 0 -10000 0 0
LAT2 -0.16 0.25 -9999 0 -0.66 76 76
AP1 -0.2 0.27 -9999 0 -0.64 113 113
mol:PIP3 -0.16 0.29 -9999 0 -0.65 91 91
IKBKB -0.072 0.16 -9999 0 -0.34 82 82
AKT1 -0.18 0.24 -9999 0 -0.67 72 72
IKBKG -0.072 0.16 -9999 0 -0.33 83 83
MS4A2 -0.17 0.32 -9999 0 -0.74 118 118
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.006 0.005 -9999 0 -10000 0 0
MAP3K1 -0.1 0.23 -9999 0 -0.53 85 85
mol:Ca2+ -0.11 0.21 -9999 0 -0.46 91 91
LYN 0.005 0.049 -9999 0 -0.76 2 2
CBLB -0.16 0.24 -9999 0 -0.64 76 76
SHC1 0.001 0.004 -9999 0 -10000 0 0
RasGAP/p62DOK -0.052 0.14 -9999 0 -0.44 59 59
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.001 0.033 -9999 0 -0.74 1 1
PLD2 -0.21 0.28 -9999 0 -0.75 76 76
PTPN13 -0.13 0.24 -9999 0 -0.6 76 76
PTPN11 0.005 0.011 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.083 0.19 -9999 0 -0.41 78 78
SYK 0.006 0.035 -9999 0 -0.77 1 1
GRB2 0 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.2 0.27 -9999 0 -0.69 91 91
LAT -0.16 0.24 -9999 0 -0.64 76 76
PAK2 -0.13 0.26 -9999 0 -0.6 90 90
NFATC2 -0.18 0.32 -9999 0 -0.92 71 71
HRAS -0.15 0.29 -9999 0 -0.68 90 90
GAB2 -0.021 0.12 -9999 0 -0.74 14 14
PLA2G1B -0.002 0.037 -9999 0 -10000 0 0
Fc epsilon R1 -0.26 0.34 -9999 0 -0.63 205 205
Antigen/IgE/Fc epsilon R1 -0.24 0.32 -9999 0 -0.58 205 205
mol:GDP -0.16 0.32 -9999 0 -0.74 91 91
JUN 0 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.006 0.005 -9999 0 -10000 0 0
FOS -0.09 0.24 -9999 0 -0.74 61 61
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.17 0.26 -9999 0 -0.54 125 125
CHUK -0.072 0.16 -9999 0 -0.34 79 79
KLRG1 -0.16 0.24 -9999 0 -0.63 77 77
VAV1 -0.16 0.25 -9999 0 -0.66 77 77
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.16 0.24 -9999 0 -0.64 76 76
negative regulation of mast cell degranulation -0.14 0.22 -9999 0 -0.58 76 76
BTK -0.21 0.33 -9999 0 -0.8 95 95
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.2 0.31 -9999 0 -0.56 157 157
GAB2/PI3K/SHP2 -0.2 0.27 -9999 0 -0.75 72 72
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.17 0.25 -9999 0 -0.72 69 69
RAF1 0.025 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.23 0.32 -9999 0 -0.84 74 74
FCER1G -0.015 0.13 -9999 0 -0.75 14 14
FCER1A -0.22 0.35 -9999 0 -0.75 148 148
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.3 -9999 0 -0.55 205 205
MAPK3 0.033 0.023 -9999 0 -10000 0 0
MAPK1 0.033 0.023 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.022 0.071 -9999 0 -10000 0 0
DUSP1 -0.087 0.24 -9999 0 -0.74 59 59
NF-kappa-B/RelA -0.06 0.076 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.14 0.25 -9999 0 -0.62 76 76
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.16 0.24 -9999 0 -0.62 85 85
FER -0.16 0.24 -9999 0 -0.64 76 76
RELA 0 0 -9999 0 -10000 0 0
ITK -0.078 0.18 -9999 0 -0.66 38 38
SOS1 0.001 0.004 -9999 0 -10000 0 0
PLCG1 -0.16 0.32 -9999 0 -0.73 92 92
cytokine secretion -0.044 0.055 -9999 0 -10000 0 0
SPHK1 -0.16 0.24 -9999 0 -0.64 76 76
PTK2 -0.14 0.26 -9999 0 -0.66 76 76
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.21 0.29 -9999 0 -0.72 91 91
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.15 0.28 -9999 0 -0.63 91 91
MAP2K2 0.03 0.024 -9999 0 -10000 0 0
MAP2K1 0.03 0.024 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.15 0.22 -9999 0 -0.58 76 76
MAP2K4 0.009 0.013 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.24 0.33 -9999 0 -0.59 206 206
mol:Choline -0.2 0.28 -9999 0 -0.74 76 76
SHC/Grb2/SOS1 -0.15 0.22 -9999 0 -0.6 75 75
FYN -0.001 0.033 -9999 0 -0.74 1 1
DOK1 0 0 -9999 0 -10000 0 0
PXN -0.13 0.24 -9999 0 -0.6 75 75
HCLS1 -0.16 0.24 -9999 0 -0.64 76 76
PRKCB -0.12 0.22 -9999 0 -0.48 91 91
FCGR2B -0.013 0.098 -9999 0 -0.74 9 9
IGHE -0.005 0.009 -9999 0 -10000 0 0
KLRG1/SHIP -0.15 0.22 -9999 0 -0.6 76 76
LCP2 -0.009 0.081 -9999 0 -0.74 6 6
PLA2G4A -0.16 0.24 -9999 0 -0.64 78 78
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.2 0.28 -9999 0 -0.74 76 76
IKK complex -0.04 0.12 -9999 0 -0.28 25 25
WIPF1 0 0 -9999 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.23 0.14 -9999 0 -0.68 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.064 0.041 -9999 0 -10000 0 0
AURKB -0.41 0.26 -9999 0 -0.57 359 359
AURKC -0.003 0.042 -9999 0 -0.66 2 2
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.4 0.54 -10000 0 -1.2 106 106
STAT6 (cleaved dimer) -0.46 0.48 -10000 0 -1.2 128 128
IGHG1 -0.12 0.19 -10000 0 -0.4 4 4
IGHG3 -0.39 0.52 -10000 0 -1.1 122 122
AKT1 -0.14 0.26 -10000 0 -0.94 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.1 0.22 -10000 0 -1.1 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.16 0.27 -10000 0 -1 7 7
THY1 -0.4 0.54 -10000 0 -1.2 109 109
MYB -0.02 0.11 -10000 0 -0.59 17 17
HMGA1 -0.005 0.051 -10000 0 -0.57 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.2 0.31 -10000 0 -0.68 51 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.27 -10000 0 -1.1 7 7
SP1 0.017 0.002 -10000 0 -10000 0 0
INPP5D -0.001 0.033 -10000 0 -0.74 1 1
SOCS5 0.019 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.45 0.48 -10000 0 -1.2 115 115
SOCS1 -0.23 0.36 -10000 0 -0.77 74 74
SOCS3 -0.16 0.27 -10000 0 -1.1 6 6
FCER2 -0.34 0.5 -10000 0 -1.1 91 91
PARP14 0.008 0.005 -10000 0 -10000 0 0
CCL17 -0.47 0.62 -10000 0 -1.3 131 131
GRB2 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.12 0.22 -10000 0 -0.89 6 6
T cell proliferation -0.39 0.55 -10000 0 -1.2 109 109
IL4R/JAK1 -0.4 0.54 -10000 0 -1.2 109 109
EGR2 -0.42 0.57 -10000 0 -1.2 116 116
JAK2 -0.004 0.034 -10000 0 -10000 0 0
JAK3 0.013 0.007 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
JAK1 0.009 0.014 -10000 0 -10000 0 0
COL1A2 -0.1 0.18 -10000 0 -0.66 2 2
CCL26 -0.43 0.56 -10000 0 -1.2 121 121
IL4R -0.42 0.58 -10000 0 -1.3 110 110
PTPN6 0.019 0.014 -10000 0 -10000 0 0
IL13RA2 -0.43 0.57 -10000 0 -1.3 122 122
IL13RA1 -0.004 0.034 -10000 0 -10000 0 0
IRF4 -0.17 0.36 -10000 0 -0.88 83 83
ARG1 -0.12 0.24 -10000 0 -0.78 36 36
CBL -0.18 0.29 -10000 0 -0.76 20 20
GTF3A 0.013 0.013 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.003 0.051 -10000 0 -10000 0 0
IRF4/BCL6 -0.18 0.31 -10000 0 -0.83 80 80
CD40LG -0.11 0.28 -10000 0 -0.74 86 86
MAPK14 -0.18 0.29 -10000 0 -0.8 17 17
mitosis -0.14 0.25 -10000 0 -0.86 7 7
STAT6 -0.47 0.64 -10000 0 -1.4 111 111
SPI1 -0.045 0.2 -10000 0 -0.74 37 37
RPS6KB1 -0.13 0.24 -10000 0 -0.87 6 6
STAT6 (dimer) -0.47 0.64 -10000 0 -1.4 111 111
STAT6 (dimer)/PARP14 -0.43 0.58 -10000 0 -1.3 111 111
mast cell activation 0.008 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.29 -10000 0 -0.82 31 31
FRAP1 -0.14 0.26 -10000 0 -0.94 7 7
LTA -0.4 0.54 -10000 0 -1.2 109 109
FES -0.001 0.033 -10000 0 -0.74 1 1
T-helper 1 cell differentiation 0.45 0.62 1.4 111 -10000 0 111
CCL11 -0.4 0.53 -10000 0 -1.2 111 111
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.26 -10000 0 -1.1 7 7
IL2RG 0.002 0.087 -10000 0 -0.73 7 7
IL10 -0.4 0.55 -10000 0 -1.2 109 109
IRS1 0 0 -10000 0 -10000 0 0
IRS2 -0.004 0.057 -10000 0 -0.74 3 3
IL4 -0.079 0.14 -10000 0 -10000 0 0
IL5 -0.4 0.54 -10000 0 -1.2 109 109
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.31 0.42 -10000 0 -0.9 110 110
COL1A1 -0.14 0.23 -10000 0 -0.66 27 27
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.41 0.55 -10000 0 -1.3 106 106
IL2R gamma/JAK3 -0.001 0.066 -10000 0 -0.55 7 7
TFF3 -0.45 0.62 -10000 0 -1.4 118 118
ALOX15 -0.63 0.77 -10000 0 -1.5 188 188
MYBL1 -0.001 0.026 -10000 0 -0.57 1 1
T-helper 2 cell differentiation -0.32 0.43 -10000 0 -0.92 112 112
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.009 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.15 0.26 -10000 0 -1.1 7 7
mol:PI-3-4-5-P3 -0.14 0.26 -10000 0 -0.94 7 7
PI3K -0.15 0.27 -10000 0 -1.1 6 6
DOK2 -0.068 0.21 -10000 0 -0.74 46 46
ETS1 0.001 0.11 -10000 0 -0.7 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.11 0.21 -10000 0 -0.86 6 6
ITGB3 -0.41 0.56 -10000 0 -1.3 108 108
PIGR -0.81 0.83 -10000 0 -1.6 264 264
IGHE 0.029 0.044 -10000 0 -10000 0 0
MAPKKK cascade -0.11 0.21 -10000 0 -0.84 6 6
BCL6 0.001 0.004 -10000 0 -10000 0 0
OPRM1 -0.4 0.54 -10000 0 -1.2 106 106
RETNLB -0.4 0.54 -10000 0 -1.2 108 108
SELP -0.58 0.75 -10000 0 -1.6 161 161
AICDA -0.39 0.52 -10000 0 -1.2 106 106
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.059 0.098 -10000 0 -10000 0 0
SMARCC2 0.012 0 -10000 0 -10000 0 0
SMARCC1 0.012 0 -10000 0 -10000 0 0
TBX21 -0.2 0.35 -10000 0 -0.88 81 81
SUMO2 0.002 0.006 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0 -10000 0 -10000 0 0
FKBP4 -0.001 0.026 -10000 0 -0.57 1 1
FKBP5 0 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.13 0.1 0.34 42 -10000 0 42
PRL -0.083 0.12 -10000 0 -0.63 1 1
cortisol/GR alpha (dimer)/TIF2 0.31 0.25 0.58 166 -10000 0 166
RELA -0.046 0.1 -10000 0 -0.33 2 2
FGG -0.13 0.47 0.54 55 -0.62 234 289
GR beta/TIF2 0.14 0.12 0.35 59 -0.38 1 60
IFNG -0.34 0.24 -10000 0 -0.68 100 100
apoptosis 0.026 0.12 0.46 2 -0.57 2 4
CREB1 0.001 0.028 -10000 0 -10000 0 0
histone acetylation -0.011 0.15 0.39 1 -0.41 17 18
BGLAP -0.094 0.14 -10000 0 -0.55 8 8
GR/PKAc 0.12 0.099 0.33 32 -10000 0 32
NF kappa B1 p50/RelA -0.084 0.18 -10000 0 -0.48 38 38
SMARCD1 0.012 0 -10000 0 -10000 0 0
MDM2 0.11 0.097 0.29 57 -0.31 1 58
GATA3 -0.013 0.13 -10000 0 -0.71 17 17
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.16 0.41 -10000 0 -1.3 51 51
GSK3B 0.002 0.006 -10000 0 -10000 0 0
NR1I3 0.045 0.11 0.47 1 -10000 0 1
CSN2 0.16 0.16 0.44 43 -10000 0 43
BRG1/BAF155/BAF170/BAF60A 0 0 -10000 0 -10000 0 0
NFATC1 0.001 0.034 -10000 0 -0.74 1 1
POU2F1 0.005 0.014 -10000 0 -10000 0 0
CDKN1A 0.025 0.024 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
SFN -0.057 0.17 -10000 0 -0.58 49 49
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.093 0.14 0.33 32 -10000 0 32
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.031 0.16 0.46 1 -0.9 11 12
JUN -0.29 0.16 -10000 0 -0.5 121 121
IL4 -0.11 0.15 -10000 0 -0.52 15 15
CDK5R1 -0.01 0.081 -10000 0 -0.58 10 10
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.45 0.24 -10000 0 -0.61 267 267
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.099 0.34 27 -10000 0 27
cortisol/GR alpha (monomer) 0.36 0.32 0.71 170 -10000 0 170
NCOA2 -0.001 0.033 -10000 0 -0.74 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.25 -10000 0 -0.82 61 61
AP-1/NFAT1-c-4 -0.53 0.25 -10000 0 -0.68 290 290
AFP -0.19 0.15 -10000 0 -0.69 12 12
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.18 0.15 0.49 38 -10000 0 38
TP53 0.028 0.034 -10000 0 -0.72 1 1
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.54 0.25 -10000 0 -0.68 316 316
KRT14 -0.37 0.23 -10000 0 -0.64 105 105
TBP 0.018 0 -10000 0 -10000 0 0
CREBBP 0.11 0.067 0.34 1 -10000 0 1
HDAC1 0 0.004 -10000 0 -10000 0 0
HDAC2 0.01 0.03 -10000 0 -10000 0 0
AP-1 -0.54 0.25 -10000 0 -0.68 294 294
MAPK14 0.002 0.005 -10000 0 -10000 0 0
MAPK10 -0.01 0.093 -10000 0 -0.74 8 8
MAPK11 0.002 0.006 -10000 0 -10000 0 0
KRT5 -0.56 0.26 -10000 0 -0.69 330 330
interleukin-1 receptor activity 0.007 0.028 -10000 0 -10000 0 0
NCOA1 0.013 0.001 -10000 0 -10000 0 0
STAT1 0.017 0 -10000 0 -10000 0 0
CGA -0.12 0.17 -10000 0 -0.53 33 33
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.19 0.49 101 -10000 0 101
MAPK3 0.002 0.006 -10000 0 -10000 0 0
MAPK1 0.002 0.005 -10000 0 -10000 0 0
ICAM1 -0.26 0.43 -10000 0 -1.1 77 77
NFKB1 -0.046 0.1 -10000 0 -0.33 2 2
MAPK8 -0.24 0.17 -10000 0 -0.47 111 111
MAPK9 0.002 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.023 0.12 0.46 2 -0.6 2 4
BAX 0.025 0.024 -10000 0 -10000 0 0
POMC -0.21 0.26 -10000 0 -0.86 29 29
EP300 0.11 0.068 0.34 1 -10000 0 1
cortisol/GR alpha (dimer)/p53 0.32 0.25 0.6 161 -10000 0 161
proteasomal ubiquitin-dependent protein catabolic process 0.075 0.074 0.27 10 -0.27 1 11
SGK1 0.17 0.077 -10000 0 -10000 0 0
IL13 -0.27 0.2 -10000 0 -0.74 46 46
IL6 -0.34 0.52 -10000 0 -1.2 114 114
PRKACG -0.001 0.026 -10000 0 -0.57 1 1
IL5 -0.24 0.17 -10000 0 -0.76 24 24
IL2 -0.34 0.2 -10000 0 -0.66 92 92
CDK5 0.001 0.004 -10000 0 -10000 0 0
PRKACB 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.2 0.28 -10000 0 -0.71 72 72
CDK5R1/CDK5 -0.006 0.059 -10000 0 -0.42 10 10
NF kappa B1 p50/RelA/PKAc -0.058 0.13 -10000 0 -0.48 6 6
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.57 153 -10000 0 153
SMARCA4 0.012 0 -10000 0 -10000 0 0
chromatin remodeling 0.19 0.14 0.41 94 -10000 0 94
NF kappa B1 p50/RelA/Cbp 0.035 0.18 0.38 14 -0.54 3 17
JUN (dimer) -0.29 0.16 -10000 0 -0.5 120 120
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.41 0.51 -10000 0 -1 185 185
NR3C1 0.2 0.2 0.5 101 -10000 0 101
NR4A1 -0.096 0.26 -10000 0 -0.73 67 67
TIF2/SUV420H1 -0.001 0.025 -10000 0 -0.56 1 1
MAPKKK cascade 0.026 0.12 0.46 2 -0.57 2 4
cortisol/GR alpha (dimer)/Src-1 0.32 0.25 0.6 157 -10000 0 157
PBX1 0.002 0.049 -10000 0 -0.74 2 2
POU1F1 -0.002 0.046 -10000 0 -0.57 3 3
SELE -0.47 0.61 -10000 0 -1.3 166 166
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.19 0.14 0.41 92 -10000 0 92
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.57 153 -10000 0 153
mol:cortisol 0.19 0.2 0.41 176 -0.23 4 180
MMP1 -0.33 0.19 -10000 0 -0.5 168 168
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.044 0.055 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.099 0.14 -9999 0 -0.43 19 19
JUN -0.063 0.14 -9999 0 -0.42 16 16
HRAS 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.22 -9999 0 -0.48 129 129
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.22 -9999 0 -0.48 129 129
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.16 0.22 -9999 0 -0.48 125 125
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.2 -9999 0 -0.43 129 129
GRB7 -0.005 0.051 -9999 0 -0.57 4 4
RET51/GFRalpha1/GDNF -0.17 0.22 -9999 0 -0.48 129 129
MAPKKK cascade -0.13 0.17 -9999 0 -0.59 18 18
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.16 0.22 -9999 0 -0.48 125 125
lamellipodium assembly -0.095 0.13 -9999 0 -0.4 19 19
RET51/GFRalpha1/GDNF/SHC -0.17 0.22 -9999 0 -0.48 129 129
PIK3CA 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.16 0.22 -9999 0 -0.48 125 125
RET9/GFRalpha1/GDNF/Shank3 -0.16 0.22 -9999 0 -0.42 191 191
MAPK3 -0.14 0.18 -9999 0 -0.62 20 20
DOK1 0 0 -9999 0 -10000 0 0
DOK6 -0.063 0.21 -9999 0 -0.74 43 43
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.14 0.18 -9999 0 -0.54 40 40
DOK5 -0.005 0.059 -9999 0 -0.66 4 4
GFRA1 -0.18 0.32 -9999 0 -0.74 125 125
MAPK8 -0.074 0.15 -9999 0 -0.44 16 16
HRAS/GTP -0.14 0.19 -9999 0 -0.44 129 129
tube development -0.15 0.2 -9999 0 -0.45 125 125
MAPK1 -0.14 0.18 -9999 0 -0.62 20 20
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.14 -9999 0 -0.33 125 125
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.19 0.25 -9999 0 -0.51 149 149
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.22 -9999 0 -0.48 129 129
RET51/GFRalpha1/GDNF/Dok5 -0.17 0.22 -9999 0 -0.49 129 129
PRKCA -0.003 0.046 -9999 0 -0.74 2 2
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.11 0.15 -9999 0 -0.36 125 125
PIK3R1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.14 -9999 0 -0.33 125 125
RET51/GFRalpha1/GDNF/Grb7 -0.17 0.22 -9999 0 -0.48 130 130
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.02 0.1 -9999 0 -0.57 17 17
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.062 0.14 -9999 0 -0.41 16 16
RET9/GFRalpha1/GDNF/FRS2 -0.16 0.22 -9999 0 -0.42 191 191
SHANK3 -0.003 0.046 -9999 0 -0.74 2 2
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.33 125 125
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.14 -9999 0 -0.47 16 16
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.1 0.14 -9999 0 -0.47 16 16
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.48 16 16
PI3K -0.14 0.2 -9999 0 -0.65 19 19
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.15 0.2 -9999 0 -0.45 125 125
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.1 0.14 -9999 0 -0.48 16 16
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.22 -9999 0 -0.48 129 129
GAB1 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
IRS2 -0.004 0.057 -9999 0 -0.74 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.14 -9999 0 -0.48 16 16
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.22 -9999 0 -0.48 130 130
GRB2 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.093 0.21 -9999 0 -0.57 81 81
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.22 -9999 0 -0.48 129 129
Rac1/GTP -0.11 0.16 -9999 0 -0.49 19 19
RET9/GFRalpha1/GDNF -0.18 0.24 -9999 0 -0.46 191 191
GFRalpha1/GDNF -0.2 0.27 -9999 0 -0.54 191 191
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.072 0.075 0.14 261 -10000 0 261
BUB1B -0.13 0.1 -10000 0 -0.22 206 206
PLK1 -0.014 0.037 -10000 0 -0.12 15 15
PLK1S1 -0.003 0.02 -10000 0 -10000 0 0
KIF2A -0.005 0.034 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.014 0.037 -10000 0 -0.12 15 15
GOLGA2 0 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.2 0.23 -10000 0 -0.41 240 240
WEE1 -0.007 0.039 -10000 0 -10000 0 0
cytokinesis -0.11 0.13 -10000 0 -0.29 54 54
PP2A-alpha B56 -0.008 0.023 -10000 0 -10000 0 0
AURKA -0.007 0.03 -10000 0 -0.12 10 10
PICH/PLK1 -0.12 0.17 -10000 0 -0.46 59 59
CENPE -0.039 0.11 -10000 0 -0.36 52 52
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.005 0.033 -10000 0 -10000 0 0
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0 0 -10000 0 -10000 0 0
TPX2 -0.061 0.049 -10000 0 -0.12 59 59
PAK1 0.003 0.026 -10000 0 -0.57 1 1
SPC24 -0.16 0.26 -10000 0 -0.57 138 138
FBXW11 0 0 -10000 0 -10000 0 0
CLSPN -0.012 0.038 -10000 0 -0.14 11 11
GORASP1 0 0 -10000 0 -10000 0 0
metaphase -0.001 0.003 -10000 0 -0.012 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.007 0.02 -10000 0 -0.064 10 10
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -10000 0 0
STAG2 0 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.011 -10000 0 -10000 0 0
spindle elongation -0.014 0.037 -10000 0 -0.12 15 15
ODF2 0.004 0.005 -10000 0 -10000 0 0
BUB1 -0.006 0.033 -10000 0 -10000 0 0
TPT1 -0.003 0.02 -10000 0 -10000 0 0
CDC25C -0.078 0.058 -10000 0 -0.15 32 32
CDC25B 0.009 0.003 -10000 0 -10000 0 0
SGOL1 -0.072 0.075 -10000 0 -0.14 261 261
RHOA 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.031 0.082 -10000 0 -0.3 5 5
CDC14B 0.01 0.002 -10000 0 -10000 0 0
CDC20 -0.38 0.27 -10000 0 -0.57 331 331
PLK1/PBIP1 -0.028 0.059 -10000 0 -0.33 15 15
mitosis -0.001 0.005 0.022 14 -10000 0 14
FBXO5 -0.004 0.032 -10000 0 -10000 0 0
CDC2 -0.001 0.004 -10000 0 -0.012 15 15
NDC80 -0.2 0.27 -10000 0 -0.57 175 175
metaphase plate congression -0.007 0.026 -10000 0 -10000 0 0
ERCC6L -0.12 0.17 -10000 0 -0.44 59 59
NLP/gamma Tubulin -0.005 0.022 -10000 0 -10000 0 0
microtubule cytoskeleton organization -0.003 0.02 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.003 0.005 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.2 0.2 -10000 0 -0.37 267 267
GRASP65/GM130/RAB1/GTP/PLK1 -0.009 0.016 -10000 0 -10000 0 0
RAB1A 0 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.001 0.029 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.045 0.035 -10000 0 -10000 0 0
microtubule-based process -0.18 0.17 -10000 0 -0.34 259 259
Golgi organization -0.014 0.037 -10000 0 -0.12 15 15
Cohesin/SA2 -0.019 0.025 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.3 0.29 -10000 0 -0.57 259 259
APC/C/CDC20 -0.23 0.16 -10000 0 -0.34 331 331
PPP2R1A 0 0 -10000 0 -10000 0 0
chromosome segregation -0.028 0.058 -10000 0 -0.32 15 15
PRC1 -0.055 0.17 -10000 0 -0.57 48 48
ECT2 -0.016 0.073 -10000 0 -0.35 18 18
C13orf34 -0.003 0.029 -10000 0 -10000 0 0
NUDC -0.007 0.026 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.13 0.099 -10000 0 -0.22 206 206
spindle assembly -0.009 0.03 -10000 0 -10000 0 0
spindle stabilization -0.003 0.02 -10000 0 -10000 0 0
APC/C/HCDH1 0 0 -10000 0 -10000 0 0
MKLP2/PLK1 -0.18 0.17 -10000 0 -0.35 259 259
CCNB1 -0.063 0.19 -10000 0 -0.57 63 63
PPP1CB 0.003 0.005 -10000 0 -10000 0 0
BTRC 0 0 -10000 0 -10000 0 0
ROCK2 0.001 0.025 -10000 0 -10000 0 0
TUBG1 -0.003 0.02 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.033 0.079 -10000 0 -0.29 5 5
MLF1IP -0.007 0.075 -10000 0 -0.43 15 15
INCENP 0.005 0.006 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.18 0.21 -9999 0 -0.56 76 76
SMAD6-7/SMURF1 -0.047 0.14 -9999 0 -0.48 49 49
NOG -0.031 0.15 -9999 0 -0.73 21 21
SMAD9 -0.1 0.21 -9999 0 -0.59 73 73
SMAD4 0 0 -9999 0 -10000 0 0
SMAD5 -0.022 0.13 -9999 0 -0.47 22 22
BMP7/USAG1 -0.24 0.27 -9999 0 -0.5 242 242
SMAD5/SKI -0.049 0.11 -9999 0 -0.46 18 18
SMAD1 0.033 0.029 -9999 0 -10000 0 0
BMP2 -0.093 0.24 -9999 0 -0.74 63 63
SMAD1/SMAD1/SMAD4 -0.031 0.091 -9999 0 -10000 0 0
BMPR1A 0 0 -9999 0 -10000 0 0
BMPR1B -0.056 0.2 -9999 0 -0.74 38 38
BMPR1A-1B/BAMBI -0.04 0.13 -9999 0 -0.48 41 41
AHSG -0.02 0.1 -9999 0 -0.57 17 17
CER1 -0.002 0.036 -9999 0 -0.57 2 2
BMP2-4/CER1 -0.073 0.18 -9999 0 -0.49 74 74
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.066 0.13 -9999 0 -0.49 29 29
BMP2-4 (homodimer) -0.082 0.2 -9999 0 -0.57 72 72
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.043 0.13 -9999 0 -0.45 48 48
RGMA -0.065 0.18 -9999 0 -0.58 56 56
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.062 0.12 -9999 0 -0.44 29 29
BMP2-4/USAG1 -0.16 0.26 -9999 0 -0.54 147 147
SMAD6/SMURF1/SMAD5 -0.049 0.11 -9999 0 -0.46 18 18
SOSTDC1 -0.14 0.29 -9999 0 -0.74 95 95
BMP7/BMPR2/BMPR1A-1B -0.14 0.19 -9999 0 -0.52 44 44
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.018 0.11 -9999 0 -0.74 12 12
HFE2 -0.002 0.036 -9999 0 -0.57 2 2
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.073 0.18 -9999 0 -0.5 72 72
SMAD5/SMAD5/SMAD4 -0.049 0.11 -9999 0 -0.47 17 17
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.05 0.1 -9999 0 -0.45 16 16
BMP7 (homodimer) -0.2 0.28 -9999 0 -0.58 170 170
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.027 0.11 -9999 0 -0.48 29 29
SMAD1/SKI 0.037 0.028 -9999 0 -10000 0 0
SMAD6 -0.072 0.22 -9999 0 -0.74 49 49
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.083 0.19 -9999 0 -0.48 87 87
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.35 0.28 -9999 0 -0.57 303 303
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.042 0.15 -9999 0 -0.56 38 38
CHRDL1 -0.39 0.37 -9999 0 -0.74 263 263
ENDOFIN/SMAD1 0.037 0.028 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.036 0.1 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.007 0.067 -9999 0 -0.67 5 5
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.3 -9999 0 -0.55 288 288
BMP2-4/GREM1 -0.28 0.22 -9999 0 -0.4 347 347
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.094 0.2 -9999 0 -0.55 73 73
SMAD1/SMAD6 0.037 0.028 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.2 0.28 -9999 0 -0.58 170 170
BMP6 -0.018 0.11 -9999 0 -0.74 12 12
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.057 0.11 -9999 0 -0.4 29 29
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.037 0.028 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL -0.001 0.033 -9999 0 -0.74 1 1
PPP1CA 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.084 0.14 -9999 0 -0.46 43 43
CHRD -0.004 0.053 -9999 0 -0.68 3 3
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.071 0.14 -9999 0 -0.49 29 29
BMP4 -0.017 0.11 -9999 0 -0.72 12 12
FST -0.097 0.22 -9999 0 -0.58 84 84
BMP2-4/NOG -0.09 0.21 -9999 0 -0.53 85 85
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.13 0.17 -9999 0 -0.49 44 44
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 -0.015 0.089 -9999 0 -0.51 15 15
ARNO/beta Arrestin1-2 -0.17 0.24 -9999 0 -0.45 191 191
EGFR -0.023 0.12 -9999 0 -0.63 18 18
EPHA2 -0.004 0.057 -9999 0 -0.74 3 3
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.027 0.12 -9999 0 -0.5 27 27
ARRB2 0.008 0.011 -9999 0 -0.22 1 1
mol:GTP 0.015 0.024 -9999 0 -0.15 2 2
ARRB1 -0.14 0.29 -9999 0 -0.74 98 98
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.017 0.098 -9999 0 -0.57 15 15
EGF -0.014 0.097 -9999 0 -0.69 10 10
somatostatin receptor activity 0 0 -9999 0 -0.001 153 153
ARAP2 -0.001 0.033 -9999 0 -0.74 1 1
mol:GDP -0.12 0.15 -9999 0 -0.33 141 141
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 105 105
ITGA2B -0.022 0.13 -9999 0 -0.74 15 15
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.033 -9999 0 -0.43 3 3
ADAP1 -0.012 0.092 -9999 0 -0.74 8 8
KIF13B -0.012 0.092 -9999 0 -0.74 8 8
HGF/MET -0.12 0.23 -9999 0 -0.56 111 111
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.15 -9999 0 -0.31 153 153
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.023 0.099 -9999 0 -0.42 27 27
ADRB2 -0.21 0.33 -9999 0 -0.74 143 143
receptor agonist activity 0 0 -9999 0 0 155 155
actin filament binding 0 0 -9999 0 -0.001 153 153
SRC 0 0 -9999 0 -10000 0 0
ITGB3 -0.016 0.11 -9999 0 -0.74 11 11
GNAQ 0 0.033 -9999 0 -0.74 1 1
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 128 128
ARF6/GDP -0.013 0.07 -9999 0 -0.35 3 3
ARF6/GDP/GULP/ACAP1 -0.11 0.14 -9999 0 -0.42 48 48
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.022 0.096 -9999 0 -0.43 26 26
ACAP1 -0.003 0.042 -9999 0 -0.66 2 2
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.001 0.014 -9999 0 -0.32 1 1
EFNA1 0 0 -9999 0 -10000 0 0
HGF -0.16 0.3 -9999 0 -0.74 108 108
CYTH3 0.01 0 -9999 0 -10000 0 0
CYTH2 0.005 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 111 111
endosomal lumen acidification 0 0 0 1 -0.001 99 100
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.013 0.098 -9999 0 -0.74 9 9
GNAQ/ARNO 0.004 0.02 -9999 0 -0.41 1 1
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 10 10
MET -0.004 0.053 -9999 0 -0.68 3 3
GNA14 -0.18 0.32 -9999 0 -0.74 123 123
GNA15 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 152 152
GNA11 0 0 -9999 0 -10000 0 0
LHCGR -0.001 0.026 -9999 0 -0.57 1 1
AGTR1 -0.3 0.36 -9999 0 -0.74 205 205
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.014 -9999 0 -0.32 1 1
IPCEF1/ARNO -0.017 0.078 -9999 0 -0.41 12 12
alphaIIb/beta3 Integrin -0.029 0.12 -9999 0 -0.56 26 26
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.032 0.03 -9999 0 -10000 0 0
VDR -0.001 0.033 -9999 0 -0.74 1 1
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.13 0.18 -9999 0 -0.54 10 10
RXRs/LXRs/DNA/Oxysterols -0.097 0.16 -9999 0 -0.64 10 10
MED1 0 0 -9999 0 -10000 0 0
mol:9cRA 0.004 0.006 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.013 0.061 -9999 0 -10000 0 0
RXRs/NUR77 -0.28 0.26 -9999 0 -0.48 289 289
RXRs/PPAR -0.18 0.2 -9999 0 -0.56 43 43
NCOR2 -0.001 0.033 -9999 0 -0.74 1 1
VDR/VDR/Vit D3 -0.001 0.025 -9999 0 -0.56 1 1
RARs/VDR/DNA/Vit D3 -0.003 0.036 -9999 0 -0.41 4 4
RARA 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.001 0.033 -9999 0 -0.74 1 1
RARs/RARs/DNA/9cRA -0.002 0.032 -9999 0 -0.41 3 3
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.057 0.053 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.013 0.063 -9999 0 -10000 0 0
THRA 0 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.025 -9999 0 -0.56 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.23 0.21 -9999 0 -0.43 265 265
NR1H4 -0.005 0.051 -9999 0 -0.57 4 4
RXRs/LXRs/DNA -0.21 0.19 -9999 0 -0.56 10 10
NR1H2 0.015 0.004 -9999 0 -10000 0 0
NR1H3 0.014 0.005 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.21 0.2 -9999 0 -0.4 266 266
NR4A1 -0.096 0.25 -9999 0 -0.74 65 65
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.12 0.14 -9999 0 -0.33 11 11
RXRG -0.38 0.37 -9999 0 -0.73 265 265
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.015 0.004 -9999 0 -10000 0 0
RXRB 0.014 0.005 -9999 0 -10000 0 0
THRB -0.026 0.14 -9999 0 -0.74 18 18
PPARG -0.084 0.23 -9999 0 -0.74 57 57
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.1 0.23 -9999 0 -1.3 12 12
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.097 0.16 -9999 0 -0.64 10 10
PPARA 0 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.004 0.057 -9999 0 -0.74 3 3
RXRs/NUR77/BCL2 -0.2 0.19 -9999 0 -0.35 289 289
SREBF1 -0.082 0.15 -9999 0 -0.6 9 9
RXRs/RXRs/DNA/9cRA -0.23 0.21 -9999 0 -0.43 265 265
ABCA1 -0.082 0.15 -9999 0 -0.6 9 9
RARs/THRs -0.017 0.08 -9999 0 -10000 0 0
RXRs/FXR -0.23 0.22 -9999 0 -0.43 265 265
BCL2 -0.001 0.026 -9999 0 -0.57 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.009 0.14 -10000 0 -0.38 67 67
CRKL -0.014 0.15 -10000 0 -0.41 63 63
HRAS -0.06 0.14 -10000 0 -0.62 14 14
mol:PIP3 -0.025 0.14 -10000 0 -0.39 61 61
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.022 0.16 -10000 0 -0.43 63 63
FOXO3 -0.007 0.14 -10000 0 -0.36 63 63
AKT1 -0.016 0.14 -10000 0 -0.4 63 63
BAD -0.007 0.14 -10000 0 -0.37 61 61
megakaryocyte differentiation -0.051 0.21 -10000 0 -0.49 84 84
GSK3B -0.007 0.14 -10000 0 -0.36 63 63
RAF1 0.004 0.14 -10000 0 -0.48 14 14
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.022 0.16 -10000 0 -0.43 63 63
STAT1 -0.075 0.36 -10000 0 -1 63 63
HRAS/SPRED1 -0.048 0.11 -10000 0 -0.48 14 14
cell proliferation -0.021 0.15 -10000 0 -0.42 63 63
PIK3CA 0 0 -10000 0 -10000 0 0
TEC -0.003 0.046 -10000 0 -0.74 2 2
RPS6KB1 -0.022 0.16 -10000 0 -0.43 63 63
HRAS/SPRED2 -0.048 0.11 -10000 0 -0.48 14 14
LYN/TEC/p62DOK -0.053 0.14 -10000 0 -0.41 64 64
MAPK3 0.018 0.1 -10000 0 -0.32 14 14
STAP1 -0.044 0.2 -10000 0 -0.5 76 76
GRAP2 -0.044 0.18 -10000 0 -0.74 30 30
JAK2 -0.11 0.28 -10000 0 -0.85 63 63
STAT1 (dimer) -0.072 0.35 -10000 0 -0.99 63 63
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.054 0.14 -10000 0 -0.4 68 68
actin filament polymerization -0.021 0.15 -10000 0 -0.42 63 63
LYN -0.003 0.046 -10000 0 -0.74 2 2
STAP1/STAT5A (dimer) -0.049 0.25 -10000 0 -0.67 63 63
PIK3R1 0 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.045 0.12 -10000 0 -0.36 61 61
PI3K -0.05 0.13 -10000 0 -0.4 63 63
PTEN -0.003 0.046 -10000 0 -0.74 2 2
SCF/KIT/EPO/EPOR -0.1 0.44 -10000 0 -1.3 63 63
MAPK8 -0.022 0.16 -10000 0 -0.43 63 63
STAT3 (dimer) -0.021 0.15 -10000 0 -0.42 63 63
positive regulation of transcription 0.019 0.085 -10000 0 -0.26 13 13
mol:GDP -0.064 0.15 -10000 0 -0.66 14 14
PIK3C2B -0.022 0.16 -10000 0 -0.43 63 63
CBL/CRKL -0.007 0.14 -10000 0 -0.38 63 63
FER -0.022 0.16 -10000 0 -0.43 63 63
SH2B3 -0.024 0.16 -10000 0 -0.43 65 65
PDPK1 -0.016 0.13 -10000 0 -0.36 61 61
SNAI2 -0.022 0.16 -10000 0 -0.43 63 63
positive regulation of cell proliferation -0.045 0.26 -10000 0 -0.74 63 63
KITLG 0.013 0.005 -10000 0 -10000 0 0
cell motility -0.045 0.26 -10000 0 -0.74 63 63
PTPN6 0.004 0.011 -10000 0 -10000 0 0
EPOR 0.01 0.1 -10000 0 -10000 0 0
STAT5A (dimer) -0.032 0.22 -10000 0 -0.61 63 63
SOCS1 -0.001 0.033 -10000 0 -0.74 1 1
cell migration 0.036 0.18 0.44 76 -10000 0 76
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.002 0.063 -10000 0 -0.57 6 6
VAV1 -0.007 0.073 -10000 0 -0.74 5 5
GRB10 -0.022 0.16 -10000 0 -0.43 63 63
PTPN11 0.003 0.009 -10000 0 -10000 0 0
SCF/KIT -0.058 0.15 -10000 0 -0.46 63 63
GO:0007205 0 0.008 -10000 0 -10000 0 0
MAP2K1 0.015 0.11 -10000 0 -0.36 14 14
CBL 0 0 -10000 0 -10000 0 0
KIT -0.13 0.47 -10000 0 -1.4 63 63
MAP2K2 0.015 0.11 -10000 0 -0.36 14 14
SHC/Grb2/SOS1 -0.05 0.13 -10000 0 -0.4 63 63
STAT5A -0.035 0.22 -10000 0 -0.63 63 63
GRB2 0 0 -10000 0 -10000 0 0
response to radiation -0.021 0.15 -10000 0 -0.42 63 63
SHC/GRAP2 -0.033 0.13 -10000 0 -0.56 30 30
PTPRO -0.053 0.21 -10000 0 -0.5 84 84
SH2B2 -0.022 0.16 -10000 0 -0.43 63 63
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.037 0.18 -10000 0 -0.46 76 76
CREBBP 0.028 0.011 -10000 0 -10000 0 0
BCL2 0.01 0.1 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB -0.001 0.033 -9999 0 -0.74 1 1
alphaV beta3 Integrin -0.012 0.081 -9999 0 -0.56 11 11
PTK2 -0.11 0.17 -9999 0 -0.6 40 40
positive regulation of JNK cascade -0.035 0.092 -9999 0 -0.34 40 40
CDC42/GDP -0.023 0.14 -9999 0 -0.47 40 40
Rac1/GDP -0.021 0.14 -9999 0 -0.46 40 40
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.043 0.11 -9999 0 -0.42 40 40
nectin-3/I-afadin -0.044 0.15 -9999 0 -0.56 40 40
RAPGEF1 -0.034 0.15 -9999 0 -0.54 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.048 0.18 -9999 0 -0.62 40 40
PDGFB-D/PDGFRB -0.001 0.033 -9999 0 -0.74 1 1
TLN1 -0.021 0.15 -9999 0 -0.52 33 33
Rap1/GTP -0.036 0.099 -9999 0 -0.37 40 40
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.044 0.15 -9999 0 -0.56 40 40
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP -0.035 0.17 -9999 0 -0.58 40 40
MLLT4 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K -0.033 0.11 -9999 0 -0.4 41 41
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.42 238 238
positive regulation of lamellipodium assembly -0.038 0.098 -9999 0 -0.36 42 42
PVRL1 -0.27 0.29 -9999 0 -0.57 238 238
PVRL3 -0.059 0.2 -9999 0 -0.74 40 40
PVRL2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
CLDN1 -0.1 0.22 -9999 0 -0.58 88 88
JAM-A/CLDN1 -0.089 0.17 -9999 0 -0.48 41 41
SRC -0.079 0.19 -9999 0 -0.71 40 40
ITGB3 -0.016 0.11 -9999 0 -0.74 11 11
nectin-1(dimer)/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.42 238 238
FARP2 -0.039 0.16 -9999 0 -0.57 40 40
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.038 0.13 -9999 0 -0.48 40 40
nectin-1/I-afadin -0.2 0.21 -9999 0 -0.42 238 238
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.39 258 258
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.035 0.092 -9999 0 -0.34 40 40
alphaV/beta3 Integrin/Talin -0.051 0.15 -9999 0 -0.78 14 14
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.052 0.16 -9999 0 -0.56 33 33
VAV2 -0.043 0.17 -9999 0 -0.58 43 43
RAP1/GDP -0.04 0.12 -9999 0 -0.43 40 40
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.038 0.13 -9999 0 -0.48 40 40
nectin-3(dimer)/I-afadin/I-afadin -0.044 0.15 -9999 0 -0.56 40 40
Rac1/GTP -0.046 0.12 -9999 0 -0.44 42 42
PTPRM -0.057 0.17 -9999 0 -0.45 64 64
E-cadherin/beta catenin/alpha catenin -0.12 0.13 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.034 0.11 -10000 0 -0.48 15 15
fibroblast growth factor receptor signaling pathway -0.033 0.11 -10000 0 -0.47 15 15
LAMA1 -0.17 0.26 -10000 0 -0.58 146 146
PRNP 0 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.14 0.25 -10000 0 -0.56 130 130
SMAD2 -0.023 0.14 -10000 0 -0.43 37 37
GPC1/PrPc/Cu2+ -0.02 0.081 -10000 0 -0.35 28 28
GPC1/Laminin alpha1 -0.14 0.22 -10000 0 -0.45 158 158
TDGF1 -0.003 0.044 -10000 0 -0.57 3 3
CRIPTO/GPC1 -0.026 0.1 -10000 0 -0.42 31 31
APP/GPC1 -0.023 0.095 -10000 0 -0.42 28 28
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.089 -10000 0 -0.35 31 31
FLT1 0 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.055 0.14 -10000 0 -0.48 37 37
SERPINC1 -0.007 0.063 -10000 0 -0.57 6 6
FYN -0.002 0.092 -10000 0 -0.35 32 32
FGR -0.037 0.16 -10000 0 -0.43 66 66
positive regulation of MAPKKK cascade -0.001 0.12 -10000 0 -0.47 16 16
SLIT2 -0.16 0.3 -10000 0 -0.74 110 110
GPC1/NRG -0.04 0.13 -10000 0 -0.46 43 43
NRG1 -0.022 0.13 -10000 0 -0.74 15 15
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.019 0.08 -10000 0 -0.35 28 28
LYN -0.003 0.094 -10000 0 -0.36 33 33
mol:Spermine -0.014 0.1 -10000 0 -0.42 28 28
cell growth -0.033 0.11 -10000 0 -0.47 15 15
BMP signaling pathway 0.032 0.13 0.57 28 -10000 0 28
SRC -0.001 0.089 -10000 0 -0.35 31 31
TGFBR1 0 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.22 0.34 -10000 0 -0.74 152 152
GPC1 -0.032 0.13 -10000 0 -0.57 28 28
TGFBR1 (dimer) 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.024 0.13 -10000 0 -0.39 57 57
HCK -0.007 0.1 -10000 0 -0.37 37 37
FGF2 -0.021 0.12 -10000 0 -0.74 14 14
FGFR1 -0.001 0.033 -10000 0 -0.74 1 1
VEGFR1 homodimer 0 0 -10000 0 -10000 0 0
TGFBR2 -0.054 0.19 -10000 0 -0.74 37 37
cell death -0.023 0.095 -10000 0 -0.41 28 28
ATIII/GPC1 -0.028 0.1 -10000 0 -0.42 34 34
PLA2G2A/GPC1 -0.19 0.27 -10000 0 -0.56 169 169
LCK -0.002 0.092 -10000 0 -0.35 32 32
neuron differentiation -0.04 0.13 -10000 0 -0.46 43 43
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.054 0.19 -10000 0 -0.74 37 37
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.12 0.39 -9999 0 -1.2 51 51
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.036 0.12 -9999 0 -0.43 8 8
ATF2/c-Jun -0.01 0.098 -9999 0 -0.43 3 3
MAPK11 -0.036 0.12 -9999 0 -0.43 8 8
MITF -0.041 0.16 -9999 0 -0.46 19 19
MAPKAPK5 -0.032 0.15 -9999 0 -0.36 75 75
KRT8 -0.032 0.15 -9999 0 -0.36 75 75
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.054 0.18 -9999 0 -0.46 75 75
CEBPB -0.032 0.15 -9999 0 -0.53 8 8
SLC9A1 -0.032 0.15 -9999 0 -0.36 75 75
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.026 0.15 -9999 0 -0.52 8 8
p38alpha-beta/MNK1 -0.065 0.13 -9999 0 -0.58 8 8
JUN -0.009 0.098 -9999 0 -0.42 3 3
PPARGC1A -0.13 0.28 -9999 0 -0.49 151 151
USF1 -0.032 0.15 -9999 0 -0.36 75 75
RAB5/GDP/GDI1 -0.045 0.095 -9999 0 -0.4 8 8
NOS2 -0.097 0.32 -9999 0 -1.2 32 32
DDIT3 -0.032 0.15 -9999 0 -0.53 8 8
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.018 0.12 -9999 0 -0.44 8 8
p38alpha-beta/HBP1 -0.065 0.13 -9999 0 -0.58 8 8
CREB1 -0.03 0.15 -9999 0 -0.38 75 75
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.021 0.13 -9999 0 -0.52 8 8
RPS6KA4 -0.032 0.15 -9999 0 -0.36 75 75
PLA2G4A -0.025 0.14 -9999 0 -0.53 13 13
GDI1 -0.032 0.15 -9999 0 -0.36 75 75
TP53 -0.044 0.19 -9999 0 -0.46 75 75
RPS6KA5 -0.032 0.15 -9999 0 -0.36 75 75
ESR1 -0.055 0.2 -9999 0 -0.6 31 31
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.044 0.18 -9999 0 -0.4 84 84
MEF2A -0.032 0.15 -9999 0 -0.36 75 75
EIF4EBP1 -0.032 0.16 -9999 0 -0.38 75 75
KRT19 -0.038 0.17 -9999 0 -0.69 12 12
ELK4 -0.032 0.15 -9999 0 -0.36 75 75
ATF6 -0.032 0.15 -9999 0 -0.36 75 75
ATF1 -0.03 0.15 -9999 0 -0.38 75 75
p38alpha-beta/MAPKAPK2 -0.065 0.13 -9999 0 -0.58 8 8
p38alpha-beta/MAPKAPK3 -0.065 0.13 -9999 0 -0.58 8 8
Nongenotropic Androgen signaling

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.095 0.18 -10000 0 -0.44 109 109
regulation of S phase of mitotic cell cycle -0.062 0.13 -10000 0 -0.31 103 103
GNAO1 -0.004 0.049 -10000 0 -0.63 3 3
HRAS 0 0 -10000 0 -10000 0 0
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
MAP2K1 -0.049 0.16 -10000 0 -0.46 18 18
T-DHT/AR -0.12 0.23 -10000 0 -0.56 103 103
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 61 61
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.033 -10000 0 -0.74 1 1
mol:GDP -0.11 0.22 -10000 0 -0.55 103 103
cell proliferation -0.058 0.2 -10000 0 -0.65 18 18
PIK3CA 0 0 -10000 0 -10000 0 0
FOS -0.09 0.3 -10000 0 -0.86 61 61
mol:Ca2+ -0.012 0.022 -10000 0 -0.085 8 8
MAPK3 -0.052 0.18 -10000 0 -0.58 18 18
MAPK1 -0.022 0.096 -10000 0 -0.3 18 18
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.004 61 61
cAMP biosynthetic process 0.011 0.021 -10000 0 -10000 0 0
GNG2 -0.007 0.073 -10000 0 -0.74 5 5
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 61 61
HRAS/GTP -0.084 0.16 -10000 0 -0.4 103 103
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0 0 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 61 61
PI3K 0 0 -10000 0 -10000 0 0
apoptosis 0.048 0.18 0.45 61 -10000 0 61
T-DHT/AR/PELP1 -0.1 0.2 -10000 0 -0.49 103 103
HRAS/GDP -0.11 0.21 -10000 0 -0.52 103 103
CREB1 -0.053 0.19 -10000 0 -0.48 61 61
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.15 0.3 -10000 0 -0.74 103 103
GNB1 -0.001 0.033 -10000 0 -0.74 1 1
RAF1 -0.056 0.17 -10000 0 -0.38 103 103
RAC1-CDC42/GDP -0.1 0.2 -10000 0 -0.5 103 103
T-DHT/AR/PELP1/Src -0.091 0.18 -10000 0 -0.44 103 103
MAP2K2 -0.049 0.16 -10000 0 -0.46 18 18
T-DHT/AR/PELP1/Src/PI3K -0.063 0.13 -10000 0 -0.31 103 103
GNAZ -0.009 0.08 -10000 0 -0.74 6 6
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.023 0.064 -10000 0 -0.62 3 3
mol:T-DHT 0 0.001 -10000 0 -0.003 43 43
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.007 0.036 -10000 0 -0.56 2 2
Gi family/GTP -0.042 0.084 -10000 0 -0.48 4 4
CDC42 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.2 0.44 -9999 0 -1.2 42 42
HDAC7 -0.006 0.013 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.34 -9999 0 -0.9 38 38
SMAD4 0 0.002 -9999 0 -10000 0 0
ID2 -0.2 0.44 -9999 0 -1.2 40 40
AP1 -0.07 0.18 -9999 0 -0.56 61 61
ABCG2 -0.25 0.5 -9999 0 -1.3 63 63
HIF1A -0.024 0.071 -9999 0 -10000 0 0
TFF3 -0.24 0.48 -9999 0 -1.3 49 49
GATA2 -0.073 0.23 -9999 0 -0.74 55 55
AKT1 -0.033 0.059 -9999 0 -10000 0 0
response to hypoxia -0.047 0.065 -9999 0 -10000 0 0
MCL1 -0.2 0.44 -9999 0 -1.2 42 42
NDRG1 -0.21 0.44 -9999 0 -1.2 39 39
SERPINE1 -0.2 0.44 -9999 0 -1.2 42 42
FECH -0.2 0.44 -9999 0 -1.2 38 38
FURIN -0.2 0.44 -9999 0 -1.2 36 36
NCOA2 0.008 0.034 -9999 0 -0.74 1 1
EP300 -0.024 0.09 -9999 0 -10000 0 0
HMOX1 -0.21 0.44 -9999 0 -1.2 40 40
BHLHE40 -0.2 0.44 -9999 0 -1.2 38 38
BHLHE41 -0.21 0.45 -9999 0 -1.2 44 44
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.033 0.084 -9999 0 -0.49 8 8
ENG 0.001 0.14 -9999 0 -0.83 9 9
JUN 0.008 0.005 -9999 0 -10000 0 0
RORA -0.2 0.44 -9999 0 -1.2 42 42
ABCB1 -0.2 0.44 -9999 0 -1.4 59 59
TFRC -0.2 0.44 -9999 0 -1.2 41 41
CXCR4 -0.2 0.44 -9999 0 -1.2 39 39
TF -0.23 0.46 -9999 0 -1.2 46 46
CITED2 -0.21 0.45 -9999 0 -1.3 39 39
HIF1A/ARNT -0.25 0.5 -9999 0 -1.4 46 46
LDHA -0.034 0.047 -9999 0 -10000 0 0
ETS1 -0.21 0.45 -9999 0 -1.3 43 43
PGK1 -0.2 0.44 -9999 0 -1.2 38 38
NOS2 -0.25 0.48 -9999 0 -1.2 55 55
ITGB2 -0.22 0.46 -9999 0 -1.3 46 46
ALDOA -0.2 0.44 -9999 0 -1.2 39 39
Cbp/p300/CITED2 -0.25 0.44 -9999 0 -1.2 44 44
FOS -0.082 0.25 -9999 0 -0.74 61 61
HK2 -0.2 0.44 -9999 0 -1.2 42 42
SP1 0.011 0.025 -9999 0 -10000 0 0
GCK -0.03 0.14 -9999 0 -0.74 1 1
HK1 -0.2 0.44 -9999 0 -1.2 35 35
NPM1 -0.2 0.44 -9999 0 -1.2 42 42
EGLN1 -0.2 0.44 -9999 0 -1.2 36 36
CREB1 0.017 0 -9999 0 -10000 0 0
PGM1 -0.2 0.44 -9999 0 -1.2 40 40
SMAD3 0 0.002 -9999 0 -10000 0 0
EDN1 -0.17 0.4 -9999 0 -1.2 53 53
IGFBP1 -0.21 0.44 -9999 0 -1.2 42 42
VEGFA -0.24 0.32 -9999 0 -0.85 31 31
HIF1A/JAB1 -0.018 0.029 -9999 0 -10000 0 0
CP -0.23 0.47 -9999 0 -1.3 43 43
CXCL12 -0.23 0.49 -9999 0 -1.3 51 51
COPS5 0.009 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.004 -9999 0 -10000 0 0
BNIP3 -0.2 0.44 -9999 0 -1.2 38 38
EGLN3 -0.25 0.47 -9999 0 -1.2 54 54
CA9 -0.43 0.47 -9999 0 -1.3 71 71
TERT -0.31 0.49 -9999 0 -1.3 52 52
ENO1 -0.2 0.44 -9999 0 -1.2 38 38
PFKL -0.2 0.44 -9999 0 -1.2 39 39
NCOA1 0.003 0.005 -9999 0 -10000 0 0
ADM -0.21 0.44 -9999 0 -1.2 40 40
ARNT -0.024 0.07 -9999 0 -10000 0 0
HNF4A 0.002 0.074 -9999 0 -0.58 8 8
ADFP -0.21 0.44 -9999 0 -1.2 44 44
SLC2A1 -0.44 0.36 -9999 0 -0.96 90 90
LEP -0.26 0.48 -9999 0 -1.2 56 56
HIF1A/ARNT/Cbp/p300 -0.21 0.35 -9999 0 -0.91 47 47
EPO -0.084 0.25 -9999 0 -0.79 4 4
CREBBP -0.024 0.09 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.26 0.38 -9999 0 -0.97 51 51
PFKFB3 -0.2 0.44 -9999 0 -1.2 42 42
NT5E -0.21 0.44 -9999 0 -1.2 42 42
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.031 0.13 -9999 0 -0.56 28 28
alphaV beta3 Integrin -0.024 0.11 -9999 0 -0.49 24 24
PTK2 -0.19 0.23 -9999 0 -0.7 43 43
IGF1R 0 0 -9999 0 -10000 0 0
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
CDKN1B -0.22 0.29 -9999 0 -0.58 189 189
VEGFA 0 0 -9999 0 -10000 0 0
ILK -0.22 0.29 -9999 0 -0.58 189 189
ROCK1 0 0 -9999 0 -10000 0 0
AKT1 -0.21 0.27 -9999 0 -0.54 189 189
PTK2B 0.002 0.13 -9999 0 -0.8 7 7
alphaV/beta3 Integrin/JAM-A -0.17 0.22 -9999 0 -0.84 13 13
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.013 0.076 -9999 0 -0.48 11 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.016 0.081 -9999 0 -0.43 18 18
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.12 0.16 -9999 0 -0.66 20 20
alphaV/beta3 Integrin/Syndecan-1 -0.011 0.073 -9999 0 -0.48 12 12
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.041 0.14 -9999 0 -0.78 11 11
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.19 0.18 -9999 0 -0.59 11 11
RPS6KB1 -0.038 0.13 -9999 0 -0.72 11 11
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.1 0.18 -9999 0 -0.75 24 24
GPR124 -0.001 0.033 -9999 0 -0.74 1 1
MAPK1 -0.1 0.18 -9999 0 -0.75 24 24
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.31 0.25 -9999 0 -0.49 313 313
cell adhesion -0.014 0.073 -9999 0 -0.44 11 11
ANGPTL3 -0.005 0.051 -9999 0 -0.57 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.027 0.11 -9999 0 -0.48 28 28
IGF-1R heterotetramer 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.054 0.19 -9999 0 -0.74 37 37
ITGB3 -0.016 0.11 -9999 0 -0.74 11 11
IGF1 -0.028 0.14 -9999 0 -0.73 19 19
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.011 0.072 -9999 0 -0.47 12 12
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.004 0.057 -9999 0 -0.74 3 3
alphaV/beta3 Integrin/CD47 -0.013 0.078 -9999 0 -0.48 14 14
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.04 0.14 -9999 0 -0.5 40 40
CSF1 -0.006 0.066 -9999 0 -0.74 4 4
PIK3C2A -0.22 0.29 -9999 0 -0.58 189 189
PI4 Kinase/Pyk2 -0.16 0.21 -9999 0 -0.76 25 25
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.033 0.14 -9999 0 -0.52 32 32
FAK1/Vinculin -0.14 0.18 -9999 0 -0.52 43 43
alphaV beta3/Integrin/ppsTEM5 -0.011 0.073 -9999 0 -0.48 12 12
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.28 0.36 -9999 0 -0.74 191 191
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.021 0.12 -9999 0 -0.74 14 14
F11R 0.004 0.095 -9999 0 -0.56 14 14
alphaV/beta3 Integrin/Lactadherin -0.01 0.07 -9999 0 -0.48 11 11
alphaV/beta3 Integrin/TGFBR2 -0.045 0.16 -9999 0 -0.55 41 41
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.038 -9999 0 -0.43 4 4
HSP90AA1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.01 0.064 -9999 0 -0.44 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.019 0.12 -9999 0 -0.74 13 13
alphaV/beta3 Integrin/Pyk2 -0.031 0.13 -9999 0 -0.8 7 7
SDC1 -0.001 0.033 -9999 0 -0.74 1 1
VAV3 0.031 0.043 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.14 0.18 -9999 0 -0.52 43 43
cell migration -0.13 0.16 -9999 0 -0.49 32 32
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.15 0.2 -9999 0 -0.76 13 13
SPP1 -0.29 0.29 -9999 0 -0.57 255 255
KDR -0.041 0.17 -9999 0 -0.74 28 28
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.46 0.36 -9999 0 -0.74 313 313
angiogenesis -0.11 0.22 -9999 0 -0.74 26 26
Rac1/GTP -0.004 0.036 -9999 0 -10000 0 0
EDIL3 -0.046 0.18 -9999 0 -0.74 31 31
cell proliferation -0.045 0.16 -9999 0 -0.55 41 41
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.26 0.34 -10000 0 -0.83 53 53
PCK1 -0.13 0.21 -10000 0 -0.74 17 17
HNF4A -0.31 0.4 -10000 0 -1.1 50 50
KCNJ11 -0.27 0.38 -10000 0 -1 37 37
AKT1 0 0.088 -10000 0 -10000 0 0
response to starvation -0.01 0.034 -10000 0 -10000 0 0
DLK1 -0.29 0.37 -10000 0 -0.95 45 45
NKX2-1 -0.77 0.79 -10000 0 -1.5 260 260
ACADM -0.26 0.34 -10000 0 -0.83 52 52
TAT -0.12 0.19 -10000 0 -0.75 9 9
CEBPB 0.003 0.006 -10000 0 -10000 0 0
CEBPA 0.002 0.034 -10000 0 -0.74 1 1
TTR -0.052 0.19 -10000 0 -0.79 16 16
PKLR -0.27 0.34 -10000 0 -0.84 56 56
APOA1 -0.43 0.56 -10000 0 -1.4 87 87
CPT1C -0.26 0.34 -10000 0 -0.83 52 52
ALAS1 -0.11 0.18 -10000 0 -10000 0 0
TFRC -0.16 0.25 -10000 0 -0.93 9 9
FOXF1 0 0.24 0.3 2 -0.62 58 60
NF1 0.016 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.012 0.081 -10000 0 -0.6 8 8
CPT1A -0.26 0.34 -10000 0 -0.83 53 53
HMGCS1 -0.26 0.34 -10000 0 -0.83 53 53
NR3C1 0.017 0.012 -10000 0 -10000 0 0
CPT1B -0.26 0.34 -10000 0 -0.86 40 40
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.005 0.029 -10000 0 -10000 0 0
GCK -0.26 0.34 -10000 0 -0.84 54 54
CREB1 0.007 0.017 -10000 0 -10000 0 0
IGFBP1 -0.12 0.17 -10000 0 -0.67 3 3
PDX1 -0.17 0.24 -10000 0 -0.69 19 19
UCP2 -0.26 0.34 -10000 0 -0.83 53 53
ALDOB -0.26 0.36 -10000 0 -0.93 28 28
AFP 0.017 0.14 -10000 0 -0.68 5 5
BDH1 -0.26 0.34 -10000 0 -0.84 54 54
HADH -0.26 0.36 -10000 0 -0.89 32 32
F2 -0.34 0.42 -10000 0 -1.1 49 49
HNF1A -0.012 0.082 -10000 0 -0.6 8 8
G6PC 0.01 0.088 -10000 0 -0.74 1 1
SLC2A2 -0.17 0.23 -10000 0 -0.87 2 2
INS -0.009 0.011 -10000 0 -10000 0 0
FOXA1 0.072 0.14 0.31 30 -0.57 11 41
FOXA3 -0.009 0.15 -10000 0 -0.72 17 17
FOXA2 -0.31 0.41 -10000 0 -0.89 77 77
ABCC8 -0.28 0.38 -10000 0 -0.99 41 41
ALB 0.025 0.13 -10000 0 -0.63 6 6
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.011 0.037 -9999 0 -0.53 1 1
NFATC2 -0.06 0.18 -9999 0 -0.51 70 70
NFATC3 0.012 0.028 -9999 0 -10000 0 0
CD40LG -0.17 0.38 -9999 0 -0.78 115 115
PTGS2 -0.14 0.34 -9999 0 -0.77 74 74
JUNB -0.001 0.033 -9999 0 -0.74 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.011 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.011 -9999 0 -10000 0 0
CALM1 -0.001 0.003 -9999 0 -10000 0 0
JUN -0.001 0.003 -9999 0 -10000 0 0
mol:Ca2+ -0.006 0.01 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 -0.003 0.044 -9999 0 -0.57 3 3
CREM 0 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.1 0.17 -9999 0 -0.56 45 45
FOS -0.091 0.24 -9999 0 -0.74 61 61
IFNG -0.11 0.29 -9999 0 -0.63 80 80
AP-1/NFAT1-c-4 -0.21 0.3 -9999 0 -0.75 94 94
FASLG -0.12 0.31 -9999 0 -0.74 59 59
NFAT1-c-4/ICER1 -0.082 0.16 -9999 0 -0.5 47 47
IL2RA -0.11 0.29 -9999 0 -0.66 66 66
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.14 0.34 -9999 0 -0.7 101 101
JunB/Fra1/NFAT1-c-4 -0.08 0.15 -9999 0 -0.49 45 45
IL4 -0.11 0.29 -9999 0 -0.64 73 73
IL2 -0.004 0.014 -9999 0 -10000 0 0
IL3 -0.019 0.023 -9999 0 -10000 0 0
FKBP1A 0 0 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0 0.003 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.01 0.059 -9999 0 -0.37 12 12
Syndecan-3/Neurocan -0.02 0.073 -9999 0 -10000 0 0
POMC -0.055 0.17 -9999 0 -0.59 47 47
EGFR -0.023 0.12 -9999 0 -0.63 18 18
Syndecan-3/EGFR -0.012 0.061 -9999 0 -0.32 18 18
AGRP -0.34 0.37 -9999 0 -0.74 233 233
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.04 0.15 -9999 0 -0.57 35 35
long-term memory -0.001 0.017 -9999 0 -0.38 1 1
Syndecan-3/IL8 -0.011 0.059 -9999 0 -0.31 18 18
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN -0.001 0.033 -9999 0 -0.74 1 1
limb bud formation 0 0 -9999 0 -10000 0 0
MC4R -0.024 0.12 -9999 0 -0.57 21 21
SRC 0 0 -9999 0 -10000 0 0
PTN -0.021 0.12 -9999 0 -0.7 15 15
FGFR/FGF/Syndecan-3 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.027 0.082 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.19 0.2 -9999 0 -0.4 233 233
Syndecan-3/AgRP/MC4R -0.19 0.2 -9999 0 -0.39 233 233
Fyn/Cortactin -0.001 0.025 -9999 0 -0.56 1 1
SDC3 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.011 0.058 -9999 0 -0.31 18 18
IL8 -0.022 0.11 -9999 0 -0.61 18 18
Syndecan-3/Fyn/Cortactin -0.001 0.017 -9999 0 -0.38 1 1
Syndecan-3/CASK 0 0 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.057 0.15 -9999 0 -0.43 67 67
Gamma Secretase 0 0 -9999 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.14 0.44 -10000 0 -1.3 39 39
IL23A -0.14 0.43 -10000 0 -1.2 38 38
NF kappa B1 p50/RelA/I kappa B alpha -0.21 0.36 -10000 0 -1.1 51 51
positive regulation of T cell mediated cytotoxicity -0.15 0.46 -10000 0 -1.2 51 51
ITGA3 -0.13 0.41 -10000 0 -1.2 37 37
IL17F -0.064 0.28 -10000 0 -0.74 29 29
IL12B 0.016 0.025 -10000 0 -10000 0 0
STAT1 (dimer) -0.21 0.38 -10000 0 -1.1 51 51
CD4 -0.13 0.43 -10000 0 -1.2 45 45
IL23 -0.15 0.41 -10000 0 -1.2 38 38
IL23R 0.003 0.085 -10000 0 -10000 0 0
IL1B -0.14 0.44 -10000 0 -1.3 39 39
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.13 0.4 -10000 0 -1.1 44 44
TYK2 0.011 0.019 -10000 0 -10000 0 0
STAT4 -0.012 0.092 -10000 0 -0.74 8 8
STAT3 0 0 -10000 0 -10000 0 0
IL18RAP -0.023 0.15 -10000 0 -0.74 21 21
IL12RB1 -0.038 0.19 -10000 0 -0.77 32 32
PIK3CA 0 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.026 0.15 -10000 0 -0.59 32 32
IL23R/JAK2 0.002 0.1 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.15 0.46 -10000 0 -1.2 51 51
natural killer cell activation 0 0.007 -10000 0 -10000 0 0
JAK2 0.018 0.023 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
NFKB1 0.006 0.006 -10000 0 -10000 0 0
RELA 0.006 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.14 0.39 -10000 0 -1.1 38 38
ALOX12B -0.17 0.42 -10000 0 -1.1 52 52
CXCL1 -0.15 0.46 -10000 0 -1.2 54 54
T cell proliferation -0.15 0.46 -10000 0 -1.2 51 51
NFKBIA 0.006 0.006 -10000 0 -10000 0 0
IL17A -0.043 0.24 -10000 0 -0.59 22 22
PI3K -0.21 0.36 -10000 0 -1.1 51 51
IFNG 0 0.028 0.099 1 -0.12 10 11
STAT3 (dimer) -0.2 0.34 -10000 0 -1 51 51
IL18R1 0 0.074 -10000 0 -0.73 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 -0.062 0.28 -10000 0 -0.82 24 24
IL18/IL18R -0.026 0.12 -10000 0 -0.54 25 25
macrophage activation -0.012 0.017 -10000 0 -0.045 27 27
TNF -0.15 0.45 -10000 0 -1.3 40 40
STAT3/STAT4 -0.21 0.36 -10000 0 -1.1 52 52
STAT4 (dimer) -0.22 0.39 -10000 0 -1.2 52 52
IL18 0.003 0.058 -10000 0 -0.74 3 3
IL19 -0.13 0.4 -10000 0 -1.1 43 43
STAT5A (dimer) -0.21 0.38 -10000 0 -1.1 51 51
STAT1 0 0 -10000 0 -10000 0 0
SOCS3 -0.003 0.046 -10000 0 -0.74 2 2
CXCL9 -0.14 0.43 -10000 0 -1.2 42 42
MPO -0.15 0.46 -10000 0 -1.2 60 60
positive regulation of humoral immune response -0.15 0.46 -10000 0 -1.2 51 51
IL23/IL23R/JAK2/TYK2 -0.16 0.52 -10000 0 -1.3 51 51
IL6 -0.24 0.58 -10000 0 -1.3 101 101
STAT5A 0 0 -10000 0 -10000 0 0
IL2 0.006 0.008 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.007 -10000 0 -10000 0 0
CD3E -0.12 0.41 -10000 0 -1.1 44 44
keratinocyte proliferation -0.15 0.46 -10000 0 -1.2 51 51
NOS2 -0.17 0.48 -10000 0 -1.3 53 53
Coregulation of Androgen receptor activity

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.002 0.004 -9999 0 -10000 0 0
SVIL 0.002 0.004 -9999 0 -10000 0 0
ZNF318 0 0.005 -9999 0 -10000 0 0
JMJD2C -0.004 0.026 -9999 0 -0.081 50 50
T-DHT/AR/Ubc9 -0.13 0.2 -9999 0 -0.52 103 103
CARM1 0 0 -9999 0 -10000 0 0
PRDX1 0 0.001 -9999 0 -10000 0 0
PELP1 0 0.001 -9999 0 -10000 0 0
CTNNB1 0.001 0.004 -9999 0 -10000 0 0
AKT1 0 0.002 -9999 0 -10000 0 0
PTK2B 0.001 0.004 -9999 0 -10000 0 0
MED1 0 0.002 -9999 0 -10000 0 0
MAK -0.066 0.21 -9999 0 -0.74 45 45
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.002 0.004 -9999 0 -10000 0 0
GSN 0.002 0.004 -9999 0 -10000 0 0
NCOA2 -0.001 0.033 -9999 0 -0.74 1 1
NCOA6 0.002 0.004 -9999 0 -10000 0 0
DNA-PK 0 0.006 -9999 0 -10000 0 0
NCOA4 0 0 -9999 0 -10000 0 0
PIAS3 0.001 0.004 -9999 0 -10000 0 0
cell proliferation -0.11 0.27 -9999 0 -0.94 45 45
XRCC5 0 0.002 -9999 0 -10000 0 0
UBE3A 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.14 0.22 -9999 0 -0.54 114 114
FHL2 -0.054 0.08 -9999 0 -0.56 2 2
RANBP9 0.002 0.004 -9999 0 -10000 0 0
JMJD1A -0.034 0.07 -9999 0 -0.13 162 162
CDK6 -0.002 0.036 -9999 0 -0.57 2 2
TGFB1I1 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.14 0.21 -9999 0 -0.53 108 108
XRCC6 0 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.14 0.24 -9999 0 -0.55 104 104
CTDSP1 0.001 0.004 -9999 0 -10000 0 0
CTDSP2 0 0.004 -9999 0 -10000 0 0
BRCA1 0.002 0.004 -9999 0 -10000 0 0
TCF4 -0.004 0.057 -9999 0 -0.74 3 3
CDKN2A -0.27 0.29 -9999 0 -0.58 233 233
SRF 0.016 0.007 -9999 0 -10000 0 0
NKX3-1 -0.11 0.14 -9999 0 -0.95 2 2
KLK3 0.031 0.054 -9999 0 -10000 0 0
TMF1 0.001 0.003 -9999 0 -10000 0 0
HNRNPA1 0 0.002 -9999 0 -10000 0 0
AOF2 0 0.002 -9999 0 -10000 0 0
APPL1 0.02 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.13 0.21 -9999 0 -0.52 103 103
AR -0.16 0.31 -9999 0 -0.76 103 103
UBA3 0.001 0.004 -9999 0 -10000 0 0
PATZ1 0 0.002 -9999 0 -10000 0 0
PAWR 0.001 0.003 -9999 0 -10000 0 0
PRKDC 0 0.002 -9999 0 -10000 0 0
PA2G4 0 0.003 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.12 0.19 -9999 0 -0.48 103 103
RPS6KA3 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.13 0.2 -9999 0 -0.52 103 103
LATS2 0 0.002 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.12 0.19 -9999 0 -0.48 103 103
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 0 0.033 -9999 0 -0.74 1 1
KLK2 -0.093 0.14 -9999 0 -0.51 28 28
CASP8 0 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.19 -9999 0 -0.48 104 104
TMPRSS2 -0.4 0.54 -9999 0 -1.2 161 161
CCND1 -0.01 0.084 -9999 0 -0.71 7 7
PIAS1 0.002 0.004 -9999 0 -10000 0 0
mol:T-DHT -0.019 0.036 -9999 0 -0.078 118 118
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.002 0.005 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.21 -9999 0 -0.52 105 105
CMTM2 -0.09 0.24 -9999 0 -0.74 61 61
SNURF -0.024 0.13 -9999 0 -0.74 16 16
ZMIZ1 -0.007 0.047 -9999 0 -0.8 1 1
CCND3 0 0.001 -9999 0 -10000 0 0
TGIF1 0 0.002 -9999 0 -10000 0 0
FKBP4 0 0.026 -9999 0 -0.57 1 1
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.015 0.042 -9999 0 -10000 0 0
BIRC5 -0.49 0.2 -9999 0 -0.57 426 426
NFKBIA 0.018 0.042 -9999 0 -10000 0 0
CPEB1 -0.05 0.18 -9999 0 -0.74 34 34
AKT1 0.018 0.042 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.014 0.037 -9999 0 -10000 0 0
NDEL1/TACC3 0.017 0.04 -9999 0 -0.29 2 2
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.013 0.006 -9999 0 -10000 0 0
PAK1/Aurora A 0.015 0.045 -9999 0 -0.35 1 1
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
JUB 0 0 -9999 0 -10000 0 0
TPX2 -0.28 0.2 -9999 0 -0.42 349 349
TP53 0.018 0.033 -9999 0 -0.35 1 1
DLG7 0.01 0.042 -9999 0 -10000 0 0
AURKAIP1 0 0 -9999 0 -10000 0 0
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.018 0.043 -9999 0 -0.31 2 2
G2/M transition of mitotic cell cycle 0.014 0.037 -9999 0 -10000 0 0
AURKA 0.016 0.052 -9999 0 -10000 0 0
AURKB -0.088 0.051 -9999 0 -0.12 343 343
CDC25B 0.019 0.036 -9999 0 -10000 0 0
G2/M transition checkpoint 0.014 0.037 -9999 0 -10000 0 0
mRNA polyadenylation -0.018 0.12 -9999 0 -0.44 34 34
Aurora A/CPEB -0.018 0.12 -9999 0 -0.44 34 34
Aurora A/TACC1/TRAP/chTOG 0.022 0.045 -9999 0 -0.4 2 2
BRCA1 0 0 -9999 0 -10000 0 0
centrosome duplication 0.015 0.045 -9999 0 -0.35 1 1
regulation of centrosome cycle 0.017 0.04 -9999 0 -0.28 2 2
spindle assembly 0.015 0.044 -9999 0 -0.4 2 2
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.24 0.1 -9999 0 -0.42 24 24
CENPA -0.076 0.043 -9999 0 -0.18 23 23
Aurora A/PP2A 0.015 0.042 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.028 0.033 -9999 0 -10000 0 0
negative regulation of DNA binding 0.018 0.033 -9999 0 -0.35 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.014 0.037 -9999 0 -10000 0 0
mitotic prometaphase 0.025 0.017 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.052 -9999 0 -10000 0 0
TACC1 -0.003 0.046 -9999 0 -0.74 2 2
TACC3 -0.002 0.036 -9999 0 -0.57 2 2
Aurora A/Antizyme1 0.02 0.038 -9999 0 -10000 0 0
Aurora A/RasGAP 0.015 0.042 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.006 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.001 0.015 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.28 0.2 -9999 0 -0.42 349 349
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.22 0.16 -9999 0 -0.46 24 24
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
CKAP5 0 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.004 0.018 -10000 0 -10000 0 0
AES 0.003 0.015 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0 0 -10000 0 -10000 0 0
DKK2 -0.14 0.29 -10000 0 -0.74 93 93
TLE1 0.002 0.031 -10000 0 -0.61 1 1
MACF1 0.004 0.047 -10000 0 -0.74 2 2
CTNNB1 0.066 0.099 0.29 10 -10000 0 10
WIF1 -0.47 0.36 -10000 0 -0.74 318 318
beta catenin/RanBP3 0.002 0.091 0.44 15 -10000 0 15
KREMEN2 -0.37 0.28 -10000 0 -0.57 325 325
DKK1 -0.039 0.15 -10000 0 -0.62 31 31
beta catenin/beta TrCP1 0.068 0.093 0.3 3 -10000 0 3
FZD1 0.004 0.005 -10000 0 -10000 0 0
AXIN2 -0.036 0.28 -10000 0 -1.5 17 17
AXIN1 0.008 0.005 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.021 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.092 0.054 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.02 0.063 0.24 30 -10000 0 30
Axin1/APC/GSK3/beta catenin/Macf1 0.065 0.042 -10000 0 -10000 0 0
HNF1A -0.006 0.075 -10000 0 -0.58 8 8
CTBP1 0.004 0.017 -10000 0 -10000 0 0
MYC 0.008 0.048 -10000 0 -10000 0 0
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.31 0.25 -10000 0 -0.71 93 93
NKD1 -0.071 0.22 -10000 0 -0.72 49 49
TCF4 -0.001 0.058 -10000 0 -0.72 3 3
TCF3 0.004 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.002 0.023 -10000 0 -10000 0 0
Ran/GTP 0 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.017 0.094 0.45 21 -10000 0 21
LEF1 0.002 0.031 -10000 0 -0.58 1 1
DVL1 0.08 0.061 0.21 1 -10000 0 1
CSNK2A1 0.003 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.097 0.071 -10000 0 -0.56 1 1
DKK1/LRP6/Kremen 2 -0.25 0.19 -10000 0 -0.68 25 25
LRP6 0.007 0.005 -10000 0 -10000 0 0
CSNK1A1 0.004 0.018 -10000 0 -10000 0 0
NLK 0.01 0.002 -10000 0 -10000 0 0
CCND1 -0.008 0.17 -10000 0 -1.5 6 6
WNT1 0.003 0.045 -10000 0 -0.57 3 3
GSK3A 0.008 0.005 -10000 0 -10000 0 0
GSK3B 0.003 0.004 -10000 0 -10000 0 0
FRAT1 -0.001 0.033 -10000 0 -0.74 1 1
PPP2R5D 0.076 0.1 0.37 49 -10000 0 49
APC 0 0.023 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.16 0.12 0.26 315 -10000 0 315
CREBBP 0.004 0.017 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.016 0.13 -9999 0 -0.5 33 33
ADCY5 -0.028 0.15 -9999 0 -0.49 45 45
ADCY6 0.015 0.039 -9999 0 -0.48 3 3
ADCY7 0.017 0.022 -9999 0 -0.48 1 1
ADCY1 0.016 0.032 -9999 0 -0.48 2 2
ADCY2 -0.025 0.13 -9999 0 -0.41 50 50
ADCY3 0.017 0.022 -9999 0 -0.48 1 1
ADCY8 -0.14 0.23 -9999 0 -0.48 158 158
PRKCE 0.009 0.026 -9999 0 -0.56 1 1
ADCY9 0.016 0.032 -9999 0 -0.48 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.069 0.13 -9999 0 -0.44 27 27
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.001 0.093 -10000 0 -0.59 12 12
NFATC2 -0.054 0.3 -10000 0 -0.73 72 72
NFATC3 0.013 0.054 -10000 0 -10000 0 0
CD40LG -0.17 0.45 -10000 0 -1.1 70 70
ITCH -0.008 0.11 -10000 0 -10000 0 0
CBLB -0.008 0.11 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.28 -10000 0 -1.1 29 29
JUNB -0.001 0.033 -10000 0 -0.74 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.053 0.12 -10000 0 -0.33 81 81
T cell anergy -0.061 0.18 -10000 0 -0.45 81 81
TLE4 -0.021 0.23 -10000 0 -0.73 28 28
Jun/NFAT1-c-4/p21SNFT -0.12 0.27 -10000 0 -1.1 23 23
AP-1/NFAT1-c-4 -0.23 0.39 -10000 0 -1.3 38 38
IKZF1 -0.031 0.28 -10000 0 -1 24 24
T-helper 2 cell differentiation -0.045 0.28 -10000 0 -0.8 46 46
AP-1/NFAT1 -0.14 0.24 -10000 0 -0.62 68 68
CALM1 -0.028 0.064 -10000 0 -10000 0 0
EGR2 -0.022 0.33 -10000 0 -1.4 18 18
EGR3 -0.024 0.33 -10000 0 -1.4 19 19
NFAT1/FOXP3 -0.09 0.21 -10000 0 -0.7 29 29
EGR1 -0.007 0.11 -10000 0 -0.74 11 11
JUN 0.003 0.022 -10000 0 -10000 0 0
EGR4 -0.005 0.086 -10000 0 -0.58 11 11
mol:Ca2+ -0.032 0.073 -10000 0 -10000 0 0
GBP3 -0.038 0.28 -10000 0 -0.9 31 31
FOSL1 -0.003 0.044 -10000 0 -0.57 3 3
NFAT1-c-4/MAF/IRF4 -0.099 0.27 -10000 0 -1.1 22 22
DGKA -0.018 0.23 -10000 0 -0.76 22 22
CREM 0 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.3 -10000 0 -1.1 29 29
CTLA4 -0.017 0.21 -10000 0 -0.78 16 16
NFAT1-c-4 (dimer)/EGR1 -0.11 0.29 -10000 0 -1.2 22 22
NFAT1-c-4 (dimer)/EGR4 -0.11 0.27 -10000 0 -1.1 21 21
FOS -0.088 0.25 -10000 0 -0.74 61 61
IFNG -0.16 0.35 -10000 0 -0.99 56 56
T cell activation -0.04 0.24 -10000 0 -0.79 22 22
MAF 0 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.003 0.2 0.86 13 -10000 0 13
TNF -0.037 0.3 -10000 0 -1 25 25
FASLG -0.089 0.46 -10000 0 -1.6 36 36
TBX21 -0.062 0.23 -10000 0 -0.74 51 51
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.059 0.22 -10000 0 -0.74 47 47
PTPN1 -0.018 0.23 -10000 0 -0.78 20 20
NFAT1-c-4/ICER1 -0.1 0.27 -10000 0 -1.1 23 23
GATA3 -0.023 0.13 -10000 0 -0.71 17 17
T-helper 1 cell differentiation -0.15 0.34 -10000 0 -0.88 69 69
IL2RA -0.15 0.28 -10000 0 -0.9 42 42
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.018 0.23 -10000 0 -0.77 21 21
E2F1 0.015 0.004 -10000 0 -10000 0 0
PPARG -0.084 0.23 -10000 0 -0.74 57 57
SLC3A2 -0.018 0.23 -10000 0 -0.8 19 19
IRF4 -0.009 0.08 -10000 0 -0.74 6 6
PTGS2 -0.15 0.41 -10000 0 -1.1 54 54
CSF2 -0.14 0.41 -10000 0 -1.1 46 46
JunB/Fra1/NFAT1-c-4 -0.097 0.25 -10000 0 -1.1 21 21
IL4 -0.049 0.3 -10000 0 -0.86 45 45
IL5 -0.11 0.36 -10000 0 -1.1 34 34
IL2 -0.041 0.24 -10000 0 -0.81 22 22
IL3 -0.037 0.048 -10000 0 -10000 0 0
RNF128 -0.097 0.31 -10000 0 -0.8 81 81
NFATC1 0.002 0.2 -10000 0 -0.86 13 13
CDK4 0.008 0.16 0.62 10 -10000 0 10
PTPRK -0.018 0.23 -10000 0 -0.77 21 21
IL8 -0.12 0.37 -10000 0 -1.1 36 36
POU2F1 0 0.003 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0 0 -10000 0 -10000 0 0
HDAC1 0.001 0.005 -10000 0 -10000 0 0
AES 0 0.002 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.002 0.036 -10000 0 -0.57 2 2
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 -0.001 0.032 -10000 0 -0.73 1 1
AP1 -0.08 0.19 -10000 0 -0.43 92 92
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 0 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.002 0.042 -10000 0 -0.55 1 1
NICD/RBPSUH 0 0 -10000 0 -10000 0 0
WIF1 -0.47 0.36 -10000 0 -0.74 318 318
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0 0 -10000 0 -10000 0 0
KREMEN2 -0.37 0.28 -10000 0 -0.57 325 325
DKK1 -0.039 0.15 -10000 0 -0.62 31 31
beta catenin/beta TrCP1 0.016 0.06 -10000 0 -10000 0 0
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 -0.004 0.026 0.3 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES -0.001 0.027 -10000 0 -10000 0 0
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.09 0.24 -10000 0 -0.74 61 61
JUN 0 0 -10000 0 -10000 0 0
MAP3K7 0 0.003 -10000 0 -10000 0 0
CTNNB1 0.01 0.065 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.31 0.25 -10000 0 -0.71 93 93
HNF1A -0.009 0.072 -10000 0 -0.58 8 8
CTBP1 0 0.002 -10000 0 -10000 0 0
MYC 0.002 0.012 -10000 0 -10000 0 0
NKD1 -0.071 0.22 -10000 0 -0.72 49 49
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.001 0.018 -10000 0 -10000 0 0
apoptosis -0.079 0.19 -10000 0 -0.42 92 92
Delta 1/NOTCHprecursor 0 0 -10000 0 -10000 0 0
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.002 0.012 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.004 0.026 0.3 1 -10000 0 1
DVL1 -0.045 0.043 -10000 0 -0.67 1 1
CSNK2A1 0.01 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.25 0.19 -10000 0 -0.68 25 25
LRP6 0 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.001 -10000 0 -10000 0 0
NLK 0.001 0.006 -10000 0 -10000 0 0
CCND1 -0.015 0.16 -10000 0 -1.4 6 6
WNT1 -0.003 0.044 -10000 0 -0.58 3 3
Axin1/APC/beta catenin 0.011 0.045 0.27 1 -0.36 1 2
DKK2 -0.14 0.29 -10000 0 -0.74 93 93
NOTCH1 precursor/DVL1 -0.022 0.028 -10000 0 -0.55 1 1
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 -0.001 0.033 -10000 0 -0.74 1 1
NOTCH/Deltex homolog 1 -0.001 0.018 -10000 0 -10000 0 0
PPP2R5D 0.01 0.1 0.31 49 -10000 0 49
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.28 0.21 -10000 0 -0.43 317 317
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 -0.008 0.058 -9999 0 -0.42 10 10
VLDLR -0.003 0.046 -9999 0 -0.74 2 2
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.001 0.033 -9999 0 -0.74 1 1
ITGA3 -0.006 0.066 -9999 0 -0.74 4 4
RELN/VLDLR/Fyn -0.086 0.19 -9999 0 -0.48 90 90
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.001 0.022 -9999 0 -10000 0 0
AKT1 -0.035 0.13 -9999 0 -0.49 3 3
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.033 0.13 -9999 0 -0.57 29 29
RELN/LRP8/DAB1 -0.098 0.18 -9999 0 -0.45 88 88
LRPAP1/LRP8 -0.002 0.032 -9999 0 -0.42 3 3
RELN/LRP8/DAB1/Fyn -0.092 0.17 -9999 0 -0.43 88 88
DAB1/alpha3/beta1 Integrin -0.085 0.16 -9999 0 -0.69 6 6
long-term memory -0.12 0.19 -9999 0 -0.73 16 16
DAB1/LIS1 -0.085 0.16 -9999 0 -0.64 5 5
DAB1/CRLK/C3G -0.082 0.15 -9999 0 -0.62 5 5
PIK3CA 0 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.086 0.16 -9999 0 -0.64 5 5
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.065 0.2 -9999 0 -0.66 50 50
CDK5R1 -0.011 0.08 -9999 0 -0.57 10 10
RELN -0.13 0.28 -9999 0 -0.73 89 89
PIK3R1 0 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.087 0.18 -9999 0 -0.47 92 92
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.2 -9999 0 -0.45 106 106
MAPK8 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.097 0.18 -9999 0 -0.42 115 115
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.092 0.17 -9999 0 -0.42 90 90
RELN/LRP8 -0.086 0.18 -9999 0 -0.48 86 86
GRIN2B/RELN/LRP8/DAB1/Fyn -0.094 0.17 -9999 0 -0.42 88 88
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.004 0.049 -9999 0 -0.56 4 4
RAP1A -0.076 0.14 -9999 0 -0.58 5 5
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.003 0.042 -9999 0 -0.66 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.006 0.057 -9999 0 -0.57 5 5
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.013 0.097 -9999 0 -0.4 3 3
neuron adhesion -0.073 0.14 -9999 0 -0.62 5 5
LRP8 -0.003 0.044 -9999 0 -0.57 3 3
GSK3B -0.026 0.12 -9999 0 -0.46 3 3
RELN/VLDLR/DAB1/Fyn -0.091 0.17 -9999 0 -0.43 89 89
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.065 0.12 -9999 0 -0.32 89 89
CDK5 0 0 -9999 0 -10000 0 0
MAPT 0.003 0.083 -9999 0 -0.66 7 7
neuron migration -0.03 0.17 -9999 0 -0.55 6 6
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.043 0.082 -9999 0 -0.4 3 3
RELN/VLDLR -0.079 0.17 -9999 0 -0.44 87 87
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.25 -10000 0 -0.75 13 13
CRP -0.15 0.25 -10000 0 -0.74 15 15
cell cycle arrest -0.17 0.28 -10000 0 -0.66 57 57
TIMP1 -0.11 0.21 -10000 0 -0.66 8 8
IL6ST -0.018 0.14 -10000 0 -0.74 18 18
Rac1/GDP -0.064 0.19 -10000 0 -0.7 20 20
AP1 -0.007 0.16 -10000 0 -0.55 15 15
GAB2 -0.004 0.12 -10000 0 -0.73 14 14
TNFSF11 -0.16 0.26 -10000 0 -0.67 35 35
HSP90B1 0 0.05 -10000 0 -10000 0 0
GAB1 0.014 0.008 -10000 0 -10000 0 0
MAPK14 -0.028 0.17 -10000 0 -0.72 17 17
AKT1 0.042 0.057 -10000 0 -10000 0 0
FOXO1 0.049 0.053 -10000 0 -10000 0 0
MAP2K6 -0.051 0.18 -10000 0 -0.75 17 17
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.075 0.2 -10000 0 -0.73 17 17
MITF -0.069 0.19 -10000 0 -0.65 27 27
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0 0 -10000 0 -10000 0 0
A2M -0.47 0.69 -10000 0 -1.5 165 165
CEBPB 0.016 0.004 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.029 0.12 0.23 4 -0.62 6 10
STAT3 -0.18 0.29 -10000 0 -0.69 57 57
STAT1 -0.007 0.016 -10000 0 -10000 0 0
CEBPD -0.14 0.25 -10000 0 -0.83 12 12
PIK3CA 0.01 0.003 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
JUN 0.006 0.005 -10000 0 -10000 0 0
PIAS3/MITF -0.085 0.17 -10000 0 -0.64 24 24
MAPK11 -0.028 0.17 -10000 0 -0.72 17 17
STAT3 (dimer)/FOXO1 -0.19 0.31 -10000 0 -0.77 56 56
GRB2/SOS1/GAB family -0.03 0.17 -10000 0 -0.67 19 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.051 0.19 -10000 0 -0.56 37 37
GRB2 0.014 0.008 -10000 0 -10000 0 0
JAK2 0 0 -10000 0 -10000 0 0
LBP -0.11 0.21 -10000 0 -0.68 7 7
PIK3R1 0.008 0.005 -10000 0 -10000 0 0
JAK1 0.011 0.005 -10000 0 -10000 0 0
MYC -0.14 0.25 -10000 0 -0.75 13 13
FGG -0.48 0.57 -10000 0 -1.1 234 234
macrophage differentiation -0.17 0.28 -10000 0 -0.66 57 57
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.089 0.2 -10000 0 -0.53 62 62
JUNB -0.14 0.24 -10000 0 -0.74 14 14
FOS -0.084 0.24 -10000 0 -0.74 61 61
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.07 0.19 -10000 0 -0.5 59 59
STAT1/PIAS1 -0.084 0.18 -10000 0 -0.49 50 50
GRB2/SOS1/GAB family/SHP2/PI3K 0.02 0.061 -10000 0 -10000 0 0
STAT3 (dimer) -0.18 0.29 -10000 0 -0.68 57 57
PRKCD -0.09 0.22 -10000 0 -0.74 16 16
IL6R -0.004 0.1 -10000 0 -0.74 10 10
SOCS3 -0.014 0.17 -10000 0 -0.84 10 10
gp130 (dimer)/JAK1/JAK1/LMO4 -0.011 0.092 -10000 0 -0.46 19 19
Rac1/GTP -0.1 0.17 -10000 0 -0.7 21 21
HCK -0.004 0.081 -10000 0 -0.74 6 6
MAPKKK cascade 0.044 0.13 -10000 0 -0.56 14 14
bone resorption -0.15 0.25 -10000 0 -0.64 35 35
IRF1 -0.14 0.25 -10000 0 -0.75 13 13
mol:GDP -0.065 0.19 -10000 0 -0.72 21 21
SOS1 0.015 0.013 -10000 0 -10000 0 0
VAV1 -0.068 0.2 -10000 0 -0.74 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.043 0.18 -10000 0 -0.81 17 17
PTPN11 -0.006 0.014 -10000 0 -10000 0 0
IL6/IL6RA -0.098 0.23 -10000 0 -0.59 86 86
gp130 (dimer)/TYK2/TYK2/LMO4 -0.014 0.091 -10000 0 -0.47 18 18
gp130 (dimer)/JAK2/JAK2/LMO4 -0.014 0.091 -10000 0 -0.47 18 18
IL6 -0.11 0.28 -10000 0 -0.74 82 82
PIAS3 0 0 -10000 0 -10000 0 0
PTPRE 0.011 0.049 -10000 0 -0.73 2 2
PIAS1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.075 0.18 -10000 0 -0.46 62 62
LMO4 0.007 0.029 -10000 0 -0.6 1 1
STAT3 (dimer)/PIAS3 -0.21 0.23 -10000 0 -0.66 57 57
MCL1 0.05 0.051 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.02 0 -9999 0 -10000 0 0
SMARCC1 0.006 0.008 -9999 0 -10000 0 0
REL 0 0.002 -9999 0 -10000 0 0
HDAC7 -0.029 0.12 -9999 0 -10000 0 0
JUN 0.001 0.004 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.001 0.033 -9999 0 -0.74 1 1
KAT5 0 0.001 -9999 0 -10000 0 0
MAPK14 0.012 0.026 -9999 0 -0.45 1 1
FOXO1 0 0 -9999 0 -10000 0 0
T-DHT/AR -0.036 0.13 -9999 0 -0.44 1 1
MAP2K6 0.006 0.028 -9999 0 -0.6 1 1
BRM/BAF57 -0.001 0.025 -9999 0 -0.56 1 1
MAP2K4 0.007 0.007 -9999 0 -10000 0 0
SMARCA2 0 0.033 -9999 0 -0.74 1 1
PDE9A -0.11 0.23 -9999 0 -0.85 28 28
NCOA2 0.005 0.034 -9999 0 -0.74 1 1
CEBPA -0.001 0.033 -9999 0 -0.74 1 1
EHMT2 0.001 0.004 -9999 0 -10000 0 0
cell proliferation -0.047 0.17 -9999 0 -0.52 24 24
NR0B1 -0.18 0.27 -9999 0 -0.57 161 161
EGR1 -0.015 0.11 -9999 0 -0.74 11 11
RXRs/9cRA -0.23 0.22 -9999 0 -0.44 265 265
AR/RACK1/Src -0.014 0.074 -9999 0 -10000 0 0
AR/GR -0.063 0.12 -9999 0 -0.34 42 42
GNB2L1 0.005 0.005 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.013 0.016 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.013 0.074 -9999 0 -0.45 1 1
SRC 0.018 0.04 -9999 0 -10000 0 0
NR3C1 0 0 -9999 0 -10000 0 0
KLK3 -0.13 0.15 -9999 0 -0.55 27 27
APPBP2 0.008 0.006 -9999 0 -10000 0 0
TRIM24 0.001 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.037 0.053 -9999 0 -10000 0 0
TMPRSS2 -0.42 0.57 -9999 0 -1.2 161 161
RXRG -0.39 0.37 -9999 0 -0.74 265 265
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0.006 0.005 -9999 0 -10000 0 0
NR2C2 0 0 -9999 0 -10000 0 0
KLK2 -0.019 0.13 -9999 0 -0.48 3 3
AR -0.052 0.15 -9999 0 -0.33 103 103
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
SRY -0.005 0.051 -9999 0 -0.57 4 4
GATA2 -0.081 0.23 -9999 0 -0.74 55 55
MYST2 0 0.001 -9999 0 -10000 0 0
HOXB13 -0.34 0.28 -9999 0 -0.57 294 294
T-DHT/AR/RACK1/Src -0.014 0.07 -9999 0 -10000 0 0
positive regulation of transcription -0.081 0.23 -9999 0 -0.74 55 55
DNAJA1 0.008 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.006 -9999 0 -10000 0 0
NCOA1 0.014 0.004 -9999 0 -10000 0 0
SPDEF -0.096 0.25 -9999 0 -0.73 67 67
T-DHT/AR/TIF2 0.013 0.056 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 -0.037 0.053 -9999 0 -10000 0 0
GSK3B 0.007 0.006 -9999 0 -10000 0 0
NR2C1 0 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.012 0.043 -9999 0 -0.38 1 1
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0 0.002 -9999 0 -10000 0 0
POU2F1 -0.001 0.042 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.13 0.15 -9999 0 -0.47 24 24
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 0.001 0.004 -9999 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0 0 -9999 0 -10000 0 0
CCL5 -0.013 0.098 -9999 0 -0.74 9 9
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.09 0.1 -9999 0 -0.43 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.093 0.079 -9999 0 -0.4 5 5
Syndecan-1/Syntenin -0.092 0.078 -9999 0 -0.4 4 4
MAPK3 -0.059 0.087 -9999 0 -0.48 1 1
HGF/MET -0.12 0.23 -9999 0 -0.56 111 111
TGFB1/TGF beta receptor Type II 0 0 -9999 0 -10000 0 0
BSG 0 0 -9999 0 -10000 0 0
keratinocyte migration -0.092 0.078 -9999 0 -0.39 5 5
Syndecan-1/RANTES -0.1 0.1 -9999 0 -0.52 12 12
Syndecan-1/CD147 -0.084 0.072 -9999 0 -0.43 2 2
Syndecan-1/Syntenin/PIP2 -0.089 0.075 -9999 0 -0.39 4 4
LAMA5 -0.001 0.033 -9999 0 -0.74 1 1
positive regulation of cell-cell adhesion -0.087 0.074 -9999 0 -0.38 4 4
MMP7 -0.039 0.15 -9999 0 -0.62 31 31
HGF -0.16 0.3 -9999 0 -0.74 108 108
Syndecan-1/CASK -0.086 0.094 -9999 0 -0.41 4 4
Syndecan-1/HGF/MET -0.17 0.17 -9999 0 -0.54 61 61
regulation of cell adhesion -0.05 0.086 -9999 0 -0.46 1 1
HPSE 0 0 -9999 0 -10000 0 0
positive regulation of cell migration -0.09 0.1 -9999 0 -0.43 4 4
SDC1 -0.09 0.1 -9999 0 -0.43 4 4
Syndecan-1/Collagen -0.09 0.1 -9999 0 -0.43 4 4
PPIB 0 0 -9999 0 -10000 0 0
MET -0.004 0.053 -9999 0 -0.68 3 3
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.032 0.13 -9999 0 -0.57 28 28
MAPK1 -0.059 0.087 -9999 0 -0.48 1 1
homophilic cell adhesion -0.089 0.1 -9999 0 -0.42 4 4
MMP1 -0.36 0.28 -9999 0 -0.57 310 310
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.012 0.081 -9999 0 -0.56 11 11
AKT1 -0.012 0.2 -9999 0 -0.65 28 28
PTK2B -0.06 0.26 -9999 0 -0.89 31 31
VEGFR2 homodimer/Frs2 -0.12 0.27 -9999 0 -0.99 28 28
CAV1 -0.2 0.33 -9999 0 -0.74 137 137
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.11 0.25 -9999 0 -0.93 28 28
endothelial cell proliferation -0.009 0.2 -9999 0 -0.62 30 30
mol:Ca2+ -0.054 0.24 -9999 0 -0.84 28 28
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.1 0.23 -9999 0 -0.88 28 28
RP11-342D11.1 -0.061 0.24 -9999 0 -0.84 28 28
CDH5 -0.15 0.3 -9999 0 -0.74 102 102
VEGFA homodimer 0 0 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.004 0.057 -9999 0 -0.74 3 3
HRAS/GDP -0.08 0.19 -9999 0 -0.71 28 28
SH2D2A -0.001 0.033 -9999 0 -0.74 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.077 0.18 -9999 0 -0.67 29 29
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.11 0.25 -9999 0 -0.93 28 28
VEGFR1 homodimer 0 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.09 0.21 -9999 0 -0.81 28 28
GRB10 -0.054 0.24 -9999 0 -0.84 28 28
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.17 0.32 -9999 0 -0.95 57 57
HRAS 0 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.057 0.13 -9999 0 -0.46 31 31
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.098 0.23 -9999 0 -0.86 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.038 0.16 -9999 0 -0.74 26 26
Nck/Pak -0.001 0.019 -9999 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.11 0.25 -9999 0 -0.94 28 28
mol:GDP -0.087 0.2 -9999 0 -0.77 28 28
mol:NADP -0.01 0.18 -9999 0 -0.56 29 29
eNOS/Hsp90 -0.005 0.17 -9999 0 -0.52 29 29
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 -0.056 0.24 -9999 0 -0.86 28 28
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0 0 -9999 0 -10000 0 0
VEGFA 0 0 -9999 0 -10000 0 0
VEGFC -0.003 0.046 -9999 0 -0.74 2 2
FAK1/Vinculin -0.045 0.25 -9999 0 -0.85 31 31
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.26 -9999 0 -0.96 31 31
PTPN6 0 0 -9999 0 -10000 0 0
EPAS1 -0.13 0.29 -9999 0 -0.71 95 95
mol:L-citrulline -0.01 0.18 -9999 0 -0.56 29 29
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.1 0.23 -9999 0 -0.88 28 28
VEGFR2 homodimer/VEGFA homodimer -0.11 0.25 -9999 0 -0.94 28 28
VEGFR2/3 heterodimer -0.14 0.31 -9999 0 -0.96 42 42
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 -0.053 0.25 -9999 0 -0.87 28 28
VEGFR2 homodimer -0.11 0.31 -9999 0 -0.7 95 95
FLT1 0 0 -9999 0 -10000 0 0
NEDD4 -0.001 0.033 -9999 0 -0.74 1 1
MAPK3 -0.048 0.23 -9999 0 -0.78 30 30
MAPK1 -0.048 0.23 -9999 0 -0.78 30 30
VEGFA145/NRP2 -0.004 0.049 -9999 0 -0.56 4 4
VEGFR1/2 heterodimer -0.12 0.27 -9999 0 -0.99 28 28
KDR -0.11 0.31 -9999 0 -0.7 95 95
VEGFA165/NRP1/VEGFR2 homodimer -0.099 0.24 -9999 0 -0.9 28 28
SRC 0 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.049 0.24 -9999 0 -0.8 30 30
PI3K -0.09 0.21 -9999 0 -0.82 28 28
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.11 0.25 -9999 0 -0.93 28 28
FES -0.058 0.25 -9999 0 -0.89 28 28
GAB1 -0.094 0.22 -9999 0 -0.84 28 28
VEGFR2 homodimer/VEGFA homodimer/Src -0.11 0.25 -9999 0 -0.93 28 28
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.095 0.24 -9999 0 -0.57 63 63
VEGFR2 homodimer/VEGFA homodimer/Yes -0.11 0.25 -9999 0 -0.93 28 28
PI3K/GAB1 -0.013 0.2 -9999 0 -0.67 28 28
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.096 0.22 -9999 0 -0.86 28 28
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.13 0.29 -9999 0 -1.1 31 31
HSP90AA1 0 0 -9999 0 -10000 0 0
CDC42 -0.057 0.25 -9999 0 -0.88 28 28
actin cytoskeleton reorganization -0.11 0.24 -9999 0 -0.91 28 28
PTK2 -0.056 0.28 -9999 0 -0.95 31 31
EDG1 -0.061 0.24 -9999 0 -0.84 28 28
mol:DAG -0.056 0.24 -9999 0 -0.86 28 28
CaM/Ca2+ -0.088 0.21 -9999 0 -0.78 28 28
MAP2K3 -0.046 0.24 -9999 0 -0.82 28 28
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.1 0.24 -9999 0 -0.89 28 28
PLCG1 -0.057 0.25 -9999 0 -0.88 28 28
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.1 0.23 -9999 0 -0.88 28 28
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.11 0.25 -9999 0 -0.93 28 28
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.11 0.25 -9999 0 -0.93 28 28
cell migration -0.041 0.24 -9999 0 -0.75 31 31
mol:PI-3-4-5-P3 -0.083 0.19 -9999 0 -0.73 28 28
FYN -0.001 0.033 -9999 0 -0.74 1 1
VEGFB/NRP1 -0.091 0.21 -9999 0 -0.79 28 28
mol:NO -0.01 0.18 -9999 0 -0.56 29 29
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.08 0.19 -9999 0 -0.71 28 28
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.1 0.24 -9999 0 -0.89 28 28
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.016 0.11 -9999 0 -0.74 11 11
NOS3 -0.017 0.2 -9999 0 -0.65 29 29
VEGFR2 homodimer/VEGFA homodimer/Sck -0.11 0.25 -9999 0 -0.94 29 29
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.045 0.23 -9999 0 -0.8 29 29
PRKCB -0.065 0.26 -9999 0 -0.89 29 29
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.097 0.22 -9999 0 -0.85 28 28
VEGFR1/2 heterodimer/VEGFA homodimer -0.11 0.25 -9999 0 -0.93 28 28
VEGFA165/NRP2 -0.004 0.049 -9999 0 -0.56 4 4
MAPKKK cascade -0.08 0.19 -9999 0 -0.71 28 28
NRP2 -0.006 0.066 -9999 0 -0.74 4 4
VEGFC homodimer -0.003 0.046 -9999 0 -0.74 2 2
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.045 0.25 -9999 0 -0.85 31 31
MAP3K13 -0.057 0.25 -9999 0 -0.88 28 28
PDPK1 -0.014 0.19 -9999 0 -0.63 28 28
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.053 -9999 0 -0.42 8 8
Metarhodopsin II/Arrestin -0.001 0.023 -9999 0 -0.36 2 2
PDE6G/GNAT1/GTP -0.015 0.081 -9999 0 -0.43 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.009 0.072 -9999 0 -0.57 8 8
GRK1 -0.002 0.036 -9999 0 -0.57 2 2
CNG Channel -0.054 0.13 -9999 0 -0.6 7 7
mol:Na + -0.096 0.15 -9999 0 -0.53 23 23
mol:ADP -0.002 0.036 -9999 0 -0.57 2 2
RGS9-1/Gbeta5/R9AP -0.059 0.16 -9999 0 -0.49 60 60
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.098 0.15 -9999 0 -0.54 23 23
CNGB1 -0.051 0.16 -9999 0 -0.57 44 44
RDH5 -0.003 0.046 -9999 0 -0.74 2 2
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.091 0.14 -9999 0 -0.51 23 23
Na + (4 Units) -0.089 0.14 -9999 0 -0.49 23 23
RGS9 -0.078 0.23 -9999 0 -0.74 53 53
GNB1/GNGT1 -0.13 0.19 -9999 0 -0.42 157 157
GNAT1/GDP -0.055 0.14 -9999 0 -0.43 60 60
GUCY2D 0 0 -9999 0 -10000 0 0
GNGT1 -0.18 0.27 -9999 0 -0.57 156 156
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.031 0.11 -9999 0 -0.43 30 30
mol:11-cis-retinal -0.003 0.046 -9999 0 -0.74 2 2
mol:cGMP -0.081 0.13 -9999 0 -10000 0 0
GNB1 -0.001 0.033 -9999 0 -0.74 1 1
Rhodopsin -0.004 0.044 -9999 0 -0.49 4 4
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.007 0.063 -9999 0 -0.57 6 6
Metarhodopsin II -0.003 0.029 -9999 0 -0.32 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.086 0.14 -9999 0 -10000 0 0
RGS9BP -0.013 0.098 -9999 0 -0.74 9 9
Metarhodopsin II/Transducin -0.052 0.077 -9999 0 -0.37 2 2
GCAP Family/Ca ++ -0.088 0.14 -9999 0 -0.32 137 137
PDE6A/B -0.025 0.11 -9999 0 -0.54 23 23
mol:Pi -0.058 0.16 -9999 0 -0.49 60 60
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.1 0.15 -9999 0 -0.56 3 3
PDE6B -0.016 0.11 -9999 0 -0.72 11 11
PDE6A -0.017 0.11 -9999 0 -0.71 12 12
PDE6G -0.015 0.1 -9999 0 -0.74 10 10
RHO -0.002 0.036 -9999 0 -0.57 2 2
PDE6 -0.071 0.17 -9999 0 -0.8 11 11
GUCA1A -0.16 0.26 -9999 0 -0.57 137 137
GC2/GCAP Family -0.088 0.14 -9999 0 -10000 0 0
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0 0 -9999 0 -10000 0 0
ErbB4 signaling events

Figure 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
ErbB4/ErbB4/HBEGF/HBEGF -0.08 0.12 -10000 0 -0.52 19 19
epithelial cell differentiation -0.036 0.1 -10000 0 -0.56 10 10
ITCH 0.023 0.027 -10000 0 -10000 0 0
WWP1 -0.038 0.088 -10000 0 -10000 0 0
FYN -0.001 0.033 -10000 0 -0.74 1 1
EGFR -0.023 0.12 -10000 0 -0.63 18 18
PRL -0.009 0.072 -10000 0 -0.57 8 8
neuron projection morphogenesis 0.002 0.089 -10000 0 -10000 0 0
PTPRZ1 -0.38 0.27 -10000 0 -0.58 332 332
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.043 0.077 -10000 0 -0.48 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.057 0.097 -10000 0 -0.49 15 15
ADAM17 0.023 0.027 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.058 0.11 -10000 0 -0.49 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.18 0.22 -10000 0 -0.53 131 131
NCOR1 0 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.053 0.091 -10000 0 -0.55 8 8
GRIN2B -0.028 0.1 -10000 0 -0.52 8 8
ErbB4/ErbB2/betacellulin -0.072 0.13 -10000 0 -0.54 21 21
STAT1 0 0 -10000 0 -10000 0 0
HBEGF -0.026 0.14 -10000 0 -0.74 18 18
PRLR -0.04 0.16 -10000 0 -0.63 32 32
E4ICDs/ETO2 -0.071 0.1 -10000 0 -0.6 8 8
axon guidance 0.054 0.073 -10000 0 -10000 0 0
NEDD4 0.021 0.042 -10000 0 -0.71 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.036 0.13 -10000 0 -0.47 39 39
CBFA2T3 -0.012 0.092 -10000 0 -0.74 8 8
ErbB4/ErbB2/HBEGF -0.056 0.093 -10000 0 -0.53 8 8
MAPK3 -0.038 0.071 -10000 0 -10000 0 0
STAT1 (dimer) -0.064 0.079 -10000 0 -0.42 1 1
MAPK1 -0.038 0.071 -10000 0 -10000 0 0
JAK2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.053 0.088 -10000 0 -0.53 7 7
NRG1 0.013 0.1 -10000 0 -0.56 15 15
NRG3 -0.19 0.32 -10000 0 -0.74 130 130
NRG2 -0.078 0.23 -10000 0 -0.74 53 53
NRG4 -0.07 0.19 -10000 0 -0.57 61 61
heart development 0.054 0.073 -10000 0 -10000 0 0
neural crest cell migration -0.053 0.087 -10000 0 -0.52 7 7
ERBB2 0.029 0.032 -10000 0 -0.42 2 2
WWOX/E4ICDs -0.064 0.079 -10000 0 -0.43 1 1
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.1 0.14 -10000 0 -0.48 33 33
apoptosis 0.2 0.26 0.66 87 -10000 0 87
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.16 -10000 0 -0.53 53 53
ErbB4/ErbB2/epiregulin -0.12 0.18 -10000 0 -0.53 48 48
ErbB4/ErbB4/betacellulin/betacellulin -0.098 0.15 -10000 0 -0.55 38 38
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.085 0.14 -10000 0 -0.62 17 17
MDM2 -0.042 0.098 -10000 0 -0.43 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.041 0.081 -10000 0 -0.46 15 15
STAT5A 0.057 0.068 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.064 0.12 -10000 0 -0.62 12 12
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.058 0.072 -10000 0 -0.4 1 1
STAT5A (dimer) -0.039 0.11 -10000 0 -0.61 10 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.045 0.068 -10000 0 -10000 0 0
LRIG1 -0.001 0.033 -10000 0 -0.74 1 1
EREG -0.15 0.29 -10000 0 -0.72 104 104
BTC -0.056 0.2 -10000 0 -0.74 38 38
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.054 0.074 -10000 0 -10000 0 0
ERBB4 -0.076 0.098 -10000 0 -0.49 1 1
STAT5B 0 0 -10000 0 -10000 0 0
YAP1 -0.02 0.025 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.077 0.11 -10000 0 -0.6 2 2
glial cell differentiation 0.058 0.072 0.4 1 -10000 0 1
WWOX 0 0 -10000 0 -10000 0 0
cell proliferation -0.02 0.15 -10000 0 -0.72 7 7
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.25 0.35 -9999 0 -0.74 168 168
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0 0 -9999 0 -10000 0 0
TCEB1 0 0 -9999 0 -10000 0 0
HIF1A/p53 -0.01 0.03 -9999 0 -0.46 1 1
HIF1A -0.011 0.026 -9999 0 -10000 0 0
COPS5 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.27 0.29 -9999 0 -0.58 233 233
ARNT/IPAS -0.19 0.26 -9999 0 -0.56 168 168
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.009 0.022 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.009 0.022 -9999 0 -10000 0 0
PHD1-3/OS9 -0.047 0.11 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.007 0.017 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.009 0.022 -9999 0 -10000 0 0
EGLN3 -0.087 0.21 -9999 0 -0.57 76 76
EGLN2 0 0 -9999 0 -10000 0 0
EGLN1 0 0 -9999 0 -10000 0 0
TP53 -0.001 0.033 -9999 0 -0.74 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.14 0.14 -9999 0 -0.36 39 39
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0 0.13 -10000 0 -0.41 18 18
TBX21 -0.093 0.5 -10000 0 -1.4 57 57
B2M 0.006 0.058 -10000 0 -0.74 3 3
TYK2 0.016 0.017 -10000 0 -10000 0 0
IL12RB1 -0.033 0.19 -10000 0 -0.77 32 32
GADD45B -0.028 0.36 -10000 0 -1.1 38 38
IL12RB2 -0.046 0.18 -10000 0 -0.57 54 54
GADD45G -0.015 0.33 -10000 0 -1 31 31
natural killer cell activation 0.006 0.019 -10000 0 -10000 0 0
RELB -0.001 0.026 -10000 0 -0.57 1 1
RELA 0 0 -10000 0 -10000 0 0
IL18 0.009 0.059 -10000 0 -0.75 3 3
IL2RA -0.008 0.072 -10000 0 -0.66 6 6
IFNG -0.008 0.075 -10000 0 -0.68 6 6
STAT3 (dimer) -0.003 0.29 -10000 0 -0.84 35 35
HLA-DRB5 -0.062 0.22 -10000 0 -0.74 48 48
FASLG -0.047 0.41 -10000 0 -1.3 36 36
NF kappa B2 p52/RelB -0.13 0.3 -10000 0 -1 38 38
CD4 -0.013 0.13 -10000 0 -0.74 15 15
SOCS1 -0.001 0.033 -10000 0 -0.74 1 1
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D -0.006 0.11 -10000 0 -0.74 11 11
CD3E -0.003 0.1 -10000 0 -0.74 9 9
CD3G -0.037 0.18 -10000 0 -0.74 32 32
IL12Rbeta2/JAK2 -0.02 0.14 -10000 0 -0.41 54 54
CCL3 -0.027 0.35 -10000 0 -1.1 36 36
CCL4 -0.03 0.36 -10000 0 -1.1 33 33
HLA-A 0.009 0.034 -10000 0 -0.74 1 1
IL18/IL18R 0.019 0.14 -10000 0 -0.57 25 25
NOS2 -0.077 0.44 -10000 0 -1.3 50 50
IL12/IL12R/TYK2/JAK2/SPHK2 0.001 0.13 -10000 0 -0.4 20 20
IL1R1 -0.025 0.34 -10000 0 -1 36 36
IL4 -0.004 0.019 -10000 0 -10000 0 0
JAK2 0.016 0.017 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.03 0.31 -10000 0 -1.1 26 26
RAB7A 0.01 0.28 -10000 0 -0.79 33 33
lysosomal transport 0.014 0.26 -10000 0 -0.75 33 33
FOS -0.16 0.5 -10000 0 -1.3 81 81
STAT4 (dimer) -0.006 0.34 -10000 0 -0.96 39 39
STAT5A (dimer) -0.13 0.3 -10000 0 -1 40 40
GZMA -0.033 0.37 -10000 0 -1.3 29 29
GZMB -0.033 0.37 -10000 0 -1.2 35 35
HLX 0 0 -10000 0 -10000 0 0
LCK -0.036 0.39 -10000 0 -1.1 38 38
TCR/CD3/MHC II/CD4 -0.089 0.33 -10000 0 -0.9 50 50
IL2/IL2R -0.013 0.1 -10000 0 -0.69 8 8
MAPK14 -0.012 0.34 -10000 0 -0.99 37 37
CCR5 -0.023 0.35 -10000 0 -1.1 32 32
IL1B -0.001 0.12 -10000 0 -0.76 11 11
STAT6 0.018 0.1 -10000 0 -10000 0 0
STAT4 -0.012 0.092 -10000 0 -0.74 8 8
STAT3 0 0 -10000 0 -10000 0 0
STAT1 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B 0.017 0.016 -10000 0 -10000 0 0
CD8A 0 0.088 -10000 0 -0.74 7 7
CD8B -0.013 0.13 -10000 0 -0.7 17 17
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0 0.13 0.41 18 -10000 0 18
IL2RB -0.004 0.057 -10000 0 -0.74 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.003 0.3 -10000 0 -0.85 39 39
IL2RG -0.01 0.087 -10000 0 -0.74 7 7
IL12 0.017 0.08 -10000 0 -0.57 8 8
STAT5A 0 0 -10000 0 -10000 0 0
CD247 -0.008 0.12 -10000 0 -0.74 12 12
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.098 -10000 0 -0.75 8 8
IL12/IL12R/TYK2/JAK2 -0.051 0.44 -10000 0 -1.3 39 39
MAP2K3 -0.016 0.34 -10000 0 -1 37 37
RIPK2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.016 0.34 -10000 0 -1 37 37
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.059 0.22 -10000 0 -0.74 46 46
IL18RAP -0.018 0.15 -10000 0 -0.75 21 21
IL12Rbeta1/TYK2 -0.015 0.15 -10000 0 -0.59 32 32
EOMES -0.028 0.23 -10000 0 -1.4 13 13
STAT1 (dimer) -0.001 0.29 -10000 0 -0.82 35 35
T cell proliferation 0.008 0.25 -10000 0 -0.69 37 37
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.006 0.076 -10000 0 -0.75 5 5
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.1 0.22 -10000 0 -0.77 38 38
ATF2 0 0.31 -10000 0 -0.91 35 35
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.14 0.14 -9999 0 -0.66 4 4
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.11 -9999 0 -0.58 4 4
alphaV/beta3 Integrin/Osteopontin/Src -0.21 0.2 -9999 0 -0.4 255 255
AP1 -0.16 0.16 -9999 0 -0.61 33 33
ILK -0.14 0.17 -9999 0 -0.7 4 4
bone resorption -0.12 0.12 -9999 0 -0.59 5 5
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.14 0.14 -9999 0 -0.65 4 4
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.001 0.025 -9999 0 -0.56 1 1
alphaV/beta3 Integrin/Osteopontin -0.18 0.18 -9999 0 -0.58 11 11
MAP3K1 -0.14 0.18 -9999 0 -0.53 11 11
JUN 0 0 -9999 0 -10000 0 0
MAPK3 -0.12 0.17 -9999 0 -0.66 4 4
MAPK1 -0.12 0.17 -9999 0 -0.58 6 6
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.12 0.17 -9999 0 -0.6 6 6
ITGB3 -0.016 0.11 -9999 0 -0.73 11 11
NFKBIA -0.1 0.16 -9999 0 -0.64 4 4
FOS -0.09 0.24 -9999 0 -0.74 61 61
CD44 -0.001 0.033 -9999 0 -0.74 1 1
CHUK 0 0 -9999 0 -10000 0 0
PLAU -0.099 0.17 -9999 0 -0.57 8 8
NF kappa B1 p50/RelA -0.12 0.12 -9999 0 -0.56 4 4
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.012 0.081 -9999 0 -0.55 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.14 0.18 -9999 0 -0.57 8 8
VAV3 -0.12 0.17 -9999 0 -0.76 4 4
MAP3K14 -0.14 0.18 -9999 0 -0.52 11 11
ROCK2 0 0 -9999 0 -10000 0 0
SPP1 -0.29 0.28 -9999 0 -0.57 255 255
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.13 -9999 0 -0.7 4 4
MMP2 -0.1 0.17 -9999 0 -0.64 9 9
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.024 0.11 -10000 0 -0.45 27 27
ER alpha/Gai/GDP/Gbeta gamma -0.027 0.11 -10000 0 -0.46 25 25
AKT1 -0.007 0.18 -10000 0 -0.82 24 24
PIK3CA 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.011 0.18 -10000 0 -0.83 24 24
mol:Ca2+ -0.093 0.23 -10000 0 -0.48 124 124
IGF1R 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.023 0.1 -10000 0 -0.48 24 24
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.005 0.17 0.78 24 -10000 0 24
RhoA/GTP -0.017 0.076 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.029 0.12 -10000 0 -0.52 25 25
regulation of stress fiber formation -0.031 0.076 0.57 2 -10000 0 2
E2/ERA-ERB (dimer) -0.023 0.1 -10000 0 -0.48 24 24
KRAS 0 0 -10000 0 -10000 0 0
G13/GTP -0.021 0.095 -10000 0 -0.44 24 24
pseudopodium formation 0.031 0.076 -10000 0 -0.57 2 2
E2/ER alpha (dimer)/PELP1 -0.023 0.1 -10000 0 -0.48 24 24
GRB2 0 0 -10000 0 -10000 0 0
GNG2 -0.007 0.073 -10000 0 -0.74 5 5
GNAO1 -0.004 0.049 -10000 0 -0.63 3 3
HRAS 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.014 0.13 -10000 0 -0.54 25 25
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.024 0.11 -10000 0 -0.5 24 24
mol:NADP 0.014 0.13 -10000 0 -0.54 25 25
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.098 0.24 -10000 0 -0.5 124 124
IGF-1R heterotetramer 0 0 -10000 0 -10000 0 0
PLCB1 -0.13 0.23 -10000 0 -0.51 124 124
PLCB2 -0.13 0.23 -10000 0 -0.52 128 128
IGF1 -0.028 0.14 -10000 0 -0.73 19 19
mol:L-citrulline 0.014 0.13 -10000 0 -0.54 25 25
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.007 0.045 -10000 0 -0.67 1 1
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0 0 -10000 0 -10000 0 0
GNAQ -0.001 0.033 -10000 0 -0.74 1 1
ESR1 -0.035 0.16 -10000 0 -0.74 24 24
Gq family/GDP/Gbeta gamma -0.075 0.14 -10000 0 -0.81 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.018 0.074 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.029 0.12 -10000 0 -0.52 25 25
GNAZ -0.009 0.08 -10000 0 -0.74 6 6
E2/ER alpha (dimer) -0.027 0.12 -10000 0 -0.56 24 24
STRN 0 0 -10000 0 -10000 0 0
GNAL -0.004 0.057 -10000 0 -0.74 3 3
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.016 0 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.033 -10000 0 -0.74 1 1
HBEGF 0.013 0.12 -10000 0 -0.68 6 6
cAMP biosynthetic process -0.021 0.091 -10000 0 -0.4 26 26
SRC 0.018 0.11 -10000 0 -0.64 5 5
PI3K 0 0 -10000 0 -10000 0 0
GNB1 -0.001 0.033 -10000 0 -0.74 1 1
G13/GDP/Gbeta gamma -0.025 0.11 -10000 0 -0.48 24 24
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.032 0.11 -10000 0 -0.59 10 10
Gs family/GTP -0.021 0.093 -10000 0 -0.41 26 26
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation 0.015 0.13 -10000 0 -0.52 25 25
mol:DAG -0.098 0.24 -10000 0 -0.5 124 124
Gs family/GDP/Gbeta gamma -0.025 0.1 -10000 0 -0.45 24 24
MSN 0.031 0.082 -10000 0 -0.64 2 2
Gq family/GTP -0.14 0.24 -10000 0 -0.54 123 123
mol:PI-3-4-5-P3 -0.009 0.18 -10000 0 -0.79 24 24
NRAS 0 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.015 0.13 0.52 25 -10000 0 25
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.022 0.1 -10000 0 -0.47 24 24
NOS3 0.013 0.14 -10000 0 -0.57 25 25
GNA11 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.018 0.15 -10000 0 -0.63 24 24
E2/ER alpha (dimer)/PELP1/Src -0.03 0.12 -10000 0 -0.54 25 25
ruffle organization 0.031 0.076 -10000 0 -0.57 2 2
ROCK2 -0.016 0.07 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.74 123 123
GNA15 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
MMP9 0.008 0.12 -10000 0 -0.59 5 5
MMP2 0.022 0.12 -10000 0 -0.79 5 5
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.065 0.1 -10000 0 -0.37 4 4
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.56 153 153
NT3 (dimer)/TRKB -0.12 0.19 -10000 0 -0.54 39 39
SHC/Grb2/SOS1/GAB1/PI3K 0 0 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.093 0.24 -10000 0 -0.74 63 63
PIK3CA 0 0 -10000 0 -10000 0 0
DYNLT1 0 0 -10000 0 -10000 0 0
NTRK1 -0.007 0.073 -10000 0 -0.74 5 5
NTRK2 -0.14 0.26 -10000 0 -0.62 112 112
NTRK3 -0.22 0.34 -10000 0 -0.73 148 148
NT-4/5 (dimer)/TRKB -0.12 0.19 -10000 0 -0.54 39 39
neuron apoptosis 0.13 0.19 0.46 91 -10000 0 91
SHC 2-3/Grb2 -0.14 0.21 -10000 0 -0.63 47 47
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.056 0.1 -10000 0 -0.55 9 9
SHC3 -0.16 0.26 -10000 0 -0.68 90 90
STAT3 (dimer) -0.005 0.042 -10000 0 -0.37 6 6
NT3 (dimer)/TRKA -0.043 0.12 -10000 0 -0.37 57 57
RIN/GDP -0.045 0.092 -10000 0 -0.27 2 2
GIPC1 0 0 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
DNAJA3 -0.024 0.07 -10000 0 -0.46 3 3
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.014 0.11 -10000 0 -0.88 7 7
MAGED1 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.092 -10000 0 -0.74 8 8
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.035 0.12 -10000 0 -0.47 38 38
TRKA/NEDD4-2 -0.006 0.055 -10000 0 -0.56 5 5
ELMO1 -0.013 0.098 -10000 0 -0.74 9 9
RhoG/GTP/ELMO1/DOCK1 -0.009 0.064 -10000 0 -0.48 9 9
NGF -0.02 0.12 -10000 0 -0.7 14 14
HRAS 0 0 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.021 0.12 -10000 0 -0.74 14 14
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
DNM1 -0.002 0.036 -10000 0 -0.57 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.03 0.085 -10000 0 -0.41 12 12
mol:GDP -0.067 0.13 -10000 0 -0.39 4 4
NGF (dimer) -0.02 0.12 -10000 0 -0.7 14 14
RhoG/GDP -0.01 0.075 -10000 0 -0.56 9 9
RIT1/GDP -0.041 0.092 -10000 0 -0.28 1 1
TIAM1 -0.001 0.033 -10000 0 -0.74 1 1
PIK3R1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.14 0.23 -10000 0 -0.45 161 161
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.013 0.093 -10000 0 -0.7 9 9
RAP1/GDP -0.047 0.067 -10000 0 -10000 0 0
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.093 0.24 -10000 0 -0.74 63 63
ubiquitin-dependent protein catabolic process -0.017 0.087 -10000 0 -0.45 19 19
Schwann cell development -0.054 0.036 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.007 0.041 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.22 0.27 -10000 0 -0.72 77 77
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.049 0.076 -10000 0 -10000 0 0
STAT3 -0.005 0.042 -10000 0 -0.37 6 6
axon guidance -0.21 0.25 -10000 0 -0.68 77 77
MAPK3 -0.005 0.12 -10000 0 -0.43 35 35
MAPK1 -0.005 0.12 -10000 0 -0.43 35 35
CDC42/GDP -0.041 0.092 -10000 0 -0.27 2 2
NTF3 -0.013 0.094 -10000 0 -0.7 9 9
NTF4 -0.012 0.092 -10000 0 -0.74 8 8
NGF (dimer)/TRKA/FAIM -0.017 0.088 -10000 0 -0.46 19 19
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.27 0.2 -10000 0 -0.42 311 311
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.13 0.24 -10000 0 -0.48 155 155
RGS19 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.055 0.081 -10000 0 -10000 0 0
Rac1/GDP -0.041 0.092 -10000 0 -0.28 1 1
NGF (dimer)/TRKA/GRIT -0.018 0.089 -10000 0 -0.46 19 19
neuron projection morphogenesis 0.003 0.075 -10000 0 -0.47 1 1
NGF (dimer)/TRKA/NEDD4-2 -0.017 0.088 -10000 0 -0.46 19 19
MAP2K1 0.035 0 -10000 0 -10000 0 0
NGFR -0.049 0.16 -10000 0 -0.57 43 43
NGF (dimer)/TRKA/GIPC/GAIP -0.011 0.055 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.048 0.12 -10000 0 -0.66 16 16
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.006 0.055 -10000 0 -0.56 5 5
SQSTM1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.13 0.21 -10000 0 -0.5 83 83
NGF (dimer)/TRKA/p62/Atypical PKCs -0.015 0.074 -10000 0 -0.4 16 16
MATK -0.028 0.14 -10000 0 -0.74 19 19
NEDD4L 0 0 -10000 0 -10000 0 0
RAS family/GDP -0.043 0.064 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.026 0.076 -10000 0 -0.34 16 16
Rac1/GTP -0.17 0.13 -10000 0 -0.33 130 130
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.003 0.046 -9999 0 -0.74 2 2
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.086 0.18 -9999 0 -0.48 86 86
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.053 0.18 -9999 0 -0.43 86 86
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.033 0.13 -9999 0 -0.57 29 29
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.006 0.066 -9999 0 -0.74 4 4
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.002 0.032 -9999 0 -0.42 3 3
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.011 0.08 -9999 0 -0.57 10 10
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.15 0.25 -9999 0 -0.57 131 131
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.11 0.2 -9999 0 -0.46 115 115
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.093 0.14 -9999 0 -0.48 29 29
MAP1B -0.002 0.019 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.072 0.15 -9999 0 -0.62 3 3
RELN -0.13 0.28 -9999 0 -0.73 89 89
PAFAH/LIS1 -0.004 0.042 -9999 0 -0.48 4 4
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.069 0.11 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.062 0.12 -9999 0 -0.31 86 86
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.1 0.15 -9999 0 -0.51 29 29
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.02 0 -9999 0 -10000 0 0
PAFAH1B3 -0.006 0.061 -9999 0 -0.61 5 5
PAFAH1B2 0 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.001 0.012 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.087 0.14 -9999 0 -0.46 29 29
LRP8 -0.003 0.044 -9999 0 -0.57 3 3
NDEL1/Katanin 60 -0.093 0.14 -9999 0 -0.48 29 29
P39/CDK5 -0.14 0.19 -9999 0 -0.66 27 27
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.042 0.16 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.089 0.17 -9999 0 -0.42 89 89
RELN/VLDLR -0.079 0.17 -9999 0 -0.44 87 87
CDC42 0 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.013 0.03 -10000 0 -10000 0 0
oxygen homeostasis -0.01 0.013 -10000 0 -10000 0 0
TCEB2 0 0 -10000 0 -10000 0 0
TCEB1 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.1 0.12 -10000 0 -0.45 13 13
EPO -0.15 0.22 -10000 0 -0.67 17 17
FIH (dimer) 0.003 0.009 -10000 0 -10000 0 0
APEX1 0.004 0.013 -10000 0 -10000 0 0
SERPINE1 -0.2 0.25 -10000 0 -0.8 18 18
FLT1 -0.038 0.16 -10000 0 -1 12 12
ADORA2A -0.19 0.24 -10000 0 -0.72 24 24
germ cell development -0.2 0.24 -10000 0 -0.77 21 21
SLC11A2 -0.2 0.25 -10000 0 -0.79 18 18
BHLHE40 -0.2 0.25 -10000 0 -0.8 17 17
HIF1AN 0.003 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.14 0.16 -10000 0 -0.49 44 44
ETS1 0.004 0.12 -10000 0 -0.75 12 12
CITED2 -0.037 0.18 -10000 0 -1.3 10 10
KDR -0.096 0.34 -10000 0 -1.3 34 34
PGK1 -0.2 0.25 -10000 0 -0.8 17 17
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.21 0.3 -10000 0 -0.83 40 40
EPAS1 -0.12 0.16 -10000 0 -0.41 77 77
SP1 0.017 0 -10000 0 -10000 0 0
ABCG2 -0.25 0.34 -10000 0 -0.96 64 64
EFNA1 -0.2 0.25 -10000 0 -0.8 17 17
FXN -0.19 0.24 -10000 0 -0.77 17 17
POU5F1 -0.2 0.25 -10000 0 -0.81 21 21
neuron apoptosis 0.21 0.29 0.8 40 -10000 0 40
EP300 0 0 -10000 0 -10000 0 0
EGLN3 -0.087 0.21 -10000 0 -0.59 76 76
EGLN2 0.003 0.01 -10000 0 -10000 0 0
EGLN1 0.003 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.004 0.013 -10000 0 -10000 0 0
SLC2A1 -0.38 0.29 -10000 0 -0.8 78 78
TWIST1 -0.27 0.31 -10000 0 -0.76 70 70
ELK1 0.016 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.14 0.16 -10000 0 -0.54 17 17
VEGFA -0.2 0.25 -10000 0 -0.8 17 17
CREBBP 0 0 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.045 0.091 -9999 0 -0.68 2 2
FZD6 0 0 -9999 0 -10000 0 0
WNT6 -0.094 0.21 -9999 0 -0.57 82 82
WNT4 -0.01 0.083 -9999 0 -0.66 8 8
FZD3 0 0 -9999 0 -10000 0 0
WNT5A -0.014 0.093 -9999 0 -0.6 12 12
WNT11 -0.038 0.16 -9999 0 -0.68 28 28
Ephrin A reverse 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
MAPKKK cascade -0.018 0.079 -9999 0 -0.37 24 24
EFNA5 -0.004 0.057 -9999 0 -0.74 3 3
FYN 0.002 0.078 -9999 0 -0.33 25 25
neuron projection morphogenesis -0.018 0.079 -9999 0 -0.37 24 24
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.018 0.08 -9999 0 -0.37 24 24
EPHA5 -0.024 0.12 -9999 0 -0.57 21 21
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.041 0.14 -10000 0 -0.64 21 21
FYN 0.001 0.23 -10000 0 -0.85 28 28
LAT/GRAP2/SLP76 -0.056 0.18 -10000 0 -0.66 35 35
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
AKT1 0.022 0.14 -10000 0 -0.47 32 32
B2M 0.006 0.058 -10000 0 -0.74 3 3
IKBKG -0.01 0.031 -10000 0 -0.18 1 1
MAP3K8 -0.003 0.046 -10000 0 -0.74 2 2
mol:Ca2+ -0.006 0.021 -10000 0 -0.13 7 7
integrin-mediated signaling pathway -0.001 0.021 -10000 0 -0.48 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.008 0.21 -10000 0 -0.73 32 32
TRPV6 -0.017 0.11 -10000 0 -0.7 13 13
CD28 0.002 0.075 -10000 0 -0.74 5 5
SHC1 0.005 0.21 -10000 0 -0.78 27 27
receptor internalization -0.011 0.23 -10000 0 -0.81 32 32
PRF1 -0.037 0.32 -10000 0 -1.2 32 32
KRAS 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
COT/AKT1 0.026 0.11 -10000 0 -0.4 24 24
LAT 0.005 0.21 -10000 0 -0.77 28 28
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D -0.006 0.11 -10000 0 -0.75 11 11
CD3E -0.003 0.1 -10000 0 -0.75 9 9
CD3G -0.037 0.18 -10000 0 -0.74 32 32
RASGRP2 -0.013 0.066 -10000 0 -0.18 68 68
RASGRP1 0.022 0.15 -10000 0 -0.49 28 28
HLA-A 0.009 0.034 -10000 0 -0.75 1 1
RASSF5 -0.001 0.033 -10000 0 -0.74 1 1
RAP1A/GTP/RAPL -0.001 0.022 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.05 -10000 0 -0.13 22 22
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.018 0.055 -10000 0 -0.25 14 14
PRKCA -0.024 0.077 -10000 0 -0.31 25 25
GRAP2 -0.044 0.18 -10000 0 -0.74 30 30
mol:IP3 -0.036 0.13 0.25 9 -0.49 29 38
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.017 0.23 -10000 0 -0.83 28 28
ORAI1 0.009 0.061 0.35 13 -0.57 1 14
CSK 0.003 0.21 -10000 0 -0.8 27 27
B7 family/CD28 -0.064 0.22 -10000 0 -0.85 32 32
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.01 0.25 -10000 0 -0.94 28 28
PTPN6 0 0.21 -10000 0 -0.81 27 27
VAV1 0.002 0.21 -10000 0 -0.81 27 27
Monovalent TCR/CD3 -0.025 0.21 -10000 0 -0.62 39 39
CBL 0 0 -10000 0 -10000 0 0
LCK -0.002 0.23 -10000 0 -0.88 27 27
PAG1 0 0.22 -10000 0 -0.81 27 27
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.011 0.25 -10000 0 -0.94 28 28
CD80 -0.016 0.14 -10000 0 -0.74 17 17
CD86 0.002 0.075 -10000 0 -0.74 5 5
PDK1/CARD11/BCL10/MALT1 -0.021 0.066 -10000 0 -0.29 18 18
HRAS 0 0 -10000 0 -10000 0 0
GO:0035030 0.005 0.19 -10000 0 -0.66 32 32
CD8A 0 0.089 -10000 0 -0.75 7 7
CD8B -0.013 0.13 -10000 0 -0.7 17 17
PTPRC -0.04 0.19 -10000 0 -0.74 33 33
PDK1/PKC theta 0.016 0.18 -10000 0 -0.6 32 32
CSK/PAG1 0.006 0.2 -10000 0 -0.83 23 23
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.004 0.058 -10000 0 -0.72 3 3
GRAP2/SLP76 -0.066 0.21 -10000 0 -0.78 35 35
STIM1 0.006 0.03 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.059 -10000 0 -0.18 14 14
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.016 0.26 -10000 0 -0.91 32 32
mol:DAG -0.034 0.11 -10000 0 -0.43 29 29
RAP1A/GDP 0.01 0.022 -10000 0 -10000 0 0
PLCG1 0.001 0.003 -10000 0 -10000 0 0
CD247 -0.008 0.12 -10000 0 -0.75 12 12
cytotoxic T cell degranulation -0.03 0.29 -10000 0 -1.1 32 32
RAP1A/GTP -0.009 0.022 -10000 0 -0.071 1 1
mol:PI-3-4-5-P3 0.016 0.17 -10000 0 -0.57 32 32
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.047 0.17 0.27 9 -0.65 29 38
NRAS 0 0 -10000 0 -10000 0 0
ZAP70 -0.011 0.093 -10000 0 -0.74 8 8
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.052 0.16 -10000 0 -0.64 32 32
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.025 0.13 -10000 0 -0.65 19 19
CARD11 -0.004 0.049 -10000 0 -0.63 3 3
PRKCB -0.035 0.1 -10000 0 -0.37 36 36
PRKCE -0.024 0.075 -10000 0 -0.3 25 25
PRKCQ 0.004 0.21 -10000 0 -0.68 36 36
LCP2 -0.008 0.08 -10000 0 -0.74 6 6
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.025 0.12 -10000 0 -0.39 32 32
IKK complex 0.035 0.047 -10000 0 -0.13 11 11
RAS family/GDP -0.003 0.008 -10000 0 -10000 0 0
MAP3K14 0.031 0.089 -10000 0 -0.31 20 20
PDPK1 0.025 0.13 -10000 0 -0.47 27 27
TCR/CD3/MHC I/CD8/Fyn -0.013 0.25 -10000 0 -0.94 27 27
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.003 0.087 -9999 0 -0.73 7 7
PDGF/PDGFRA/CRKL -0.008 0.063 -9999 0 -0.53 7 7
positive regulation of JUN kinase activity -0.006 0.047 -9999 0 -0.42 6 6
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.095 0.21 -9999 0 -0.56 83 83
AP1 -0.14 0.36 -9999 0 -1.1 61 61
mol:IP3 0.008 0.07 -9999 0 -0.55 7 7
PLCG1 0.008 0.07 -9999 0 -0.55 7 7
PDGF/PDGFRA/alphaV Integrin -0.008 0.063 -9999 0 -0.53 7 7
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.008 0.07 -9999 0 -0.55 7 7
CAV3 -0.11 0.26 -9999 0 -0.74 76 76
CAV1 -0.2 0.33 -9999 0 -0.74 137 137
SHC/Grb2/SOS1 -0.006 0.048 -9999 0 -0.42 6 6
PDGF/PDGFRA/Shf -0.008 0.063 -9999 0 -0.53 7 7
FOS -0.096 0.36 -9999 0 -1.1 61 61
JUN -0.008 0.02 -9999 0 -10000 0 0
oligodendrocyte development -0.008 0.063 -9999 0 -0.53 7 7
GRB2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG 0.008 0.07 -9999 0 -0.55 7 7
PDGF/PDGFRA -0.003 0.087 -9999 0 -0.72 7 7
actin cytoskeleton reorganization -0.008 0.063 -9999 0 -0.53 7 7
SRF 0.021 0.009 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.006 0.053 -9999 0 -0.47 6 6
PDGF/PDGFRA/Crk/C3G -0.006 0.053 -9999 0 -0.47 6 6
JAK1 0.011 0.065 -9999 0 -0.53 7 7
ELK1/SRF -0.007 0.048 -9999 0 -0.43 6 6
SHB 0 0 -9999 0 -10000 0 0
SHF 0 0 -9999 0 -10000 0 0
CSNK2A1 0.007 0.019 -9999 0 -10000 0 0
GO:0007205 0.008 0.072 -9999 0 -0.56 7 7
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.006 0.047 -9999 0 -0.42 6 6
PDGF/PDGFRA/SHB -0.008 0.063 -9999 0 -0.53 7 7
PDGF/PDGFRA/Caveolin-1 -0.16 0.26 -9999 0 -0.58 141 141
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 0.011 0.071 -9999 0 -0.53 6 6
PIK3CA 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.008 0.063 -9999 0 -0.53 7 7
JAK-STAT cascade 0.011 0.065 -9999 0 -0.53 7 7
cell proliferation -0.008 0.063 -9999 0 -0.53 7 7
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.003 0.04 -10000 0 -0.51 3 3
CRKL -0.027 0.12 -10000 0 -0.37 4 4
mol:PIP3 -0.014 0.043 0.66 2 -10000 0 2
AKT1 0.004 0.028 0.43 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.018 0.11 -10000 0 -0.4 2 2
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.1 0.2 -10000 0 -0.48 110 110
MAP3K5 -0.011 0.11 -10000 0 -0.44 4 4
HGF/MET/CIN85/CBL/ENDOPHILINS -0.097 0.18 -10000 0 -0.44 110 110
AP1 -0.061 0.16 -10000 0 -0.5 61 61
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.079 0.24 -10000 0 -0.73 61 61
STAT3 (dimer) -0.035 0.14 -10000 0 -10000 0 0
GAB1/CRKL/SHP2/PI3K -0.045 0.086 -10000 0 -10000 0 0
INPP5D -0.001 0.033 -10000 0 -0.74 1 1
CBL/CRK -0.02 0.11 -10000 0 -0.4 2 2
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.003 0.046 -10000 0 -0.74 2 2
ELK1 -0.004 0.022 -10000 0 -0.24 3 3
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.04 0.076 -10000 0 -0.46 2 2
PAK1 0.01 0.029 0.4 2 -10000 0 2
HGF/MET/RANBP10 -0.1 0.2 -10000 0 -0.48 110 110
HRAS -0.081 0.16 -10000 0 -0.59 4 4
DOCK1 -0.018 0.11 -10000 0 -0.4 2 2
GAB1 -0.035 0.12 -10000 0 -0.39 4 4
CRK -0.027 0.12 -10000 0 -0.43 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.12 0.22 -10000 0 -0.54 110 110
JUN 0 0 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.055 0.1 -10000 0 -0.25 110 110
PIK3R1 0 0 -10000 0 -10000 0 0
cell morphogenesis -0.012 0.14 -10000 0 -10000 0 0
GRB2/SHC -0.046 0.088 -10000 0 -0.5 2 2
FOS -0.09 0.24 -10000 0 -0.74 61 61
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.004 0.022 -10000 0 -0.24 3 3
HGF/MET/MUC20 -0.11 0.2 -10000 0 -0.48 111 111
cell migration -0.045 0.087 -10000 0 -0.49 2 2
GRB2 0 0 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.003 0.04 -10000 0 -0.51 3 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.067 0.13 -10000 0 -10000 0 0
MET/MUC20 -0.003 0.04 -10000 0 -0.52 3 3
RAP1B -0.01 0.11 -10000 0 -0.37 2 2
RAP1A -0.01 0.11 -10000 0 -0.37 2 2
HGF/MET/RANBP9 -0.1 0.2 -10000 0 -0.48 110 110
RAF1 -0.045 0.16 -10000 0 -0.55 4 4
STAT3 -0.064 0.12 -10000 0 -10000 0 0
cell proliferation -0.049 0.19 -10000 0 -0.52 4 4
RPS6KB1 -0.019 0.036 -10000 0 -10000 0 0
MAPK3 -0.007 0.019 -10000 0 -10000 0 0
MAPK1 -0.007 0.019 -10000 0 -0.23 2 2
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.095 -10000 0 -0.39 1 1
SRC -0.032 0.13 -10000 0 -10000 0 0
PI3K -0.046 0.088 -10000 0 -0.5 2 2
MET/Glomulin -0.003 0.036 -10000 0 -0.46 3 3
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.035 0.15 -10000 0 -0.59 2 2
MET -0.004 0.053 -10000 0 -0.68 3 3
MAP4K1 -0.019 0.12 -10000 0 -0.47 4 4
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.035 0.15 -10000 0 -0.59 2 2
BAD 0.011 0.025 0.4 2 -10000 0 2
MAP2K4 -0.003 0.1 -10000 0 -0.45 2 2
SHP2/GRB2/SOS1/GAB1 -0.048 0.091 -10000 0 -0.44 2 2
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 -0.003 0.046 -10000 0 -0.74 2 2
HGS -0.049 0.095 -10000 0 -0.42 4 4
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.16 0.3 -10000 0 -0.74 108 108
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ -0.003 0.046 -10000 0 -0.74 2 2
NCK/PLCgamma1 -0.052 0.099 -10000 0 -0.52 2 2
PDPK1 -0.004 0.032 0.5 2 -10000 0 2
HGF/MET/SHIP -0.11 0.2 -10000 0 -0.48 110 110
p75(NTR)-mediated signaling

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.007 0.06 -9999 0 -0.56 6 6
Necdin/E2F1 -0.009 0.07 -9999 0 -0.56 8 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.04 0.11 -9999 0 -0.7 3 3
NGF (dimer)/p75(NTR)/BEX1 -0.099 0.2 -9999 0 -0.45 111 111
NT-4/5 (dimer)/p75(NTR) -0.044 0.13 -9999 0 -0.44 51 51
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
AKT1 -0.004 0.12 -9999 0 -0.48 11 11
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.093 0.24 -9999 0 -0.74 63 63
MGDIs/NGR/p75(NTR)/LINGO1 -0.061 0.14 -9999 0 -0.69 7 7
FURIN 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.095 0.19 -9999 0 -0.51 68 68
LINGO1 -0.051 0.16 -9999 0 -0.57 44 44
Sortilin/TRAF6/NRIF -0.004 0.038 -9999 0 -10000 0 0
proBDNF (dimer) -0.093 0.24 -9999 0 -0.74 63 63
NTRK1 -0.007 0.073 -9999 0 -0.74 5 5
RTN4R -0.003 0.042 -9999 0 -0.66 2 2
neuron apoptosis -0.031 0.16 -9999 0 -0.6 10 10
IRAK1 0 0 -9999 0 -10000 0 0
SHC1 -0.021 0.13 -9999 0 -0.56 11 11
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.043 0.12 -9999 0 -0.48 17 17
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.05 0.13 -9999 0 -0.49 24 24
Mammalian IAPs/DIABLO -0.005 0.047 -9999 0 -0.43 6 6
proNGF (dimer) -0.02 0.12 -9999 0 -0.7 14 14
MAGED1 0 0 -9999 0 -10000 0 0
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.092 -9999 0 -0.74 8 8
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.035 0.11 -9999 0 -0.48 11 11
NGF -0.02 0.12 -9999 0 -0.7 14 14
cell cycle arrest -0.023 0.14 -9999 0 -0.52 8 8
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.02 0.064 -9999 0 -0.47 3 3
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.037 0.11 -9999 0 -0.48 8 8
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.042 0.13 -9999 0 -0.56 11 11
PSENEN 0 0 -9999 0 -10000 0 0
mol:ceramide -0.017 0.13 -9999 0 -0.48 17 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.015 0.049 -9999 0 -0.37 3 3
p75(NTR)/beta APP -0.036 0.12 -9999 0 -0.42 43 43
BEX1 -0.091 0.23 -9999 0 -0.68 67 67
mol:GDP -0.029 0.13 -9999 0 -0.4 54 54
NGF (dimer) -0.036 0.12 -9999 0 -0.51 19 19
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.055 0.13 -9999 0 -0.63 7 7
PIK3R1 0 0 -9999 0 -10000 0 0
RAC1/GTP -0.036 0.11 -9999 0 -0.49 11 11
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.042 0.13 -9999 0 -0.56 11 11
RHOB 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0 0 -9999 0 -10000 0 0
NT3 (dimer) -0.013 0.093 -9999 0 -0.7 9 9
TP53 -0.075 0.15 -9999 0 -0.67 7 7
PRDM4 -0.017 0.13 -9999 0 -0.48 17 17
BDNF (dimer) -0.27 0.24 -9999 0 -0.65 86 86
PIK3CA 0 0 -9999 0 -10000 0 0
SORT1 -0.009 0.08 -9999 0 -0.74 6 6
activation of caspase activity -0.039 0.11 -9999 0 -0.68 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.043 0.12 -9999 0 -0.48 17 17
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.014 0.14 -9999 0 -0.56 9 9
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.017 0.13 -9999 0 -0.48 17 17
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.048 0.14 -9999 0 -0.53 17 17
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.045 0.13 -9999 0 -0.43 52 52
MAPK8 -0.01 0.14 -9999 0 -0.55 7 7
MAPK9 -0.01 0.14 -9999 0 -0.55 7 7
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.013 0.094 -9999 0 -0.7 9 9
NTF4 -0.012 0.092 -9999 0 -0.74 8 8
NDN -0.012 0.092 -9999 0 -0.74 8 8
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.032 0.097 -9999 0 -0.65 3 3
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.047 -9999 0 -0.43 6 6
RhoA-B-C/GTP -0.042 0.12 -9999 0 -0.56 11 11
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.08 0.16 -9999 0 -0.71 7 7
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.086 0.17 -9999 0 -0.46 68 68
PRKACB 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.07 0.18 -9999 0 -0.56 63 63
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.009 0.08 -9999 0 -0.74 6 6
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.015 0.13 -9999 0 -0.5 11 11
BAD -0.003 0.14 -9999 0 -0.54 7 7
RIPK2 0 0 -9999 0 -10000 0 0
NGFR -0.049 0.16 -9999 0 -0.57 43 43
CYCS -0.009 0.12 -9999 0 -0.57 5 5
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.038 0.11 -9999 0 -0.51 11 11
BCL2L11 -0.003 0.14 -9999 0 -0.54 7 7
BDNF (dimer)/p75(NTR) -0.1 0.22 -9999 0 -0.52 100 100
PI3K -0.038 0.11 -9999 0 -0.51 11 11
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.043 0.12 -9999 0 -0.48 17 17
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.05 0.15 -9999 0 -0.46 54 54
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.043 0.12 -9999 0 -0.48 17 17
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG -0.006 0.057 -9999 0 -0.57 5 5
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.084 0.17 -9999 0 -0.62 18 18
SQSTM1 0 0 -9999 0 -10000 0 0
NGFRAP1 0 0 -9999 0 -10000 0 0
CASP3 0 0.13 -9999 0 -0.49 7 7
E2F1 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.019 0.075 -9999 0 -0.51 3 3
NGF (dimer)/TRKA -0.02 0.1 -9999 0 -0.53 19 19
MMP7 -0.039 0.15 -9999 0 -0.62 31 31
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.04 0.11 -9999 0 -0.7 3 3
MMP3 -0.34 0.28 -9999 0 -0.57 300 300
APAF-1/Caspase 9 -0.031 0.087 -9999 0 -0.54 4 4
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.007 0.013 -10000 0 -10000 0 0
HSPA8 0 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.027 0.11 -10000 0 -0.52 24 24
AKT1 0.006 0.022 -10000 0 -10000 0 0
GSC -0.037 0.14 -10000 0 -10000 0 0
NKX2-5 -0.3 0.29 -10000 0 -0.57 258 258
muscle cell differentiation 0.094 0.1 0.43 9 -10000 0 9
SMAD2-3/SMAD4/SP1 -0.009 0.037 -10000 0 -10000 0 0
SMAD4 0.016 0.027 -10000 0 -10000 0 0
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.01 0.035 -10000 0 -0.46 1 1
SMAD3/SMAD4/VDR 0.009 0.032 -10000 0 -10000 0 0
MYC 0.008 0.025 -10000 0 -10000 0 0
CDKN2B -0.1 0.43 -10000 0 -1.5 46 46
AP1 -0.038 0.12 -10000 0 -0.4 12 12
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.031 0.09 -10000 0 -0.42 4 4
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.044 0.16 -10000 0 -0.58 42 42
SMAD3/SMAD4/GR -0.003 0.015 -10000 0 -10000 0 0
GATA3 -0.025 0.13 -10000 0 -0.71 17 17
SKI/SIN3/HDAC complex/NCoR1 0 0.003 -10000 0 -10000 0 0
MEF2C/TIF2 -0.17 0.2 -10000 0 -0.7 34 34
endothelial cell migration -0.011 0.068 1.4 1 -10000 0 1
MAX 0 0.003 -10000 0 -10000 0 0
RBBP7 0 0.001 -10000 0 -10000 0 0
RBBP4 0 0.001 -10000 0 -10000 0 0
RUNX2 0 0 -10000 0 -10000 0 0
RUNX3 0 0 -10000 0 -10000 0 0
RUNX1 0 0 -10000 0 -10000 0 0
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 0 0.003 -10000 0 -10000 0 0
VDR -0.001 0.033 -10000 0 -0.74 1 1
CDKN1A 0.058 0.043 -10000 0 -10000 0 0
KAT2B 0.002 0.034 -10000 0 -0.74 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.045 0.11 -10000 0 -0.48 12 12
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0.001 -10000 0 -10000 0 0
SERPINE1 0.01 0.069 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 -0.001 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.003 0.039 -10000 0 -0.57 2 2
SAP30 0 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.016 0.032 -10000 0 -10000 0 0
JUN 0.004 0.14 -10000 0 -0.39 11 11
SMAD3/SMAD4/IRF7 -0.004 0.038 -10000 0 -0.54 2 2
TFE3 0.016 0.002 -10000 0 -10000 0 0
COL1A2 0.006 0.052 -10000 0 -0.4 1 1
mesenchymal cell differentiation 0.001 0.017 -10000 0 -10000 0 0
DLX1 -0.34 0.28 -10000 0 -0.57 292 292
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.076 0.24 -10000 0 -0.73 61 61
SMAD3/SMAD4/Max -0.003 0.015 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0 0.015 -10000 0 -10000 0 0
ZBTB17 0.006 0.019 -10000 0 -10000 0 0
LAMC1 0.047 0.029 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.017 -10000 0 -10000 0 0
IRF7 -0.003 0.047 -10000 0 -0.74 2 2
ESR1 -0.035 0.16 -10000 0 -0.74 24 24
HNF4A -0.009 0.072 -10000 0 -0.57 8 8
MEF2C -0.17 0.23 -10000 0 -0.74 34 34
SMAD2-3/SMAD4 -0.01 0.031 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.011 0.022 -10000 0 -10000 0 0
IGHV3OR16-13 0 0.001 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.006 0.01 -10000 0 -10000 0 0
SKIL 0 0 -10000 0 -10000 0 0
HDAC1 0 0.001 -10000 0 -10000 0 0
HDAC2 0 0.001 -10000 0 -10000 0 0
SNIP1 -0.001 0.026 -10000 0 -0.58 1 1
GCN5L2 0.003 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.003 0.022 -10000 0 -10000 0 0
MSG1/HSC70 -0.002 0.031 -10000 0 -0.49 2 2
SMAD2 0.003 0.029 -10000 0 -10000 0 0
SMAD3 0.019 0.022 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.038 0.027 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.014 0.023 -10000 0 -0.42 1 1
NCOR1 0 0.001 -10000 0 -10000 0 0
NCOA2 -0.001 0.033 -10000 0 -0.74 1 1
NCOA1 0 0 -10000 0 -10000 0 0
MYOD/E2A -0.059 0.14 -10000 0 -0.42 71 71
SMAD2-3/SMAD4/SP1/MIZ-1 0.018 0.055 -10000 0 -10000 0 0
IFNB1 0.034 0.048 -10000 0 -0.48 3 3
SMAD3/SMAD4/MEF2C -0.17 0.2 -10000 0 -0.71 34 34
CITED1 -0.003 0.042 -10000 0 -0.66 2 2
SMAD2-3/SMAD4/ARC105 -0.008 0.025 -10000 0 -10000 0 0
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.008 0.16 -10000 0 -0.48 46 46
RUNX1-3/PEBPB2 0 0 -10000 0 -10000 0 0
SMAD7 -0.025 0.097 -10000 0 -10000 0 0
MYC/MIZ-1 0.014 0.044 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.076 0.29 10 -0.45 1 11
IL10 0.026 0.11 -10000 0 -0.71 5 5
PIASy/HDAC complex 0.007 0.006 -10000 0 -10000 0 0
PIAS3 0.004 0.007 -10000 0 -10000 0 0
CDK2 0.006 0.01 -10000 0 -10000 0 0
IL5 0.023 0.095 -10000 0 -0.52 4 4
CDK4 0.005 0.028 -10000 0 -0.58 1 1
PIAS4 0.007 0.006 -10000 0 -10000 0 0
ATF3 -0.003 0.046 -10000 0 -0.74 2 2
SMAD3/SMAD4/SP1 0.001 0.027 -10000 0 -10000 0 0
FOXG1 -0.064 0.18 -10000 0 -0.58 55 55
FOXO3 0.015 0.029 -10000 0 -10000 0 0
FOXO1 0.015 0.029 -10000 0 -10000 0 0
FOXO4 0.015 0.029 -10000 0 -10000 0 0
heart looping -0.16 0.22 -10000 0 -0.72 34 34
CEBPB 0.008 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.21 0.18 -10000 0 -0.39 101 101
MYOD1 -0.082 0.2 -10000 0 -0.57 71 71
SMAD3/SMAD4/HNF4 -0.007 0.047 -10000 0 -0.37 2 2
SMAD3/SMAD4/GATA3 -0.02 0.093 -10000 0 -0.51 15 15
SnoN/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.001 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.004 0.025 -10000 0 -10000 0 0
MED15 0 0 -10000 0 -10000 0 0
SP1 0.017 0.011 -10000 0 -10000 0 0
SIN3B 0 0.001 -10000 0 -10000 0 0
SIN3A 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.2 0.19 -10000 0 -0.64 36 36
ITGB5 0.055 0.035 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.1 0.2 -10000 0 -0.5 103 103
AR -0.15 0.3 -10000 0 -0.74 103 103
negative regulation of cell growth 0.003 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.053 0.13 -10000 0 -0.39 24 24
E2F5 0 0 -10000 0 -10000 0 0
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.03 0.086 -10000 0 -0.46 3 3
SMAD2-3/SMAD4/FOXO1-3a-4 -0.02 0.098 -10000 0 -0.36 2 2
TFDP1 -0.003 0.044 -10000 0 -0.57 3 3
SMAD3/SMAD4/AP1 -0.038 0.12 -10000 0 -0.4 11 11
SMAD3/SMAD4/RUNX2 -0.001 0.017 -10000 0 -10000 0 0
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.001 0.12 -10000 0 -0.48 25 25
ACTA1 -0.011 0.16 -10000 0 -0.64 25 25
NUMA1 0.001 0.12 -10000 0 -0.48 25 25
SPTAN1 -0.009 0.15 -10000 0 -0.64 25 25
LIMK1 -0.009 0.15 -10000 0 -0.64 25 25
BIRC3 -0.009 0.08 -10000 0 -0.74 6 6
BIRC2 0 0.002 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 -0.01 0.16 -10000 0 -0.63 28 28
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.001 0.12 -10000 0 -0.48 25 25
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.009 0.15 -10000 0 -0.62 25 25
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.009 0.16 -10000 0 -0.64 25 25
MADD 0 0 -10000 0 -10000 0 0
TFAP2A -0.071 0.12 -10000 0 -0.78 12 12
BID 0.005 0.073 -10000 0 -0.3 27 27
MAP3K1 0.004 0.046 -10000 0 -0.23 10 10
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.01 0.16 -10000 0 -0.63 26 26
CASP9 0.001 0.002 -10000 0 -10000 0 0
DNA repair -0.002 0.034 -10000 0 -0.21 2 2
neuron apoptosis 0.019 0.016 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.003 0.15 -10000 0 -0.61 25 25
APAF1 0.001 0.003 -10000 0 -10000 0 0
CASP6 0.018 0.072 -10000 0 -0.35 12 12
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD -0.002 0.15 -10000 0 -0.61 25 25
CASP7 -0.005 0.042 0.36 6 -10000 0 6
KRT18 0.013 0.019 -10000 0 -10000 0 0
apoptosis -0.001 0.14 -10000 0 -0.56 25 25
DFFA -0.009 0.15 -10000 0 -0.64 25 25
DFFB -0.009 0.15 -10000 0 -0.64 25 25
PARP1 0.002 0.034 0.21 2 -10000 0 2
actin filament polymerization 0.001 0.14 0.58 25 -10000 0 25
TNF -0.019 0.12 -10000 0 -0.72 13 13
CYCS 0.008 0.055 -10000 0 -0.26 12 12
SATB1 0.021 0.078 -10000 0 -0.5 4 4
SLK -0.009 0.15 -10000 0 -0.64 25 25
p15 BID/BAX -0.014 0.061 -10000 0 -0.34 10 10
CASP2 0.035 0.051 -10000 0 -0.44 1 1
JNK cascade -0.004 0.046 0.23 10 -10000 0 10
CASP3 -0.017 0.16 -10000 0 -0.68 25 25
LMNB2 0.033 0.048 -10000 0 -0.34 3 3
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.033 -10000 0 -0.74 1 1
Mammalian IAPs/DIABLO -0.005 0.047 -10000 0 -0.43 6 6
negative regulation of DNA binding -0.07 0.12 -10000 0 -0.77 12 12
stress fiber formation -0.009 0.15 -10000 0 -0.62 25 25
GZMB -0.02 0.18 -10000 0 -0.72 27 27
CASP1 0.012 0.051 -10000 0 -0.72 2 2
LMNB1 0.033 0.048 -10000 0 -0.34 3 3
APP 0.019 0.016 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0 -10000 0 -10000 0 0
VIM -0.007 0.14 -10000 0 -0.55 25 25
LMNA 0.033 0.048 -10000 0 -0.32 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.046 -10000 0 -0.46 1 1
LRDD -0.001 0.033 -10000 0 -0.74 1 1
SREBF1 -0.009 0.15 -10000 0 -0.64 25 25
APAF-1/Caspase 9 -0.002 0.022 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.001 0.12 -10000 0 -0.47 25 25
CFL2 -0.002 0.15 -10000 0 -0.6 25 25
GAS2 -0.061 0.21 -10000 0 -0.52 72 72
positive regulation of apoptosis 0.035 0.048 -10000 0 -0.47 1 1
PRF1 -0.037 0.16 -10000 0 -0.74 25 25
Sphingosine 1-phosphate (S1P) 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
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P 0.019 0.008 -9999 0 -10000 0 0
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
mol:Sphinganine-1-P 0.02 0 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0 0.004 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.006 -9999 0 -10000 0 0
S1PR5 -0.01 0.075 -9999 0 -0.6 8 8
S1PR4 -0.065 0.21 -9999 0 -0.74 44 44
GNAI1 -0.001 0.033 -9999 0 -0.74 1 1
S1P/S1P5/G12 -0.005 0.04 -9999 0 -0.42 1 1
S1P/S1P3/Gq -0.069 0.12 -9999 0 -0.28 123 123
S1P/S1P4/Gi -0.03 0.092 -9999 0 -0.5 3 3
GNAQ -0.001 0.033 -9999 0 -0.74 1 1
GNAZ -0.009 0.08 -9999 0 -0.74 6 6
GNA14 -0.18 0.32 -9999 0 -0.74 123 123
GNA15 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
ABCC1 -0.001 0.026 -9999 0 -0.57 1 1
Noncanonical Wnt signaling pathway

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.1 0.26 -9999 0 -0.74 70 70
GNB1/GNG2 -0.042 0.091 -9999 0 -0.5 8 8
mol:DAG -0.003 0.099 -9999 0 -0.53 5 5
PLCG1 -0.003 0.1 -9999 0 -0.55 5 5
YES1 -0.012 0.098 -9999 0 -0.64 2 2
FZD3 0 0 -9999 0 -10000 0 0
FZD6 0 0 -9999 0 -10000 0 0
G protein -0.039 0.086 -9999 0 -0.56 5 5
MAP3K7 -0.016 0.14 -9999 0 -0.54 14 14
mol:Ca2+ -0.002 0.097 -9999 0 -0.51 5 5
mol:IP3 -0.003 0.099 -9999 0 -0.53 5 5
NLK -0.003 0.007 -9999 0 -10000 0 0
GNB1 -0.001 0.033 -9999 0 -0.74 1 1
CAMK2A -0.025 0.15 -9999 0 -0.58 15 15
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.045 0.091 -9999 0 -0.68 2 2
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.012 0.098 -9999 0 -0.64 2 2
GO:0007205 -0.002 0.098 -9999 0 -0.52 5 5
WNT6 -0.094 0.21 -9999 0 -0.57 82 82
WNT4 -0.01 0.083 -9999 0 -0.66 8 8
NFAT1/CK1 alpha -0.081 0.15 -9999 0 -0.56 18 18
GNG2 -0.007 0.073 -9999 0 -0.74 5 5
WNT5A -0.014 0.093 -9999 0 -0.6 12 12
WNT11 -0.038 0.16 -9999 0 -0.68 28 28
CDC42 -0.004 0.094 -9999 0 -0.6 2 2
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.017 0.093 -9999 0 -0.5 17 17
EPHB2 -0.009 0.072 -9999 0 -0.57 8 8
Syndecan-2/TACI -0.015 0.079 -9999 0 -0.42 18 18
LAMA1 -0.17 0.26 -9999 0 -0.58 146 146
Syndecan-2/alpha2 ITGB1 -0.014 0.079 -9999 0 -0.43 17 17
HRAS 0 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.005 0.048 -9999 0 -0.48 5 5
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.031 0.045 -9999 0 -10000 0 0
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.004 0.043 -9999 0 -0.43 5 5
LAMA3 -0.019 0.12 -9999 0 -0.74 13 13
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.018 0.11 -9999 0 -0.74 12 12
Syndecan-2/MMP2 -0.008 0.069 -9999 0 -0.53 8 8
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0 0 -9999 0 -10000 0 0
dendrite morphogenesis -0.01 0.064 -9999 0 -0.4 13 13
Syndecan-2/GM-CSF -0.052 0.15 -9999 0 -0.48 54 54
determination of left/right symmetry 0.012 0.057 -9999 0 -0.55 5 5
Syndecan-2/PKC delta -0.005 0.047 -9999 0 -0.48 5 5
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 -0.021 0.14 -9999 0 -0.43 54 54
MAPK1 -0.021 0.14 -9999 0 -0.43 54 54
Syndecan-2/RACK1 -0.004 0.04 -9999 0 -0.41 5 5
NF1 0 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.057 -9999 0 -0.55 5 5
ITGA2 0 0 -9999 0 -10000 0 0
MAPK8 0.025 0.05 -9999 0 -0.47 5 5
Syndecan-2/alpha2/beta1 Integrin -0.087 0.14 -9999 0 -0.55 6 6
Syndecan-2/Kininogen -0.014 0.072 -9999 0 -0.38 18 18
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.028 0.041 -9999 0 -0.38 5 5
Syndecan-2/CASK/Protein 4.1 -0.004 0.043 -9999 0 -0.44 5 5
extracellular matrix organization -0.005 0.047 -9999 0 -0.47 5 5
actin cytoskeleton reorganization -0.017 0.092 -9999 0 -0.5 17 17
Syndecan-2/Caveolin-2/Ras -0.015 0.082 -9999 0 -0.46 16 16
Syndecan-2/Laminin alpha3 -0.017 0.093 -9999 0 -0.5 17 17
Syndecan-2/RasGAP -0.004 0.038 -9999 0 -0.38 5 5
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.01 0.064 -9999 0 -0.4 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.004 0.037 -9999 0 -0.37 5 5
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.017 0.1 -9999 0 -0.64 13 13
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0 0 -9999 0 -10000 0 0
Syndecan-2/Synbindin -0.005 0.047 -9999 0 -0.48 5 5
TGFB1 0 0 -9999 0 -10000 0 0
CASP3 0.024 0.045 -9999 0 -0.43 5 5
FN1 -0.019 0.12 -9999 0 -0.74 13 13
Syndecan-2/IL8 -0.018 0.084 -9999 0 -0.4 23 23
SDC2 0.012 0.057 -9999 0 -0.56 5 5
KNG1 -0.015 0.091 -9999 0 -0.57 13 13
Syndecan-2/Neurofibromin -0.005 0.047 -9999 0 -0.48 5 5
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.072 0.22 -9999 0 -0.74 49 49
Syndecan-2/TGFB1 -0.005 0.047 -9999 0 -0.48 5 5
Syndecan-2/Syntenin/PI-4-5-P2 -0.004 0.043 -9999 0 -0.44 5 5
Syndecan-2/Ezrin -0.004 0.043 -9999 0 -0.43 5 5
PRKACA 0.024 0.045 -9999 0 -0.43 5 5
angiogenesis -0.018 0.084 -9999 0 -0.4 23 23
MMP2 -0.006 0.066 -9999 0 -0.74 4 4
IL8 -0.022 0.11 -9999 0 -0.61 18 18
calcineurin-NFAT signaling pathway -0.015 0.079 -9999 0 -0.42 18 18
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 0 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.054 0.42 8 -10000 0 8
CDKN1A 0 0.006 -10000 0 -10000 0 0
KAT2B -0.001 0.033 -10000 0 -0.74 1 1
BAX 0 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.02 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.002 0.036 -10000 0 -0.57 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.048 0.15 -10000 0 -0.42 72 72
PPARGC1A -0.15 0.3 -10000 0 -0.74 100 100
FHL2 -0.005 0.051 -10000 0 -0.57 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0 -10000 0 -10000 0 0
HIST2H4A 0.011 0.054 -10000 0 -0.42 8 8
SIRT1/FOXO3a 0 0 -10000 0 -10000 0 0
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.011 0.037 -10000 0 -10000 0 0
apoptosis 0 0 -10000 0 -10000 0 0
SIRT1/PGC1A -0.097 0.19 -10000 0 -0.48 100 100
p53/SIRT1 -0.001 0.025 -10000 0 -0.56 1 1
SIRT1/FOXO4 0 0 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.003 0.028 -10000 0 -10000 0 0
HIST1H1E 0.004 0.052 -10000 0 -10000 0 0
SIRT1/p300 0 0 -10000 0 -10000 0 0
muscle cell differentiation 0.05 0.12 0.35 72 -10000 0 72
TP53 -0.001 0.033 -10000 0 -0.74 1 1
KU70/SIRT1/BAX 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.002 0.026 -10000 0 -0.42 2 2
ACSS2 0.018 0 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.05 0.12 -10000 0 -0.35 72 72
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.02 -10000 0 -10000 0 0
RFC1 0.002 0.02 -10000 0 -10000 0 0
PRKDC 0.002 0.02 -10000 0 -10000 0 0
RIPK1 0 0.002 -10000 0 -10000 0 0
CASP7 -0.012 0.037 0.26 1 -10000 0 1
FASLG/FAS/FADD/FAF1 -0.018 0.074 0.24 4 -0.34 21 25
MAP2K4 -0.01 0.13 -10000 0 -0.51 7 7
mol:ceramide -0.006 0.11 -10000 0 -0.43 21 21
GSN 0.002 0.02 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.027 0.088 -10000 0 -0.42 20 20
FAS 0.006 0.048 -10000 0 -0.74 2 2
BID 0.003 0.028 0.31 4 -10000 0 4
MAP3K1 0.004 0.079 0.22 1 -10000 0 1
MAP3K7 0.009 0.004 -10000 0 -10000 0 0
RB1 0.001 0.029 -10000 0 -0.47 1 1
CFLAR 0 0.002 -10000 0 -10000 0 0
HGF/MET -0.11 0.2 -10000 0 -0.48 112 112
ARHGDIB 0.001 0.023 -10000 0 -0.32 1 1
FADD 0.009 0.004 -10000 0 -10000 0 0
actin filament polymerization -0.002 0.02 -10000 0 -10000 0 0
NFKB1 -0.037 0.078 -10000 0 -10000 0 0
MAPK8 -0.029 0.19 -10000 0 -0.44 80 80
DFFA 0.002 0.02 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.02 -10000 0 -10000 0 0
FAS/FADD/MET -0.005 0.045 -10000 0 -0.45 5 5
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.005 0.071 -10000 0 -0.7 5 5
FAF1 0.009 0.004 -10000 0 -10000 0 0
PARP1 0.002 0.02 -10000 0 -10000 0 0
DFFB 0.002 0.02 -10000 0 -10000 0 0
CHUK -0.032 0.069 -10000 0 -10000 0 0
FASLG -0.021 0.15 -10000 0 -0.74 20 20
FAS/FADD -0.003 0.036 -10000 0 -0.57 2 2
HGF -0.16 0.3 -10000 0 -0.74 108 108
LMNA 0.002 0.018 -10000 0 -10000 0 0
CASP6 0.002 0.02 -10000 0 -10000 0 0
CASP10 0.007 0.034 -10000 0 -0.74 1 1
CASP3 0.002 0.023 0.24 2 -10000 0 2
PTPN13 -0.004 0.057 -10000 0 -0.74 3 3
CASP8 0.004 0.04 0.43 4 -10000 0 4
IL6 -0.19 0.5 -10000 0 -1.3 82 82
MET -0.004 0.053 -10000 0 -0.68 3 3
ICAD/CAD 0.002 0.019 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.006 0.11 -10000 0 -0.43 21 21
activation of caspase activity by cytochrome c 0.003 0.028 0.31 4 -10000 0 4
PAK2 0.002 0.019 -10000 0 -10000 0 0
BCL2 0.001 0.026 -10000 0 -0.58 1 1
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.057 0.13 -9999 0 -0.56 7 7
MAP3K8 0.006 0.047 -9999 0 -0.74 2 2
FOS 0 0.1 -9999 0 -0.46 7 7
PRKCA 0.007 0.048 -9999 0 -0.74 2 2
PTPN7 0.008 0.042 -9999 0 -0.66 2 2
HRAS 0 0 -9999 0 -10000 0 0
PRKCB -0.031 0.17 -9999 0 -0.74 27 27
NRAS 0 0 -9999 0 -10000 0 0
RAS family/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.007 0.063 -9999 0 -0.45 1 1
MAP2K1 -0.003 0.13 -9999 0 -0.52 28 28
ELK1 -0.001 0.004 -9999 0 -10000 0 0
BRAF -0.032 0.12 -9999 0 -0.52 28 28
mol:GTP -0.001 0.002 -9999 0 -0.006 61 61
MAPK1 0.007 0.063 -9999 0 -0.45 1 1
RAF1 -0.032 0.12 -9999 0 -0.52 28 28
KRAS 0 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.034 0.12 -9999 0 -0.46 37 37
MAP4K1 -0.006 0.066 -9999 0 -0.74 4 4
MAP3K8 -0.003 0.046 -9999 0 -0.74 2 2
PRKCB -0.04 0.17 -9999 0 -0.74 27 27
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 0.015 0.098 -9999 0 -0.72 3 3
JUN -0.007 0.16 -9999 0 -0.66 27 27
MAP3K7 0.015 0.098 -9999 0 -0.72 3 3
GRAP2 -0.044 0.18 -9999 0 -0.74 30 30
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.022 0.1 -9999 0 -0.76 3 3
LAT 0 0 -9999 0 -10000 0 0
LCP2 -0.009 0.08 -9999 0 -0.74 6 6
MAPK8 -0.015 0.17 -9999 0 -0.7 27 27
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.025 0.095 -9999 0 -0.76 3 3
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.032 0.12 -9999 0 -0.81 3 3
Effects of Botulinum toxin

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
STX1A 0.006 0.039 -9999 0 -0.42 4 4
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.057 0.17 -9999 0 -0.56 51 51
STXBP1 -0.006 0.066 -9999 0 -0.74 4 4
ACh/CHRNA1 -0.014 0.072 -9999 0 -0.43 14 14
RAB3GAP2/RIMS1/UNC13B -0.049 0.15 -9999 0 -0.48 51 51
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.071 0.22 -9999 0 -0.73 49 49
mol:ACh 0.005 0.024 -9999 0 -0.15 12 12
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.043 0.12 -9999 0 -0.61 4 4
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.014 0.072 -9999 0 -0.42 14 14
UNC13B -0.004 0.057 -9999 0 -0.74 3 3
CHRNA1 -0.018 0.1 -9999 0 -0.63 14 14
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.014 0.07 -9999 0 -0.39 16 16
SNAP25 -0.001 0.05 -9999 0 -0.32 11 11
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.018 0.1 -9999 0 -0.57 16 16
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.007 0.053 -9999 0 -0.42 8 8
STX1A/SNAP25 fragment 1/VAMP2 -0.043 0.12 -9999 0 -0.61 4 4
BCR signaling pathway

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
JUN 0.014 0.098 -10000 0 -0.47 12 12
IKBKB 0.015 0.052 -10000 0 -0.28 2 2
AKT1 0.004 0.085 0.23 1 -0.28 13 14
IKBKG 0.017 0.055 -10000 0 -0.27 6 6
CALM1 -0.011 0.1 -10000 0 -0.49 14 14
PIK3CA 0 0 -10000 0 -10000 0 0
MAP3K1 0 0.14 -10000 0 -0.68 14 14
MAP3K7 0 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.11 0.23 4 -0.52 14 18
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.002 0.083 0.18 3 -0.27 9 12
LYN -0.003 0.047 -10000 0 -0.74 2 2
BLNK -0.001 0.033 -10000 0 -0.74 1 1
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.03 0.13 -10000 0 -0.56 27 27
CD22 -0.077 0.22 -10000 0 -0.64 51 51
CAMK2G -0.003 0.094 -10000 0 -0.48 11 11
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D -0.001 0.033 -10000 0 -0.74 1 1
SHC/GRB2/SOS1 -0.021 0.094 -10000 0 -0.73 4 4
GO:0007205 -0.019 0.11 0.23 4 -0.54 14 18
SYK -0.001 0.033 -10000 0 -0.74 1 1
ELK1 -0.011 0.1 -10000 0 -0.5 14 14
NFATC1 -0.007 0.12 -10000 0 -0.55 16 16
B-cell antigen/BCR complex -0.03 0.13 -10000 0 -0.56 27 27
PAG1/CSK -0.008 0.065 -10000 0 -0.56 7 7
NFKBIB 0.014 0.02 0.078 2 -10000 0 2
HRAS -0.003 0.097 -10000 0 -0.48 14 14
NFKBIA 0.014 0.019 0.078 2 -10000 0 2
NF-kappa-B/RelA/I kappa B beta 0.018 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.029 0.12 -10000 0 -0.77 7 7
mol:GDP -0.021 0.1 0.22 4 -0.51 14 18
PTEN -0.003 0.046 -10000 0 -0.74 2 2
CD79B -0.007 0.07 -10000 0 -0.7 5 5
NF-kappa-B/RelA/I kappa B alpha 0.018 0.016 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.015 0.15 -10000 0 -0.57 20 20
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.028 0.11 0.23 4 -0.54 14 18
CSK 0 0 -10000 0 -10000 0 0
FOS -0.05 0.16 -10000 0 -0.41 72 72
CHUK 0.017 0.055 -10000 0 -0.3 2 2
IBTK 0 0.001 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.023 0.084 -10000 0 -0.59 7 7
PTPN6 -0.071 0.2 -10000 0 -0.82 26 26
RELA 0 0.001 -10000 0 -10000 0 0
BCL2A1 0.015 0.025 -10000 0 -0.12 13 13
VAV2 -0.06 0.17 -10000 0 -0.85 15 15
ubiquitin-dependent protein catabolic process 0.018 0.019 0.081 2 -10000 0 2
BTK -0.11 0.34 -10000 0 -1.1 49 49
CD19 -0.066 0.18 -10000 0 -0.72 22 22
MAP4K1 -0.006 0.066 -10000 0 -0.74 4 4
CD72 -0.001 0.026 -10000 0 -0.57 1 1
PAG1 -0.01 0.087 -10000 0 -0.74 7 7
MAPK14 0.01 0.12 -10000 0 -0.57 13 13
SH3BP5 -0.012 0.092 -10000 0 -0.74 8 8
PIK3AP1 -0.014 0.13 0.26 4 -0.57 20 24
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.03 0.14 -10000 0 -0.62 21 21
RAF1 0.004 0.092 -10000 0 -0.56 7 7
RasGAP/p62DOK/SHIP -0.028 0.12 -10000 0 -0.74 8 8
CD79A -0.034 0.15 -10000 0 -0.68 25 25
re-entry into mitotic cell cycle -0.002 0.082 0.18 3 -0.28 9 12
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.018 0.077 -10000 0 -0.48 6 6
MAPK1 0.018 0.077 -10000 0 -0.48 6 6
CD72/SHP1 -0.065 0.19 -10000 0 -0.75 26 26
NFKB1 0 0.001 -10000 0 -10000 0 0
MAPK8 0.01 0.12 -10000 0 -0.57 13 13
actin cytoskeleton organization -0.014 0.15 -10000 0 -0.68 15 15
NF-kappa-B/RelA 0.04 0.032 0.16 2 -10000 0 2
Calcineurin -0.021 0.076 -10000 0 -0.55 6 6
PI3K -0.063 0.14 -10000 0 -0.61 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.024 0.1 0.26 4 -0.52 14 18
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.039 0.16 -10000 0 -0.9 14 14
DAPP1 -0.044 0.18 -10000 0 -1.1 13 13
cytokine secretion -0.005 0.12 -10000 0 -0.5 16 16
mol:DAG -0.028 0.11 0.23 4 -0.54 14 18
PLCG2 0 0.001 -10000 0 -10000 0 0
MAP2K1 0.011 0.085 -10000 0 -0.55 6 6
B-cell antigen/BCR complex/FcgammaRIIB -0.034 0.14 -10000 0 -0.59 24 24
mol:PI-3-4-5-P3 -0.045 0.1 0.32 1 -0.4 19 20
ETS1 -0.004 0.11 -10000 0 -0.5 17 17
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.025 0.11 -10000 0 -0.85 4 4
B-cell antigen/BCR complex/LYN -0.044 0.17 -10000 0 -0.76 20 20
MALT1 0 0.001 -10000 0 -10000 0 0
TRAF6 0.001 0.003 -10000 0 -10000 0 0
RAC1 -0.017 0.16 -10000 0 -0.74 15 15
B-cell antigen/BCR complex/LYN/SYK -0.068 0.2 -10000 0 -0.79 26 26
CARD11 -0.013 0.11 -10000 0 -0.54 14 14
FCGR2B -0.013 0.098 -10000 0 -0.74 9 9
PPP3CA 0 0 -10000 0 -10000 0 0
BCL10 0 0.001 -10000 0 -10000 0 0
IKK complex 0.016 0.026 -10000 0 -10000 0 0
PTPRC -0.049 0.18 -10000 0 -0.74 33 33
PDPK1 -0.03 0.068 0.21 1 -0.28 12 13
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.018 0.013 -10000 0 -0.1 1 1
EGFR-dependent Endothelin signaling events

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
HRAS 0 0 -9999 0 -10000 0 0
EGFR -0.023 0.12 -9999 0 -0.63 18 18
EGF/EGFR -0.058 0.15 -9999 0 -0.45 56 56
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.019 0.083 -9999 0 -0.81 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.009 0.08 -9999 0 -0.74 6 6
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.014 0.097 -9999 0 -0.69 10 10
EGF/EGFR dimer/SHC -0.023 0.098 -9999 0 -0.51 12 12
mol:GDP -0.019 0.082 -9999 0 -0.79 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.065 0.21 -9999 0 -0.74 44 44
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.017 0.075 -9999 0 -0.74 1 1
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.017 0.076 -9999 0 -0.75 1 1
FRAP1 -0.018 0.079 -9999 0 -0.77 1 1
EGF/EGFR dimer -0.027 0.12 -9999 0 -0.49 27 27
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.055 0.17 -9999 0 -0.56 50 50
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.029 0.11 0.45 32 -10000 0 32
KIRREL -0.004 0.095 -10000 0 -0.75 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.029 0.11 -10000 0 -0.45 32 32
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.022 0.085 -10000 0 -0.45 9 9
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.013 0.053 -10000 0 -0.34 8 8
FYN -0.007 0.085 -10000 0 -0.46 9 9
mol:Ca2+ -0.022 0.085 -10000 0 -0.45 9 9
mol:DAG -0.022 0.085 -10000 0 -0.45 9 9
NPHS2 -0.003 0.047 -10000 0 -0.58 3 3
mol:IP3 -0.022 0.085 -10000 0 -0.45 9 9
regulation of endocytosis -0.019 0.075 -10000 0 -0.42 9 9
Nephrin/NEPH1/podocin/Cholesterol -0.023 0.087 -10000 0 -0.46 9 9
establishment of cell polarity -0.029 0.11 -10000 0 -0.45 32 32
Nephrin/NEPH1/podocin/NCK1-2 -0.02 0.077 -10000 0 -0.51 2 2
Nephrin/NEPH1/beta Arrestin2 -0.019 0.076 -10000 0 -0.43 9 9
NPHS1 -0.021 0.12 -10000 0 -0.57 24 24
Nephrin/NEPH1/podocin -0.021 0.082 -10000 0 -0.46 9 9
TJP1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.022 0.085 -10000 0 -0.45 9 9
CD2AP 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.022 0.085 -10000 0 -0.45 9 9
GRB2 0 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.024 0.14 -10000 0 -0.5 31 31
cytoskeleton organization -0.016 0.066 -10000 0 -0.5 1 1
Nephrin/NEPH1 -0.021 0.08 -10000 0 -0.32 32 32
Nephrin/NEPH1/ZO-1 -0.023 0.088 -10000 0 -0.46 9 9
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.031 0.13 -9999 0 -0.56 28 28
PDGFRB 0.008 0.034 -9999 0 -0.74 1 1
SPHK1 -0.008 0.021 -9999 0 -10000 0 0
mol:S1P -0.01 0.029 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.001 0.14 -9999 0 -0.59 7 7
GNAO1 0.006 0.05 -9999 0 -0.64 3 3
PDGFB-D/PDGFRB/PLCgamma1 -0.04 0.1 -9999 0 -0.5 8 8
PLCG1 0.006 0.13 -9999 0 -0.54 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.008 0.034 -9999 0 -0.74 1 1
GNAI2 0.01 0.004 -9999 0 -10000 0 0
GNAI3 0.01 0.004 -9999 0 -10000 0 0
GNAI1 0.008 0.034 -9999 0 -0.75 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.013 0.11 -9999 0 -0.48 28 28
S1P1/S1P -0.033 0.092 -9999 0 -0.49 7 7
negative regulation of cAMP metabolic process 0 0.13 -9999 0 -0.57 7 7
MAPK3 -0.011 0.19 -9999 0 -0.55 51 51
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.041 0.17 -9999 0 -0.74 28 28
PLCB2 0.003 0.11 -9999 0 -0.46 8 8
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.028 0.078 -9999 0 -0.41 7 7
receptor internalization -0.031 0.087 -9999 0 -0.45 7 7
PTGS2 -0.061 0.34 -9999 0 -1.1 51 51
Rac1/GTP -0.028 0.078 -9999 0 -0.41 7 7
RHOA 0 0 -9999 0 -10000 0 0
VEGFA 0 0.001 -9999 0 -10000 0 0
negative regulation of T cell proliferation 0 0.13 -9999 0 -0.57 7 7
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.082 -9999 0 -0.74 6 6
MAPK1 -0.011 0.19 -9999 0 -0.55 51 51
S1P1/S1P/PDGFB-D/PDGFRB 0.005 0.11 -9999 0 -0.55 7 7
ABCC1 -0.001 0.026 -9999 0 -0.57 1 1
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 -0.026 0.14 -9999 0 -0.74 18 18
ENAH 0.058 0.023 -9999 0 -10000 0 0
EGFR -0.023 0.12 -9999 0 -0.63 18 18
EPHA2 -0.004 0.057 -9999 0 -0.74 3 3
MYO6 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.017 0.089 -9999 0 -0.48 18 18
AQP5 -0.17 0.25 -9999 0 -0.55 157 157
CTNND1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.11 0.17 -9999 0 -0.38 141 141
EGF -0.014 0.097 -9999 0 -0.69 10 10
NCKAP1 0 0 -9999 0 -10000 0 0
AQP3 -0.076 0.19 -9999 0 -0.55 70 70
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.033 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0 0 -9999 0 -10000 0 0
ARF6/GDP -0.002 0.025 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.033 -9999 0 -0.43 3 3
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.044 0 -9999 0 -10000 0 0
PVRL2 0 0 -9999 0 -10000 0 0
ZYX 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.03 -9999 0 -0.4 3 3
CDH1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.017 0.076 -9999 0 -0.75 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.039 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
IGF1R 0 0 -9999 0 -10000 0 0
IGF1 -0.028 0.14 -9999 0 -0.73 19 19
DIAPH1 -0.023 0.12 -9999 0 -0.64 18 18
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.024 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
VCL 0.04 0 -9999 0 -10000 0 0
EFNA1 0 0 -9999 0 -10000 0 0
LPP 0.04 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.002 0.028 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.11 0.17 -9999 0 -0.39 141 141
HGF/MET -0.081 0.15 -9999 0 -10000 0 0
HGF -0.16 0.3 -9999 0 -0.74 108 108
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0 0 -9999 0 -10000 0 0
actin cable formation 0.068 0.029 -9999 0 -10000 0 0
KIAA1543 0.039 0.018 -9999 0 -10000 0 0
KIFC3 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
EXOC3 0 0 -9999 0 -10000 0 0
ACTN1 0 0 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0 0 -9999 0 -10000 0 0
STX4 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
LIMA1 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
ROCK1 -0.002 0.021 -9999 0 -10000 0 0
adherens junction assembly 0.053 0.018 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.014 0.069 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.004 0.053 -9999 0 -0.68 3 3
PLEKHA7 0 0 -9999 0 -10000 0 0
mol:GTP -0.003 0.033 -9999 0 -0.43 3 3
establishment of epithelial cell apical/basal polarity 0 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0 0 -9999 0 -10000 0 0
Syndecan-4-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
PTK2 0.007 0.1 -9999 0 -0.61 13 13
Syndecan-4/Syndesmos 0.01 0.075 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.048 0.12 -9999 0 -0.59 12 12
Syndecan-4/ADAM12 -0.06 0.14 -9999 0 -0.57 2 2
CCL5 -0.013 0.098 -9999 0 -0.74 9 9
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.007 0.058 -9999 0 -0.58 5 5
ADAM12 -0.14 0.25 -9999 0 -0.57 121 121
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.012 0.035 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.075 0.15 -9999 0 -0.62 2 2
Syndecan-4/CXCL12/CXCR4 -0.051 0.13 -9999 0 -0.63 12 12
Syndecan-4/Laminin alpha3 0 0.099 -9999 0 -0.6 2 2
MDK -0.01 0.076 -9999 0 -0.57 9 9
Syndecan-4/FZD7 0.01 0.076 -9999 0 -10000 0 0
Syndecan-4/Midkine 0.005 0.086 -9999 0 -0.57 1 1
FZD7 -0.001 0.026 -9999 0 -0.57 1 1
Syndecan-4/FGFR1/FGF -0.03 0.089 -9999 0 -0.55 5 5
THBS1 -0.013 0.098 -9999 0 -0.74 9 9
integrin-mediated signaling pathway -0.01 0.08 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.048 0.12 -9999 0 -0.59 12 12
Syndecan-4/TACI 0.001 0.091 -9999 0 -10000 0 0
CXCR4 -0.001 0.033 -9999 0 -0.74 1 1
cell adhesion -0.008 0.062 -9999 0 -0.36 15 15
Syndecan-4/Dynamin 0.01 0.075 -9999 0 -10000 0 0
Syndecan-4/TSP1 0.003 0.11 -9999 0 -0.66 8 8
Syndecan-4/GIPC 0.01 0.075 -9999 0 -10000 0 0
Syndecan-4/RANTES 0.003 0.095 -9999 0 -0.68 2 2
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.17 0.26 -9999 0 -0.58 146 146
LAMA3 -0.019 0.12 -9999 0 -0.74 13 13
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.005 0.05 -9999 0 -0.69 2 2
Syndecan-4/alpha-Actinin 0.01 0.075 -9999 0 -10000 0 0
TFPI -0.054 0.19 -9999 0 -0.74 37 37
F2 -0.015 0.1 -9999 0 -0.57 16 16
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.076 0.16 -9999 0 -0.64 7 7
ACTN1 0 0 -9999 0 -10000 0 0
TNC -0.013 0.087 -9999 0 -0.59 11 11
Syndecan-4/CXCL12 -0.023 0.15 -9999 0 -0.65 11 11
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.062 0.2 -9999 0 -0.74 42 42
TNFRSF13B -0.017 0.1 -9999 0 -0.64 13 13
FGF2 -0.021 0.12 -9999 0 -0.74 14 14
FGFR1 -0.001 0.033 -9999 0 -0.74 1 1
Syndecan-4/PI-4-5-P2 0.004 0.075 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.017 0.12 -9999 0 -0.72 13 13
cell migration -0.005 0.014 -9999 0 -10000 0 0
PRKCD 0.002 0.006 -9999 0 -10000 0 0
vasculogenesis -0.01 0.1 -9999 0 -0.63 8 8
SDC4 0.005 0.078 -9999 0 -10000 0 0
Syndecan-4/Tenascin C 0.004 0.085 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2/PKC alpha -0.01 0.027 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.01 0.075 -9999 0 -10000 0 0
MMP9 -0.022 0.14 -9999 0 -0.58 28 28
Rac1/GTP -0.009 0.064 -9999 0 -0.37 15 15
cytoskeleton organization -0.004 0.07 -9999 0 -10000 0 0
GIPC1 0 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.019 0.14 -9999 0 -0.64 7 7
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.006 0.006 -9999 0 -10000 0 0
HDAC2 0.006 0.006 -9999 0 -10000 0 0
GNB1/GNG2 -0.007 0.057 -9999 0 -0.46 7 7
forebrain development -0.086 0.14 -9999 0 -0.49 9 9
GNAO1 0.001 0.05 -9999 0 -0.63 3 3
SMO/beta Arrestin2 -0.002 0.027 -9999 0 -0.42 2 2
SMO 0.003 0.038 -9999 0 -0.58 2 2
ARRB2 0.005 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.015 -9999 0 -10000 0 0
mol:GTP -0.003 0.004 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.005 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.004 -9999 0 -10000 0 0
GNAI1 0.004 0.034 -9999 0 -0.74 1 1
XPO1 0.006 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.1 0.11 -9999 0 -0.48 6 6
SAP30 0.006 0.006 -9999 0 -10000 0 0
mol:GDP 0.003 0.037 -9999 0 -0.58 2 2
MIM/GLI2A -0.033 0.05 -9999 0 -10000 0 0
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.005 0.005 -9999 0 -10000 0 0
GLI2 0.037 0.023 -9999 0 -10000 0 0
GLI3 0.04 0.016 -9999 0 -10000 0 0
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.006 0.006 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.007 0.073 -9999 0 -0.74 5 5
Gi family/GTP 0.002 0.049 -9999 0 -0.41 1 1
SIN3B 0.006 0.006 -9999 0 -10000 0 0
SIN3A 0.006 0.006 -9999 0 -10000 0 0
GLI3/Su(fu) -0.001 0.009 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.033 -9999 0 -10000 0 0
FOXA2 -0.6 0.6 -9999 0 -1.2 250 250
neural tube patterning -0.086 0.14 -9999 0 -0.49 9 9
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.001 0.009 -9999 0 -10000 0 0
GNB1 -0.001 0.033 -9999 0 -0.74 1 1
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 -0.033 0.05 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.086 0.14 -9999 0 -0.49 9 9
SUFU 0.012 0.017 -9999 0 -10000 0 0
LGALS3 0 0 -9999 0 -10000 0 0
catabolic process -0.001 0.013 -9999 0 -10000 0 0
GLI3A/CBP 0.005 0.033 -9999 0 -0.38 1 1
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.088 0.15 -9999 0 -0.5 9 9
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 0 0 -9999 0 -10000 0 0
RBBP7 0.006 0.006 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.001 0.009 -9999 0 -10000 0 0
GNAZ -0.004 0.081 -9999 0 -0.74 6 6
RBBP4 0.006 0.006 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP 0.039 0.021 -9999 0 -10000 0 0
STK36 0.006 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.009 0.054 -9999 0 -0.62 2 2
PTCH1 -0.079 0.16 -9999 0 -1 6 6
MIM/GLI1 -0.23 0.29 -9999 0 -0.51 250 250
CREBBP 0.005 0.032 -9999 0 -0.38 1 1
Su(fu)/SIN3/HDAC complex 0.029 0.029 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 -0.01 0.12 -9999 0 -0.74 14 14
ELF1 -0.004 0.033 -9999 0 -0.37 3 3
CCNA2 -0.15 0.25 -9999 0 -0.57 129 129
PIK3CA 0.01 0 -9999 0 -10000 0 0
JAK3 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
JAK1 0.01 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.056 0.073 -9999 0 -0.68 3 3
SHC1 0.01 0 -9999 0 -10000 0 0
SP1 -0.003 0.033 -9999 0 -0.37 4 4
IL2RA 0.018 0.083 -9999 0 -0.69 6 6
IL2RB 0.006 0.058 -9999 0 -0.74 3 3
SOS1 0.01 0 -9999 0 -10000 0 0
IL2RG 0 0.088 -9999 0 -0.74 7 7
G1/S transition of mitotic cell cycle -0.016 0.12 -9999 0 -0.9 4 4
PTPN11 0.01 0 -9999 0 -10000 0 0
CCND2 0.018 0.087 -9999 0 -0.95 4 4
LCK 0.009 0.033 -9999 0 -0.74 1 1
GRB2 0.01 0 -9999 0 -10000 0 0
IL2 0.005 0.005 -9999 0 -10000 0 0
CDK6 -0.002 0.036 -9999 0 -0.57 2 2
CCND3 0.06 0.063 -9999 0 -0.56 3 3
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
CDC42/GTP -0.028 0.086 -9999 0 -0.47 3 3
PLCG1 0.003 0.099 -9999 0 -0.48 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.028 0.084 -9999 0 -0.46 3 3
S1PR5 -0.01 0.075 -9999 0 -0.6 8 8
S1PR4 -0.065 0.21 -9999 0 -0.74 44 44
MAPK3 0.003 0.099 -9999 0 -0.48 3 3
MAPK1 0.003 0.099 -9999 0 -0.48 3 3
S1P/S1P5/Gi -0.007 0.04 -9999 0 -10000 0 0
GNAI1 -0.001 0.033 -9999 0 -0.74 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.047 -9999 0 -0.37 8 8
RHOA -0.01 0.12 -9999 0 -0.4 44 44
S1P/S1P4/Gi -0.032 0.096 -9999 0 -0.32 45 45
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.009 0.08 -9999 0 -0.74 6 6
S1P/S1P4/G12/G13 -0.038 0.12 -9999 0 -0.44 44 44
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.001 0.033 -10000 0 -0.74 1 1
Jak2/Leptin Receptor -0.026 0.097 0.19 2 -0.38 29 31
PTP1B/AKT1 -0.006 0.023 -10000 0 -10000 0 0
FYN -0.001 0.033 -10000 0 -0.74 1 1
p210 bcr-abl/PTP1B 0.024 0.036 -10000 0 -0.31 1 1
EGFR -0.013 0.12 -10000 0 -0.63 18 18
EGF/EGFR -0.02 0.084 -10000 0 -0.48 12 12
CSF1 -0.006 0.066 -10000 0 -0.74 4 4
AKT1 0.009 0.003 -10000 0 -10000 0 0
INSR 0.009 0.003 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.01 0.085 -10000 0 -0.42 8 8
Insulin Receptor/Insulin -0.004 0.018 -10000 0 -10000 0 0
HCK -0.009 0.08 -10000 0 -0.74 6 6
CRK 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.034 -10000 0 -10000 0 0
EGF -0.004 0.099 -10000 0 -0.69 10 10
YES1 0 0 -10000 0 -10000 0 0
CAV1 -0.024 0.11 -10000 0 -0.46 10 10
TXN 0.008 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.005 0.021 -10000 0 -10000 0 0
cell migration -0.024 0.036 0.31 1 -10000 0 1
STAT3 0.007 0.005 -10000 0 -10000 0 0
PRLR -0.04 0.16 -10000 0 -0.63 32 32
ITGA2B -0.022 0.13 -10000 0 -0.74 15 15
CSF1R -0.015 0.1 -10000 0 -0.74 10 10
Prolactin Receptor/Prolactin -0.036 0.13 -10000 0 -0.47 39 39
FGR -0.054 0.19 -10000 0 -0.74 37 37
PTP1B/p130 Cas 0.027 0.033 -10000 0 -10000 0 0
Crk/p130 Cas -0.005 0.021 -10000 0 -10000 0 0
DOK1 0.033 0.035 -10000 0 -0.33 1 1
JAK2 0.014 0.05 -10000 0 -0.32 2 2
Jak2/Leptin Receptor/Leptin -0.045 0.084 -10000 0 -0.46 4 4
PIK3R1 0 0 -10000 0 -10000 0 0
PTPN1 0.024 0.036 -10000 0 -0.31 1 1
LYN -0.003 0.046 -10000 0 -0.74 2 2
CDH2 -0.033 0.14 -10000 0 -0.59 28 28
SRC 0.023 0.015 -10000 0 -10000 0 0
ITGB3 -0.016 0.11 -10000 0 -0.74 11 11
CAT1/PTP1B 0.015 0.12 -10000 0 -0.53 15 15
CAPN1 0.007 0.005 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.014 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.041 0.077 -10000 0 -0.54 2 2
negative regulation of transcription 0.014 0.05 -10000 0 -0.31 2 2
FCGR2A -0.015 0.1 -10000 0 -0.74 10 10
FER 0.008 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.029 0.12 -10000 0 -0.56 26 26
BLK -0.036 0.15 -10000 0 -0.66 27 27
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.007 0.005 -10000 0 -10000 0 0
LEPR -0.038 0.17 -10000 0 -0.74 28 28
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.003 0.14 -10000 0 -0.63 17 17
PRL -0.009 0.072 -10000 0 -0.58 8 8
SOCS3 0.003 0.091 -10000 0 -1.4 2 2
SPRY2 0.004 0.048 -10000 0 -0.74 2 2
Insulin Receptor/Insulin/IRS1 0 0 -10000 0 -10000 0 0
CSF1/CSF1R -0.016 0.075 -10000 0 -0.45 12 12
Ras protein signal transduction 0.005 0.012 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.1 0.23 -10000 0 -0.57 94 94
STAT5B 0.022 0.037 -10000 0 -0.25 1 1
STAT5A 0.022 0.037 -10000 0 -0.25 1 1
GRB2 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.027 0.04 -10000 0 -0.47 1 1
CSN2 -0.012 0.041 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
LAT 0.013 0.073 -10000 0 -0.48 10 10
YBX1 0.012 0.007 -10000 0 -10000 0 0
LCK -0.001 0.033 -10000 0 -0.74 1 1
SHC1 0 0 -10000 0 -10000 0 0
NOX4 0.004 0.037 -10000 0 -0.57 2 2
TRAIL signaling pathway

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
TNFSF10 0 0 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity -0.029 0.12 -10000 0 -0.55 26 26
MAP2K4 0.041 0.011 -10000 0 -10000 0 0
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.003 0.046 -10000 0 -0.74 2 2
SMPD1 0 0 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.038 0.16 -10000 0 -0.74 26 26
TRAIL/TRAILR2 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR3 -0.072 0.19 -10000 0 -0.56 65 65
TRAIL/TRAILR1 -0.002 0.035 -10000 0 -0.56 2 2
TRAIL/TRAILR4 -0.029 0.12 -10000 0 -0.56 26 26
TRAIL/TRAILR1/DAP3/GTP -0.002 0.028 -10000 0 -0.44 2 2
IKK complex -0.001 0.009 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.02 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.009 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.038 0.16 -10000 0 -0.74 26 26
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.003 0.046 -10000 0 -0.74 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.019 -10000 0 -0.3 2 2
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP -0.002 0.025 -10000 0 -0.4 2 2
mol:ceramide 0 0 -10000 0 -10000 0 0
FADD 0 0 -10000 0 -10000 0 0
MAPK8 0.046 0.01 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.095 0.25 -10000 0 -0.74 65 65
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.03 -10000 0 -0.48 2 2
DAP3 0 0 -10000 0 -10000 0 0
CASP10 0.014 0.067 0.29 25 -0.39 1 26
JNK cascade -0.029 0.12 -10000 0 -0.55 26 26
TRAIL (trimer) 0 0 -10000 0 -10000 0 0
TNFRSF10C -0.096 0.25 -10000 0 -0.74 65 65
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.026 -10000 0 -0.41 2 2
TRAIL/TRAILR2/FADD 0 0 -10000 0 -10000 0 0
cell death 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0 -10000 0 -10000 0 0
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0 0.003 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.046 -10000 0 -0.74 2 2
ANTXR2 -0.01 0.087 -10000 0 -0.74 7 7
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.013 -10000 0 -0.1 7 7
monocyte activation -0.002 0.082 -10000 0 -0.45 16 16
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.011 -10000 0 -10000 0 0
MAP2K7 -0.001 0.011 -10000 0 -10000 0 0
MAP2K6 -0.002 0.017 -10000 0 -0.31 1 1
CYAA 0.006 0.067 -10000 0 -0.53 7 7
MAP2K4 -0.001 0.011 -10000 0 -10000 0 0
IL1B 0.004 0.072 -10000 0 -0.44 12 12
Channel -0.008 0.07 -10000 0 -0.56 7 7
NLRP1 -0.004 0.037 -10000 0 -0.47 3 3
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.015 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.013 0.1 7 -10000 0 7
MAPK3 -0.001 0.011 -10000 0 -10000 0 0
MAPK1 -0.001 0.011 -10000 0 -10000 0 0
PGR -0.092 0.18 -10000 0 -0.43 106 106
PA/Cellular Receptors -0.008 0.075 -10000 0 -0.61 7 7
apoptosis -0.001 0.013 -10000 0 -0.1 7 7
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.007 0.066 -10000 0 -0.53 7 7
macrophage activation 0.017 0.012 -10000 0 -10000 0 0
TNF -0.019 0.12 -10000 0 -0.72 13 13
VCAM1 -0.016 0.08 -10000 0 -0.45 16 16
platelet activation -0.002 0.015 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.013 0.12 2 -10000 0 2
IL18 0.011 0.045 -10000 0 -0.36 6 6
negative regulation of macrophage activation -0.001 0.013 -10000 0 -0.1 7 7
LEF -0.001 0.013 -10000 0 -0.1 7 7
CASP1 -0.003 0.031 -10000 0 -0.28 4 4
mol:cAMP -0.002 0.015 -10000 0 -10000 0 0
necrosis -0.001 0.013 -10000 0 -0.1 7 7
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.067 -10000 0 -0.54 7 7
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 0 0 -9999 0 -10000 0 0
VDR -0.001 0.033 -9999 0 -0.74 1 1
Cbp/p300/PCAF -0.001 0.021 -9999 0 -0.48 1 1
EP300 0 0 -9999 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.028 -9999 0 -0.31 1 1
KAT2B -0.001 0.033 -9999 0 -0.74 1 1
MAPK14 0 0 -9999 0 -10000 0 0
AKT1 0.02 0.037 -9999 0 -0.31 3 3
RAR alpha/9cRA/Cyclin H -0.007 0.029 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.032 0.033 -9999 0 -0.41 1 1
CDC2 0.001 0 -9999 0 -10000 0 0
response to UV 0.001 0 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.008 0.03 -9999 0 -10000 0 0
NCOR2 -0.001 0.033 -9999 0 -0.74 1 1
VDR/VDR/Vit D3 -0.001 0.025 -9999 0 -0.56 1 1
RXRs/RARs/NRIP1/9cRA -0.024 0.083 -9999 0 -0.6 2 2
NCOA2 -0.001 0.033 -9999 0 -0.74 1 1
NCOA3 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.001 0.033 -9999 0 -0.74 1 1
RARG 0.01 0 -9999 0 -10000 0 0
RAR gamma1/9cRA 0 0 -9999 0 -10000 0 0
MAPK3 0.01 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
MAPK8 0.011 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.065 0.072 -9999 0 -0.56 3 3
RARA 0.014 0.043 -9999 0 -0.29 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.031 0.035 -9999 0 -0.41 1 1
PRKCA 0.01 0.047 -9999 0 -0.74 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.041 0.091 -9999 0 -0.63 2 2
RXRG -0.22 0.22 -9999 0 -0.42 266 266
RXRA 0.021 0.041 -9999 0 -0.31 2 2
RXRB 0.006 0.065 -9999 0 -0.41 2 2
VDR/Vit D3/DNA -0.001 0.025 -9999 0 -0.56 1 1
RBP1 -0.021 0.11 -9999 0 -0.57 18 18
CRBP1/9-cic-RA -0.015 0.079 -9999 0 -0.42 18 18
RARB 0.007 0.058 -9999 0 -0.74 3 3
PRKCG -0.031 0.15 -9999 0 -0.57 36 36
MNAT1 0 0 -9999 0 -10000 0 0
RAR alpha/RXRs -0.031 0.082 -9999 0 -0.66 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.013 0.071 -9999 0 -0.5 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.038 -9999 0 -0.4 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.041 0.091 -9999 0 -0.63 2 2
positive regulation of DNA binding -0.006 0.027 -9999 0 -10000 0 0
NRIP1 -0.037 0.085 -9999 0 -0.69 1 1
RXRs/RARs -0.048 0.092 -9999 0 -0.49 4 4
RXRs/RXRs/DNA/9cRA -0.07 0.075 -9999 0 -0.69 2 2
PRKACA 0 0 -9999 0 -10000 0 0
CDK7 0 0 -9999 0 -10000 0 0
TFIIH 0 0 -9999 0 -10000 0 0
RAR alpha/9cRA -0.005 0.018 -9999 0 -10000 0 0
CCNH 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
RAR gamma2/9cRA 0 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.001 0.026 -9999 0 -0.57 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.001 0.018 -9999 0 -0.26 2 2
response to UV 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
FYN -0.001 0.033 -9999 0 -0.74 1 1
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.054 0.19 -9999 0 -0.74 37 37
p38 alpha/TAB1 -0.013 0.05 -9999 0 -0.49 2 2
PRKG1 -0.068 0.21 -9999 0 -0.74 46 46
DUSP8 -0.015 0.1 -9999 0 -0.74 10 10
PGK/cGMP/p38 alpha -0.043 0.12 -9999 0 -0.38 46 46
apoptosis -0.013 0.048 -9999 0 -0.47 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN -0.003 0.046 -9999 0 -0.74 2 2
DUSP1 -0.087 0.24 -9999 0 -0.74 59 59
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
SRC 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.03 0.087 -9999 0 -0.38 12 12
BLK -0.036 0.15 -9999 0 -0.66 27 27
HCK -0.009 0.08 -9999 0 -0.74 6 6
MAP2K3 0 0 -9999 0 -10000 0 0
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.033 -9999 0 -0.74 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.032 0.067 -9999 0 -0.45 3 3
positive regulation of innate immune response 0.036 0.094 -9999 0 -0.41 12 12
LCK -0.001 0.033 -9999 0 -0.74 1 1
p38alpha-beta/MKP7 -0.02 0.072 -9999 0 -0.64 2 2
p38alpha-beta/MKP5 -0.021 0.075 -9999 0 -0.61 3 3
PGK/cGMP -0.052 0.16 -9999 0 -0.56 46 46
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.056 0.13 -9999 0 -0.56 14 14
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.004 0.053 -9999 0 -0.68 3 3
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.004 0.026 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.003 0.07 -10000 0 -10000 0 0
IL27/IL27R/JAK1 -0.028 0.097 -10000 0 -0.58 1 1
TBX21 -0.028 0.22 -10000 0 -0.62 43 43
IL12B 0.009 0.004 -10000 0 -10000 0 0
IL12A 0.001 0.072 -10000 0 -0.56 8 8
IL6ST -0.018 0.14 -10000 0 -0.74 18 18
IL27RA/JAK1 -0.003 0.013 -10000 0 -10000 0 0
IL27 0.008 0.007 -10000 0 -10000 0 0
TYK2 0.011 0.003 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.06 0.14 -10000 0 -0.7 3 3
T-helper 2 cell differentiation -0.003 0.07 -10000 0 -10000 0 0
T cell proliferation during immune response -0.003 0.07 -10000 0 -10000 0 0
MAPKKK cascade 0.003 0.07 -10000 0 -10000 0 0
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 0.001 0.003 -10000 0 -10000 0 0
IL12RB1 -0.038 0.18 -10000 0 -0.74 32 32
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.019 0.19 -10000 0 -0.65 11 11
IL27/IL27R/JAK2/TYK2 0.002 0.071 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.003 0.07 -10000 0 -10000 0 0
STAT1 (dimer) -0.058 0.16 0.51 4 -0.75 7 11
JAK2 0.006 0.006 -10000 0 -10000 0 0
JAK1 0.001 0.003 -10000 0 -10000 0 0
STAT2 (dimer) 0.004 0.066 -10000 0 -10000 0 0
T cell proliferation -0.049 0.18 -10000 0 -0.51 27 27
IL12/IL12R/TYK2/JAK2 0.008 0.092 -10000 0 -0.59 2 2
IL17A -0.06 0.14 -10000 0 -0.7 3 3
mast cell activation -0.003 0.07 -10000 0 -10000 0 0
IFNG 0.006 0.02 -10000 0 -0.13 4 4
T cell differentiation -0.003 0.005 -10000 0 -0.022 4 4
STAT3 (dimer) 0.004 0.066 -10000 0 -10000 0 0
STAT5A (dimer) 0.004 0.066 -10000 0 -10000 0 0
STAT4 (dimer) -0.003 0.087 -10000 0 -0.48 6 6
STAT4 -0.012 0.092 -10000 0 -0.74 8 8
T cell activation -0.007 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.019 0.08 -10000 0 -10000 0 0
GATA3 -0.033 0.24 -10000 0 -1.4 14 14
IL18 0.007 0.044 -10000 0 -0.56 3 3
positive regulation of mast cell cytokine production -0.012 0.058 -10000 0 -10000 0 0
IL27/EBI3 -0.002 0.041 -10000 0 -0.52 3 3
IL27RA 0.007 0.017 -10000 0 -10000 0 0
IL6 -0.12 0.28 -10000 0 -0.74 82 82
STAT5A 0 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.001 0.006 -10000 0 -10000 0 0
IL1B -0.003 0.084 -10000 0 -0.56 11 11
EBI3 0.001 0.054 -10000 0 -0.69 3 3
TNF -0.005 0.09 -10000 0 -0.55 13 13
LPA receptor mediated events

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
GNB1/GNG2 -0.009 0.079 -9999 0 -0.66 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.046 -9999 0 -10000 0 0
AP1 -0.056 0.14 -9999 0 -0.38 64 64
mol:PIP3 -0.02 0.077 -9999 0 -0.58 3 3
AKT1 -0.006 0.05 -9999 0 -0.57 3 3
PTK2B 0.017 0.037 -9999 0 -0.34 2 2
RHOA 0.027 0.02 -9999 0 -10000 0 0
PIK3CB 0 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0 0.081 -9999 0 -0.45 3 3
MAGI3 -0.001 0.033 -9999 0 -0.74 1 1
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.011 0.057 -9999 0 -0.41 6 6
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.06 -9999 0 -0.39 8 8
NF kappa B1 p50/RelA -0.023 0.065 -9999 0 -0.64 1 1
endothelial cell migration 0.016 0.087 -9999 0 -0.82 5 5
ADCY4 0.017 0.097 -9999 0 -0.61 6 6
ADCY5 0.012 0.094 -9999 0 -0.66 4 4
ADCY6 0.031 0.069 -9999 0 -0.59 4 4
ADCY7 0.032 0.067 -9999 0 -0.66 3 3
ADCY1 0.032 0.068 -9999 0 -0.66 3 3
ADCY2 0.018 0.081 -9999 0 -0.6 4 4
ADCY3 0.032 0.067 -9999 0 -0.66 3 3
ADCY8 -0.036 0.12 -9999 0 -0.65 5 5
ADCY9 0.031 0.072 -9999 0 -0.65 4 4
GSK3B 0.024 0.035 -9999 0 -0.38 1 1
arachidonic acid secretion 0.035 0.069 -9999 0 -0.58 4 4
GNG2 -0.007 0.073 -9999 0 -0.74 5 5
TRIP6 0 0.004 -9999 0 -10000 0 0
GNAO1 0.018 0.062 -9999 0 -0.54 5 5
HRAS 0 0 -9999 0 -10000 0 0
NFKBIA 0.017 0.073 -9999 0 -0.38 1 1
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.058 -9999 0 -0.92 2 2
JUN 0 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.003 0.038 -9999 0 -0.48 3 3
TIAM1 -0.004 0.069 -9999 0 -1.1 2 2
PIK3R1 0 0.001 -9999 0 -10000 0 0
mol:IP3 -0.001 0.082 -9999 0 -0.46 3 3
PLCB3 0.022 0.036 -9999 0 -0.43 3 3
FOS -0.09 0.24 -9999 0 -0.74 61 61
positive regulation of mitosis 0.035 0.069 -9999 0 -0.58 4 4
LPA/LPA1-2-3 -0.013 0.071 -9999 0 -0.48 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.025 0.047 -9999 0 -0.42 2 2
GNAZ 0.014 0.073 -9999 0 -0.52 8 8
EGFR/PI3K-beta/Gab1 -0.02 0.08 -9999 0 -0.61 3 3
positive regulation of dendritic cell cytokine production -0.013 0.071 -9999 0 -0.48 6 6
LPA/LPA2/MAGI-3 -0.002 0.023 -9999 0 -0.48 1 1
ARHGEF1 -0.003 0.04 -9999 0 -0.54 2 2
GNAI2 0.02 0.049 -9999 0 -0.64 2 2
GNAI3 0.02 0.049 -9999 0 -0.43 5 5
GNAI1 0.019 0.064 -9999 0 -0.51 5 5
LPA/LPA3 -0.014 0.077 -9999 0 -0.46 14 14
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.005 0.054 -9999 0 -0.5 5 5
HB-EGF/EGFR -0.05 0.14 -9999 0 -0.41 61 61
HBEGF -0.025 0.14 -9999 0 -0.48 45 45
mol:DAG -0.001 0.082 -9999 0 -0.46 3 3
cAMP biosynthetic process 0.02 0.075 -9999 0 -0.66 4 4
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
GNB1 -0.001 0.033 -9999 0 -0.74 1 1
LYN 0.015 0.084 -9999 0 -0.55 3 3
GNAQ -0.009 0.05 -9999 0 -0.38 5 5
LPAR2 0 0.001 -9999 0 -10000 0 0
LPAR3 -0.017 0.1 -9999 0 -0.62 14 14
LPAR1 -0.004 0.055 -9999 0 -0.83 2 2
IL8 0.001 0.13 -9999 0 -0.44 19 19
PTK2 0.021 0.072 -9999 0 -0.45 6 6
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.011 0.058 -9999 0 -0.41 6 6
EGFR -0.015 0.12 -9999 0 -0.63 18 18
PLCG1 -0.016 0.084 -9999 0 -0.36 10 10
PLD2 0.021 0.072 -9999 0 -0.45 6 6
G12/G13 -0.004 0.043 -9999 0 -0.58 2 2
PI3K-beta -0.007 0.061 -9999 0 -0.69 3 3
cell migration 0.002 0.032 -9999 0 -0.26 2 2
SLC9A3R2 -0.004 0.057 -9999 0 -0.74 3 3
PXN 0.025 0.048 -9999 0 -0.43 2 2
HRAS/GTP -0.009 0.066 -9999 0 -0.61 4 4
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.032 0.13 -9999 0 -0.57 28 28
PRKCE 0.008 0.033 -9999 0 -0.74 1 1
PRKCD 0.006 0.079 -9999 0 -0.47 2 2
Gi(beta/gamma) -0.01 0.078 -9999 0 -0.65 5 5
mol:LPA -0.001 0.016 -9999 0 -0.21 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.001 0.059 -9999 0 -0.64 1 1
MAPKKK cascade 0.035 0.069 -9999 0 -0.58 4 4
contractile ring contraction involved in cytokinesis 0.027 0.019 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.1 0.17 -9999 0 -0.39 127 127
GNA15 -0.008 0.047 -9999 0 -0.38 4 4
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT 0.024 0.061 -9999 0 -0.4 8 8
GNA11 -0.008 0.047 -9999 0 -0.38 4 4
Rac1/GTP -0.004 0.062 -9999 0 -0.98 2 2
MMP2 0.016 0.088 -9999 0 -0.83 5 5
IGF1 pathway

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
NCK2 0 0 -9999 0 -10000 0 0
PTK2 0 0 -9999 0 -10000 0 0
CRKL 0.008 0.076 -9999 0 -0.38 18 18
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0 0 -9999 0 -10000 0 0
IRS1/Crk -0.014 0.072 -9999 0 -0.38 18 18
IGF-1R heterotetramer/IGF1/PTP1B -0.017 0.084 -9999 0 -0.45 18 18
AKT1 0.028 0.067 -9999 0 -10000 0 0
BAD 0.034 0.064 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.008 0.076 -9999 0 -0.38 18 18
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.014 0.072 -9999 0 -0.39 18 18
RAF1 0.037 0.061 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.013 0.068 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.016 0.079 -9999 0 -0.42 18 18
PIK3CA 0 0 -9999 0 -10000 0 0
RPS6KB1 0.028 0.067 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.032 0.054 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.012 0.06 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.013 0.066 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.007 0.017 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.014 0.072 -9999 0 -0.39 18 18
Crk/p130 Cas/Paxillin -0.013 0.064 -9999 0 -10000 0 0
IGF1R 0.007 0.017 -9999 0 -10000 0 0
IGF1 -0.018 0.14 -9999 0 -0.74 19 19
IRS2/Crk -0.016 0.074 -9999 0 -0.4 3 3
PI3K -0.013 0.067 -9999 0 -0.36 18 18
apoptosis 0.009 0.047 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD 0.019 0.092 -9999 0 -0.46 18 18
RAF1/14-3-3 E 0.04 0.055 -9999 0 -10000 0 0
BAD/14-3-3 0.038 0.06 -9999 0 -10000 0 0
PRKCZ 0.028 0.067 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.01 0.049 -9999 0 -10000 0 0
PTPN1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.018 0.091 -9999 0 -0.49 18 18
BCAR1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.014 0.073 -9999 0 -0.39 18 18
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.014 0.072 -9999 0 -0.38 18 18
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0.008 0.076 -9999 0 -0.38 18 18
IRS1 0.001 0.082 -9999 0 -0.42 18 18
IRS2 0.006 0.084 -9999 0 -0.39 21 21
IGF-1R heterotetramer/IGF1 -0.021 0.11 -9999 0 -0.56 19 19
GRB2 0 0 -9999 0 -10000 0 0
PDPK1 -0.012 0.063 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKD1 0.006 0.13 -9999 0 -0.48 30 30
SHC1 0 0 -9999 0 -10000 0 0
S1P3 pathway

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
PDGFRB -0.001 0.033 -9999 0 -0.74 1 1
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.006 0.039 -9999 0 -0.31 7 7
GNAO1 0.007 0.05 -9999 0 -0.63 3 3
S1P/S1P3/G12/G13 0 0.001 -9999 0 -10000 0 0
AKT1 -0.003 0.024 -9999 0 -0.46 1 1
AKT3 0.036 0.1 -9999 0 -1.3 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.033 -9999 0 -0.74 1 1
GNAI2 0.011 0.002 -9999 0 -10000 0 0
GNAI3 0.011 0.002 -9999 0 -10000 0 0
GNAI1 0.01 0.033 -9999 0 -0.74 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.011 0.002 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.033 0.043 -9999 0 -10000 0 0
MAPK3 0.038 0.041 -9999 0 -10000 0 0
MAPK1 0.038 0.041 -9999 0 -10000 0 0
JAK2 0.041 0.044 -9999 0 -0.43 1 1
CXCR4 0.038 0.049 -9999 0 -0.63 1 1
FLT1 0.012 0.001 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.038 0.041 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.033 0.043 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.033 -9999 0 -10000 0 0
VEGFA 0.012 0.001 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.03 0.04 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.022 0.005 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.078 0.14 -9999 0 -0.32 123 123
GNAQ -0.001 0.033 -9999 0 -0