PARADIGM pathway analysis of mRNA expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1G15Z1P
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1G15Z1P
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 52 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 mediated by p38-alpha and p38-beta 242
Signaling events mediated by Stem cell factor receptor (c-Kit) 221
Endothelins 145
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 145
EGFR-dependent Endothelin signaling events 144
Class IB PI3K non-lipid kinase events 125
IGF1 pathway 123
FOXM1 transcription factor network 103
Arf6 signaling events 102
Nongenotropic Androgen signaling 96
Results
Summary Table

The following list describes the columns found in ##REF##406.

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

  • 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.

Pathway.Name 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 mediated by p38-alpha and p38-beta 242 10682 44 -0.6 0.034 1000 -1000 -0.013 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 221 17240 78 -1 0.32 1000 -1000 -0.018 -1000
Endothelins 145 13938 96 -0.81 0.16 1000 -1000 -0.024 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 145 9923 68 -0.89 0.45 1000 -1000 -0.054 -1000
EGFR-dependent Endothelin signaling events 144 3026 21 -0.31 0.047 1000 -1000 -0.03 -1000
Class IB PI3K non-lipid kinase events 125 375 3 -0.11 -1000 1000 -1000 -0.021 -1000
IGF1 pathway 123 7053 57 -0.27 0.11 1000 -1000 -0.022 -1000
FOXM1 transcription factor network 103 5275 51 -0.13 0.69 1000 -1000 0.01 -1000
Arf6 signaling events 102 6372 62 -0.31 0.081 1000 -1000 -0.004 -1000
Nongenotropic Androgen signaling 96 5012 52 -0.57 0.3 1000 -1000 -0.022 -1000
Glucocorticoid receptor regulatory network 83 9547 114 -0.95 0.29 1000 -1000 -0.048 -1000
Signaling events mediated by PTP1B 78 5939 76 -0.37 0.19 1000 -1000 -0.032 -1000
Calcium signaling in the CD4+ TCR pathway 72 2257 31 -0.36 0.039 1000 -1000 -0.036 -1000
HIF-1-alpha transcription factor network 71 5396 76 -0.39 0.072 1000 -1000 -0.02 -1000
S1P1 pathway 71 2581 36 -0.62 0.045 1000 -1000 -0.024 -1000
BMP receptor signaling 69 5602 81 -0.4 0.11 1000 -1000 -0.026 -1000
PDGFR-alpha signaling pathway 69 3043 44 -0.7 0.063 1000 -1000 -0.028 -1000
Ephrin B reverse signaling 67 3240 48 -0.18 0.06 1000 -1000 -0.027 -1000
Ras signaling in the CD4+ TCR pathway 64 1094 17 -0.2 0.033 1000 -1000 -0.01 -1000
Plasma membrane estrogen receptor signaling 59 5151 86 -0.25 0.17 1000 -1000 -0.043 -1000
IL4-mediated signaling events 56 5128 91 -0.52 0.14 1000 -1000 -0.11 -1000
IL6-mediated signaling events 56 4243 75 -0.37 0.072 1000 -1000 -0.025 -1000
Integrins in angiogenesis 53 4459 84 -0.39 0.13 1000 -1000 -0.014 -1000
FAS signaling pathway (CD95) 52 2469 47 -0.88 0.059 1000 -1000 -0.025 -1000
IL23-mediated signaling events 49 2978 60 -0.79 0.064 1000 -1000 -0.004 -1000
EPHB forward signaling 48 4135 85 -0.18 0.15 1000 -1000 -0.058 -1000
Visual signal transduction: Rods 48 2509 52 -0.43 0.073 1000 -1000 -0.018 -1000
E-cadherin signaling in keratinocytes 48 2099 43 -0.27 0.036 1000 -1000 -0.019 -1000
Fc-epsilon receptor I signaling in mast cells 46 4485 97 -0.36 0.04 1000 -1000 -0.051 -1000
PLK1 signaling events 43 3706 85 -0.036 0.17 1000 -1000 -0.027 -1000
Aurora B signaling 42 2815 67 -0.38 0.23 1000 -1000 -0.019 -1000
Signaling events mediated by the Hedgehog family 41 2132 52 -0.14 0.067 1000 -1000 -0.015 -1000
Glypican 1 network 41 1973 48 -0.39 0.07 1000 -1000 -0.022 -1000
ErbB4 signaling events 40 2811 69 -0.36 0.14 1000 -1000 -0.013 -1000
S1P5 pathway 39 673 17 -0.17 0.067 1000 -1000 -0.003 -1000
Insulin Pathway 39 2918 74 -0.28 0.091 1000 -1000 -0.026 -1000
p75(NTR)-mediated signaling 38 4817 125 -0.13 0.092 1000 -1000 -0.032 -1000
Nectin adhesion pathway 36 2280 63 -0.074 0.054 1000 -1000 -0.03 -1000
TCGA08_retinoblastoma 36 295 8 -0.024 0.057 1000 -1000 -0.005 -1000
Presenilin action in Notch and Wnt signaling 35 2148 61 -0.38 0.1 1000 -1000 -0.025 -1000
Stabilization and expansion of the E-cadherin adherens junction 35 2653 74 -0.27 0.073 1000 -1000 -0.06 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 33 2858 85 -0.54 0.046 1000 -1000 -0.032 -1000
S1P4 pathway 33 834 25 -0.17 0.045 1000 -1000 -0.012 -1000
LPA receptor mediated events 32 3290 102 -0.36 0.092 1000 -1000 -0.046 -1000
ErbB2/ErbB3 signaling events 30 1974 65 -0.35 0.046 1000 -1000 -0.057 -1000
Neurotrophic factor-mediated Trk receptor signaling 30 3713 120 -0.24 0.12 1000 -1000 -0.039 -1000
Signaling events regulated by Ret tyrosine kinase 29 2411 82 -0.1 0.11 1000 -1000 -0.058 -1000
Syndecan-3-mediated signaling events 29 1015 35 -0.36 0.074 1000 -1000 -0.017 -1000
IL27-mediated signaling events 29 1514 51 -0.37 0.067 1000 -1000 -0.034 -1000
TCGA08_rtk_signaling 29 769 26 -0.27 0.042 1000 -1000 -0.022 -1000
FOXA2 and FOXA3 transcription factor networks 28 1304 46 -0.75 0.051 1000 -1000 0 -1000
TCR signaling in naïve CD8+ T cells 27 2524 93 -0.039 0.082 1000 -1000 -0.045 -1000
Regulation of nuclear SMAD2/3 signaling 26 3603 136 -0.37 0.075 1000 -1000 -0.038 -1000
amb2 Integrin signaling 26 2142 82 -0.52 0.13 1000 -1000 -0.006 -1000
mTOR signaling pathway 25 1362 53 -0.051 0.044 1000 -1000 -0.031 -1000
RXR and RAR heterodimerization with other nuclear receptor 25 1315 52 -0.38 0.1 1000 -1000 -0.024 -1000
HIF-2-alpha transcription factor network 25 1103 43 -0.22 0.26 1000 -1000 -0.1 -1000
Syndecan-4-mediated signaling events 24 1642 67 -0.39 0.15 1000 -1000 -0.031 -1000
IL12-mediated signaling events 23 2080 87 -0.83 0.087 1000 -1000 -0.033 -1000
Syndecan-2-mediated signaling events 23 1616 69 -0.32 0.13 1000 -1000 -0.018 -1000
Ceramide signaling pathway 23 1781 76 -0.25 0.083 1000 -1000 -0.025 -1000
Reelin signaling pathway 23 1294 56 -0.055 0.083 1000 -1000 -0.02 -1000
IL1-mediated signaling events 23 1456 62 -0.05 0.067 1000 -1000 -0.019 -1000
S1P3 pathway 23 984 42 -0.17 0.062 1000 -1000 -0.02 -1000
Angiopoietin receptor Tie2-mediated signaling 23 2111 88 -0.39 0.13 1000 -1000 -0.054 -1000
Canonical Wnt signaling pathway 22 1158 51 -0.38 0.16 1000 -1000 -0.041 -1000
Coregulation of Androgen receptor activity 21 1655 76 -0.22 0.053 1000 -1000 -0.012 -1000
Osteopontin-mediated events 21 829 38 -0.36 0.14 1000 -1000 -0.005 -1000
Thromboxane A2 receptor signaling 21 2265 105 -0.27 0.066 1000 -1000 -0.035 -1000
Regulation of p38-alpha and p38-beta 20 1110 54 -0.31 0.071 1000 -1000 -0.043 -1000
Regulation of Telomerase 20 2109 102 -0.36 0.085 1000 -1000 -0.007 -1000
Regulation of Androgen receptor activity 20 1413 70 -0.43 0.078 1000 -1000 -0.027 -1000
Syndecan-1-mediated signaling events 19 669 34 -0.041 0.11 1000 -1000 -0.013 -1000
IL2 signaling events mediated by PI3K 19 1113 58 -0.12 0.048 1000 -1000 -0.023 -1000
TCGA08_p53 18 126 7 -0.009 0.028 1000 -1000 -0.006 -1000
Signaling mediated by p38-gamma and p38-delta 18 275 15 -0.006 0.034 1000 -1000 -0.023 -1000
E-cadherin signaling in the nascent adherens junction 16 1223 76 -0.039 0.059 1000 -1000 -0.05 -1000
Noncanonical Wnt signaling pathway 15 395 26 -0.015 0.04 1000 -1000 -0.023 -1000
Hedgehog signaling events mediated by Gli proteins 15 1010 65 -0.17 0.077 1000 -1000 -0.022 -1000
Caspase cascade in apoptosis 14 1096 74 -0.15 0.049 1000 -1000 -0.027 -1000
Cellular roles of Anthrax toxin 14 575 39 -0.063 0.038 1000 -1000 -0.015 -1000
Signaling events mediated by PRL 14 499 34 -0.31 0.051 1000 -1000 -0.025 -1000
E-cadherin signaling events 14 74 5 0.006 0.035 1000 -1000 0.02 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 13 616 45 -0.006 0.06 1000 -1000 -0.031 -1000
FoxO family signaling 12 824 64 0.001 0.15 1000 -1000 -0.014 -1000
Wnt signaling 12 88 7 -0.015 0.04 1000 -1000 -0.011 -1000
BCR signaling pathway 12 1276 99 -0.15 0.092 1000 -1000 -0.042 -1000
Arf6 downstream pathway 11 514 43 -0.09 0.092 1000 -1000 -0.038 -1000
IFN-gamma pathway 11 798 68 -0.019 0.098 1000 -1000 -0.038 -1000
Class I PI3K signaling events mediated by Akt 11 814 68 -0.15 0.061 1000 -1000 -0.015 -1000
ceramide signaling pathway 11 587 49 -0.074 0.053 1000 -1000 -0.02 -1000
Signaling events mediated by VEGFR1 and VEGFR2 11 1419 125 -0.38 0.075 1000 -1000 -0.034 -1000
Sphingosine 1-phosphate (S1P) pathway 10 281 28 -0.17 0.053 1000 -1000 -0.014 -1000
PLK2 and PLK4 events 10 31 3 0.017 0.055 1000 -1000 0.003 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 10 548 54 -0.041 0.08 1000 -1000 -0.028 -1000
JNK signaling in the CD4+ TCR pathway 9 167 17 -0.039 0.089 1000 -1000 -0.017 -1000
EPO signaling pathway 9 516 55 -0.093 0.067 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class II 8 658 75 -0.06 0.066 1000 -1000 -0.029 -1000
TRAIL signaling pathway 8 422 48 -0.002 0.047 1000 -1000 -0.023 -1000
Effects of Botulinum toxin 8 229 26 0 0.069 1000 -1000 0 -1000
VEGFR1 specific signals 8 502 56 -0.38 0.075 1000 -1000 -0.036 -1000
Circadian rhythm pathway 7 168 22 -0.02 0.1 1000 -1000 -0.022 -1000
Paxillin-independent events mediated by a4b1 and a4b7 7 259 37 -0.019 0.084 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class III 7 310 40 -0.061 0.062 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 6 243 38 0 0.068 1000 -1000 0 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 578 83 -0.074 0.065 1000 -1000 -0.011 -1000
Paxillin-dependent events mediated by a4b1 6 229 36 -0.07 0.075 1000 -1000 -0.027 -1000
Arf6 trafficking events 6 481 71 -0.26 0.056 1000 -1000 -0.027 -1000
p38 MAPK signaling pathway 6 274 44 -0.015 0.066 1000 -1000 -0.016 -1000
Insulin-mediated glucose transport 5 160 32 -0.099 0.053 1000 -1000 -0.009 -1000
Retinoic acid receptors-mediated signaling 5 330 58 -0.053 0.08 1000 -1000 -0.02 -1000
PDGFR-beta signaling pathway 5 535 97 -0.034 0.08 1000 -1000 -0.048 -1000
Nephrin/Neph1 signaling in the kidney podocyte 4 158 34 -0.047 0.083 1000 -1000 -0.023 -1000
Canonical NF-kappaB pathway 4 173 39 0 0.074 1000 -1000 -0.011 -1000
Signaling events mediated by HDAC Class I 4 492 104 -0.21 0.081 1000 -1000 -0.033 -1000
Atypical NF-kappaB pathway 4 134 31 -0.019 0.048 1000 -1000 -0.01 -1000
IL2 signaling events mediated by STAT5 4 99 22 -0.018 0.08 1000 -1000 -0.01 -1000
Class I PI3K signaling events 4 354 73 -0.008 0.059 1000 -1000 -0.024 -1000
LPA4-mediated signaling events 2 29 12 -0.01 0.035 1000 -1000 -0.021 -1000
Aurora A signaling 2 133 60 0 0.12 1000 -1000 -0.01 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 25 23 -0.007 0.064 1000 -1000 -0.007 -1000
Ephrin A reverse signaling 1 7 7 0 0.043 1000 -1000 0 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 1 49 33 0 0.076 1000 -1000 -0.017 -1000
Rapid glucocorticoid signaling 1 25 20 0 0.043 1000 -1000 0 -1000
Arf1 pathway 1 54 54 -0.001 0.062 1000 -1000 -0.01 -1000
BARD1 signaling events 0 37 57 -0.075 0.12 1000 -1000 -0.045 -1000
a4b1 and a4b7 Integrin signaling 0 0 5 0.033 0.053 1000 -1000 0.02 -1000
Aurora C signaling 0 3 7 0 0.078 1000 -1000 -0.014 -1000
Glypican 2 network 0 0 4 0 0.032 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 25 27 0 0.077 1000 -1000 -0.026 -1000
Alternative NF-kappaB pathway 0 3 13 0 0.094 1000 -1000 0 -1000
Total 4315 262418 7203 -30 -990 131000 -131000 -3.1 -131000
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.6 0.54 0.39 4 -1 300 304
MKNK1 0.033 0.006 -10000 0 -10000 0 0
MAPK14 -0.2 0.2 -10000 0 -0.36 299 299
ATF2/c-Jun -0.26 0.32 -10000 0 -0.68 140 140
MAPK11 -0.18 0.2 -10000 0 -0.36 281 281
MITF -0.24 0.24 -10000 0 -0.42 301 301
MAPKAPK5 -0.23 0.22 -10000 0 -0.41 302 302
KRT8 -0.22 0.22 -10000 0 -0.39 299 299
MAPKAPK3 0.033 0.012 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.015 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.31 0.32 -10000 0 -0.55 303 303
CEBPB -0.21 0.23 0.3 1 -0.41 277 278
SLC9A1 -0.23 0.23 -10000 0 -0.42 298 298
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.24 0.24 -10000 0 -0.42 299 299
p38alpha-beta/MNK1 -0.24 0.28 -10000 0 -0.45 300 300
JUN -0.26 0.31 -10000 0 -0.68 140 140
PPARGC1A -0.28 0.29 0.28 1 -0.48 308 309
USF1 -0.21 0.21 -10000 0 -0.39 280 280
RAB5/GDP/GDI1 -0.17 0.18 -10000 0 -0.31 293 293
NOS2 -0.24 0.22 -10000 0 -0.41 302 302
DDIT3 -0.23 0.22 -10000 0 -0.41 297 297
RAB5A 0.034 0.005 -10000 0 -10000 0 0
HSPB1 -0.18 0.18 -10000 0 -0.34 267 267
p38alpha-beta/HBP1 -0.24 0.28 -10000 0 -0.46 298 298
CREB1 -0.25 0.24 -10000 0 -0.43 299 299
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.23 0.24 -10000 0 -0.41 289 289
RPS6KA4 -0.23 0.23 -10000 0 -0.42 298 298
PLA2G4A -0.36 0.27 -10000 0 -0.52 350 350
GDI1 -0.23 0.22 -10000 0 -0.41 297 297
TP53 -0.3 0.3 -10000 0 -0.54 292 292
RPS6KA5 -0.24 0.23 -10000 0 -0.42 309 309
ESR1 -0.29 0.27 0.31 1 -0.43 353 354
HBP1 0.034 0.005 -10000 0 -10000 0 0
MEF2C -0.26 0.26 -10000 0 -0.44 306 306
MEF2A -0.23 0.23 0.3 1 -0.41 298 299
EIF4EBP1 -0.25 0.25 -10000 0 -0.44 293 293
KRT19 -0.21 0.23 -10000 0 -0.42 256 256
ELK4 -0.21 0.21 -10000 0 -0.39 282 282
ATF6 -0.22 0.21 -10000 0 -0.39 289 289
ATF1 -0.25 0.24 -10000 0 -0.43 301 301
p38alpha-beta/MAPKAPK2 -0.22 0.24 -10000 0 -0.42 279 279
p38alpha-beta/MAPKAPK3 -0.25 0.28 -10000 0 -0.45 299 299
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.3 0.16 -10000 0 -0.38 368 368
CRKL -0.32 0.17 -10000 0 -0.4 384 384
HRAS -0.23 0.15 -10000 0 -0.34 214 214
mol:PIP3 -0.27 0.18 -10000 0 -0.39 294 294
SPRED1 0.031 0.037 -10000 0 -0.54 2 2
SPRED2 0.034 0.005 -10000 0 -10000 0 0
GAB1 -0.33 0.18 -10000 0 -0.42 394 394
FOXO3 -0.27 0.16 -10000 0 -0.37 321 321
AKT1 -0.29 0.18 -10000 0 -0.39 356 356
BAD -0.28 0.16 -10000 0 -0.37 316 316
megakaryocyte differentiation -0.32 0.18 -10000 0 -0.41 395 395
GSK3B -0.27 0.16 -10000 0 -0.37 287 287
RAF1 -0.19 0.13 -10000 0 -0.32 49 49
SHC1 0.027 0.014 -10000 0 -10000 0 0
STAT3 -0.33 0.18 -10000 0 -0.42 390 390
STAT1 -0.81 0.43 -10000 0 -1 408 408
HRAS/SPRED1 -0.19 0.14 -10000 0 -0.32 53 53
cell proliferation -0.33 0.17 -10000 0 -0.41 394 394
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
TEC 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.32 0.18 -10000 0 -0.4 393 393
HRAS/SPRED2 -0.19 0.14 -10000 0 -0.32 51 51
LYN/TEC/p62DOK -0.29 0.18 -10000 0 -0.4 323 323
MAPK3 -0.13 0.098 -10000 0 -0.3 10 10
STAP1 -0.32 0.18 -10000 0 -0.41 395 395
GRAP2 0.034 0.019 -10000 0 -10000 0 0
JAK2 -0.68 0.37 -10000 0 -0.85 400 400
STAT1 (dimer) -0.79 0.42 -10000 0 -0.97 413 413
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.28 0.19 -10000 0 -0.4 314 314
actin filament polymerization -0.32 0.17 -10000 0 -0.41 397 397
LYN 0.03 0.015 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.46 0.26 -10000 0 -0.58 403 403
PIK3R1 -0.019 0.16 -10000 0 -0.55 45 45
CBL/CRKL/GRB2 -0.28 0.17 -10000 0 -0.38 336 336
PI3K -0.32 0.2 -10000 0 -0.42 362 362
PTEN 0.026 0.068 -10000 0 -0.54 7 7
SCF/KIT/EPO/EPOR -0.94 0.51 -10000 0 -1.2 397 397
MAPK8 -0.33 0.18 -10000 0 -0.42 394 394
STAT3 (dimer) -0.32 0.17 -10000 0 -0.41 390 390
positive regulation of transcription -0.11 0.083 -10000 0 -0.25 7 7
mol:GDP -0.24 0.16 -10000 0 -0.36 227 227
PIK3C2B -0.3 0.18 -10000 0 -0.42 320 320
CBL/CRKL -0.3 0.16 -10000 0 -0.39 371 371
FER -0.33 0.18 -10000 0 -0.42 394 394
SH2B3 -0.33 0.18 -10000 0 -0.42 395 395
PDPK1 -0.24 0.17 -10000 0 -0.37 272 272
SNAI2 -0.34 0.2 -10000 0 -0.45 362 362
positive regulation of cell proliferation -0.58 0.31 -10000 0 -0.73 402 402
KITLG -0.011 0.069 -10000 0 -0.56 2 2
cell motility -0.58 0.31 -10000 0 -0.73 402 402
PTPN6 0.05 0.021 -10000 0 -10000 0 0
EPOR -0.23 0.19 -10000 0 -1.1 12 12
STAT5A (dimer) -0.48 0.26 -10000 0 -0.6 403 403
SOCS1 0.032 0.012 -10000 0 -10000 0 0
cell migration 0.32 0.17 0.41 393 -10000 0 393
SOS1 0.034 0.004 -10000 0 -10000 0 0
EPO 0.009 0.063 -10000 0 -10000 0 0
VAV1 0.038 0.025 -10000 0 -10000 0 0
GRB10 -0.34 0.18 -10000 0 -0.42 394 394
PTPN11 0.047 0.009 -10000 0 -10000 0 0
SCF/KIT -0.35 0.19 -10000 0 -0.44 397 397
GO:0007205 0.018 0.009 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.3 11 11
CBL 0.03 0.011 -10000 0 -10000 0 0
KIT -1 0.53 -10000 0 -1.3 398 398
MAP2K2 -0.15 0.11 -10000 0 -0.3 11 11
SHC/Grb2/SOS1 -0.27 0.18 -10000 0 -0.4 287 287
STAT5A -0.49 0.27 -10000 0 -0.62 403 403
GRB2 0.033 0.017 -10000 0 -10000 0 0
response to radiation -0.34 0.2 0.27 1 -0.44 363 364
SHC/GRAP2 0.039 0.026 -10000 0 -10000 0 0
PTPRO -0.33 0.18 -10000 0 -0.42 395 395
SH2B2 -0.33 0.18 -10000 0 -0.42 397 397
DOK1 0.036 0.016 -10000 0 -10000 0 0
MATK -0.33 0.18 -10000 0 -0.42 393 393
CREBBP -0.082 0.075 -10000 0 -0.18 63 63
BCL2 -0.43 0.51 -10000 0 -1.4 110 110
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.096 0.16 -10000 0 -0.35 134 134
PTK2B 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.29 -10000 0 -0.72 77 77
EDN1 -0.15 0.25 -10000 0 -0.54 147 147
EDN3 -0.39 0.25 -10000 0 -0.54 369 369
EDN2 0.096 0.077 -10000 0 -0.54 1 1
HRAS/GDP -0.25 0.23 -10000 0 -0.47 208 208
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.12 0.18 -10000 0 -0.39 114 114
ADCY4 -0.08 0.15 0.34 2 -0.3 126 128
ADCY5 -0.077 0.15 0.35 1 -0.3 129 130
ADCY6 -0.078 0.15 0.34 2 -0.3 130 132
ADCY7 -0.074 0.15 0.34 2 -0.3 125 127
ADCY1 -0.078 0.15 -10000 0 -0.3 126 126
ADCY2 -0.079 0.16 0.34 2 -0.31 132 134
ADCY3 -0.078 0.15 0.35 1 -0.3 128 129
ADCY8 -0.065 0.13 0.35 1 -0.31 68 69
ADCY9 -0.072 0.14 -10000 0 -0.3 118 118
arachidonic acid secretion -0.52 0.34 -10000 0 -0.69 372 372
ETB receptor/Endothelin-1/Gq/GTP -0.21 0.21 -10000 0 -0.37 271 271
GNAO1 0.03 0.012 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.089 0.16 -10000 0 -0.32 137 137
ETA receptor/Endothelin-1/Gs/GTP -0.085 0.15 -10000 0 -0.31 137 137
mol:GTP -0.007 0.008 -10000 0 -10000 0 0
COL3A1 -0.096 0.17 -10000 0 -0.35 126 126
EDNRB -0.21 0.29 -10000 0 -0.54 222 222
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.095 0.16 -10000 0 -0.36 80 80
CYSLTR1 -0.097 0.17 0.38 2 -0.35 132 134
SLC9A1 -0.065 0.11 -10000 0 -0.24 100 100
mol:GDP -0.27 0.25 -10000 0 -0.48 233 233
SLC9A3 -0.39 0.39 -10000 0 -0.74 230 230
RAF1 -0.35 0.27 -10000 0 -0.51 329 329
JUN -0.25 0.43 -10000 0 -1 108 108
JAK2 -0.097 0.16 -10000 0 -0.35 134 134
mol:IP3 -0.21 0.21 -10000 0 -0.43 187 187
ETA receptor/Endothelin-1 -0.12 0.19 -10000 0 -0.4 141 141
PLCB1 -0.048 0.2 -10000 0 -0.55 69 69
PLCB2 0.023 0.014 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.29 0.19 -10000 0 -0.4 368 368
FOS -0.69 0.43 -10000 0 -0.95 363 363
Gai/GDP -0.2 0.36 -10000 0 -0.95 81 81
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.26 0.26 -10000 0 -0.54 190 190
BCAR1 0.029 0.013 -10000 0 -10000 0 0
PRKCB1 -0.21 0.21 -10000 0 -0.42 194 194
GNAQ -0.008 0.009 -10000 0 -10000 0 0
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
GNAL 0.03 0.045 -10000 0 -0.54 3 3
Gs family/GDP -0.24 0.22 -10000 0 -0.46 204 204
ETA receptor/Endothelin-1/Gq/GTP -0.094 0.15 -10000 0 -0.34 85 85
MAPK14 -0.22 0.22 -10000 0 -0.42 232 232
TRPC6 -0.18 0.31 -10000 0 -0.78 77 77
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.23 -10000 0 -0.41 267 267
ETB receptor/Endothelin-2 -0.11 0.22 -10000 0 -0.32 242 242
ETB receptor/Endothelin-3 -0.42 0.27 -10000 0 -0.53 409 409
ETB receptor/Endothelin-1 -0.26 0.28 -10000 0 -0.48 292 292
MAPK3 -0.61 0.39 -10000 0 -0.83 367 367
MAPK1 -0.62 0.41 -10000 0 -0.86 367 367
Rac1/GDP -0.25 0.23 -10000 0 -0.46 222 222
cAMP biosynthetic process -0.028 0.15 0.4 5 -0.37 20 25
MAPK8 -0.18 0.3 -10000 0 -0.65 111 111
SRC 0.032 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.28 0.29 -10000 0 -0.56 217 217
p130Cas/CRK/Src/PYK2 -0.27 0.29 -10000 0 -0.57 193 193
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.25 0.23 -10000 0 -0.46 223 223
COL1A2 -0.22 0.27 0.42 1 -0.53 157 158
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.07 0.076 0.26 3 -0.4 3 6
mol:DAG -0.21 0.22 -10000 0 -0.43 189 189
MAP2K2 -0.47 0.32 -10000 0 -0.64 368 368
MAP2K1 -0.47 0.32 0.36 1 -0.64 368 369
EDNRA 0.007 0.057 -10000 0 -0.44 3 3
positive regulation of muscle contraction -0.088 0.14 -10000 0 -0.31 132 132
Gq family/GDP -0.21 0.21 -10000 0 -0.44 180 180
HRAS/GTP -0.26 0.24 -10000 0 -0.45 250 250
PRKCH -0.21 0.21 -10000 0 -0.44 179 179
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA -0.19 0.21 -10000 0 -0.44 165 165
PRKCB -0.21 0.21 -10000 0 -0.42 197 197
PRKCE -0.21 0.21 -10000 0 -0.44 179 179
PRKCD -0.21 0.21 -10000 0 -0.44 175 175
PRKCG -0.21 0.21 0.3 1 -0.44 182 183
regulation of vascular smooth muscle contraction -0.81 0.5 -10000 0 -1.1 363 363
PRKCQ -0.2 0.21 -10000 0 -0.44 175 175
PLA2G4A -0.59 0.4 -10000 0 -0.78 372 372
GNA14 0.026 0.072 -10000 0 -0.55 4 4
GNA15 0.021 0.03 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.024 -10000 0 -10000 0 0
Rac1/GTP -0.089 0.16 -10000 0 -0.32 136 136
MMP1 0.16 0.15 0.4 83 -10000 0 83
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.047 0.03 -10000 0 -10000 0 0
NFATC2 -0.084 0.23 0.5 1 -0.56 53 54
NFATC3 -0.15 0.17 0.31 1 -0.32 228 229
CD40LG -0.68 0.53 0.78 4 -1 319 323
ITCH -0.065 0.14 -10000 0 -0.52 1 1
CBLB -0.068 0.14 -10000 0 -0.25 183 183
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.31 0.74 7 -0.7 68 75
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.079 0.17 -10000 0 -0.3 190 190
T cell anergy -0.13 0.21 -10000 0 -0.4 181 181
TLE4 -0.067 0.2 -10000 0 -0.61 35 35
Jun/NFAT1-c-4/p21SNFT -0.58 0.55 0.69 3 -0.97 307 310
AP-1/NFAT1-c-4 -0.8 0.68 0.92 5 -1.2 319 324
IKZF1 -0.045 0.17 0.46 10 -0.46 26 36
T-helper 2 cell differentiation -0.12 0.29 0.52 1 -0.74 54 55
AP-1/NFAT1 -0.3 0.3 0.55 5 -0.52 281 286
CALM1 -0.037 0.11 -10000 0 -0.31 1 1
EGR2 -0.8 0.77 0.72 3 -1.5 258 261
EGR3 -0.88 0.76 0.75 2 -1.4 316 318
NFAT1/FOXP3 -0.033 0.18 0.46 8 -0.43 37 45
EGR1 -0.43 0.23 -10000 0 -0.54 409 409
JUN -0.064 0.22 0.26 1 -0.54 86 87
EGR4 0.001 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.056 0.09 -10000 0 -0.17 190 190
GBP3 -0.08 0.24 0.43 2 -0.74 43 45
FOSL1 0.034 0.01 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.54 0.53 0.66 3 -0.93 301 304
DGKA -0.053 0.16 0.46 1 -0.46 26 27
CREM 0.033 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.76 0.56 -10000 0 -1.1 342 342
CTLA4 -0.025 0.16 0.42 15 -0.41 21 36
NFAT1-c-4 (dimer)/EGR1 -0.78 0.57 -10000 0 -1.1 348 348
NFAT1-c-4 (dimer)/EGR4 -0.56 0.53 0.67 1 -0.94 308 309
FOS -0.35 0.27 0.25 1 -0.54 342 343
IFNG -0.098 0.3 0.58 6 -0.78 48 54
T cell activation -0.39 0.34 0.68 3 -0.75 157 160
MAF -0.008 0.14 -10000 0 -0.54 33 33
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.45 0.41 0.77 276 -0.7 2 278
TNF -0.67 0.48 -10000 0 -0.98 340 340
FASLG -0.89 0.79 0.85 3 -1.4 324 327
TBX21 0.028 0.15 0.28 12 -0.54 30 42
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.043 0.036 0.22 10 -10000 0 10
PTPN1 -0.049 0.16 0.42 1 -0.46 26 27
NFAT1-c-4/ICER1 -0.56 0.53 0.6 1 -0.94 304 305
GATA3 0.031 0.17 -10000 0 -0.54 34 34
T-helper 1 cell differentiation -0.096 0.3 0.58 6 -0.76 48 54
IL2RA -0.26 0.31 0.73 6 -0.69 74 80
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.052 0.16 -10000 0 -0.48 22 22
E2F1 0.055 0.047 0.24 2 -10000 0 2
PPARG -0.38 0.26 -10000 0 -0.54 365 365
SLC3A2 -0.05 0.16 -10000 0 -0.57 11 11
IRF4 0.038 0.027 -10000 0 -10000 0 0
PTGS2 -0.77 0.57 0.73 4 -1.1 332 336
CSF2 -0.68 0.53 0.78 4 -1 318 322
JunB/Fra1/NFAT1-c-4 -0.53 0.52 0.6 2 -0.91 301 303
IL4 -0.13 0.3 0.52 1 -0.78 53 54
IL5 -0.68 0.52 0.73 4 -1 318 322
IL2 -0.39 0.35 0.73 2 -0.77 148 150
IL3 -0.089 0.15 -10000 0 -0.91 13 13
RNF128 -0.21 0.33 -10000 0 -0.63 191 191
NFATC1 -0.45 0.42 0.7 2 -0.77 275 277
CDK4 0.28 0.28 0.6 83 -0.69 1 84
PTPRK -0.09 0.24 -10000 0 -0.72 49 49
IL8 -0.67 0.53 0.73 5 -1 323 328
POU2F1 0.033 0.015 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.013 -9999 0 -10000 0 0
EGFR -0.27 0.29 -9999 0 -0.54 264 264
EGF/EGFR -0.29 0.26 -9999 0 -0.43 360 360
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.19 0.21 -9999 0 -0.36 266 266
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.032 0.038 -9999 0 -0.54 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.15 0.27 -9999 0 -0.54 162 162
EGF/EGFR dimer/SHC -0.23 0.23 -9999 0 -0.41 281 281
mol:GDP -0.19 0.21 -9999 0 -0.36 266 266
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.13 0.26 -9999 0 -0.54 147 147
GRB2/SOS1 0.047 0.018 -9999 0 -10000 0 0
HRAS/GTP -0.18 0.19 -9999 0 -0.34 255 255
SHC1 0.027 0.014 -9999 0 -10000 0 0
HRAS/GDP -0.18 0.2 -9999 0 -0.35 255 255
FRAP1 -0.2 0.17 -9999 0 -0.35 259 259
EGF/EGFR dimer -0.31 0.26 -9999 0 -0.46 357 357
SOS1 0.034 0.004 -9999 0 -10000 0 0
GRB2 0.033 0.017 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.084 0.2 -9999 0 -0.39 152 152
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.11 0.25 0.54 125 -10000 0 125
PI3K Class IB/PDE3B -0.11 0.25 -10000 0 -0.54 125 125
PDE3B -0.11 0.25 -10000 0 -0.54 125 125
IGF1 pathway

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
NCK2 0.034 0.007 -10000 0 -10000 0 0
PTK2 0.027 0.014 -10000 0 -10000 0 0
CRKL -0.17 0.2 -10000 0 -0.34 254 254
GRB2/SOS1/SHC 0.051 0.033 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
IRS1/Crk -0.16 0.21 -10000 0 -0.34 257 257
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.21 -10000 0 -0.36 220 220
AKT1 -0.16 0.19 0.23 1 -0.35 219 220
BAD -0.16 0.18 0.22 1 -0.34 203 204
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.17 0.2 -10000 0 -0.34 257 257
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.21 -10000 0 -0.34 256 256
RAF1 -0.12 0.18 -10000 0 -0.46 71 71
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.22 -10000 0 -0.34 222 222
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.17 0.23 -10000 0 -0.37 258 258
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.18 0.23 1 -0.35 190 191
GNB2L1 0.033 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.1 0.15 0.33 1 -0.39 62 63
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.18 -10000 0 -0.33 166 166
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.07 0.18 -10000 0 -0.3 158 158
IGF-1R heterotetramer -0.049 0.14 -10000 0 -0.64 21 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.34 255 255
Crk/p130 Cas/Paxillin -0.13 0.21 -10000 0 -0.33 236 236
IGF1R -0.049 0.14 -10000 0 -0.64 21 21
IGF1 -0.27 0.3 -10000 0 -0.57 251 251
IRS2/Crk -0.22 0.26 -10000 0 -0.42 266 266
PI3K -0.15 0.24 -10000 0 -0.37 242 242
apoptosis 0.11 0.15 0.38 69 -0.31 1 70
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
PRKCD -0.18 0.23 -10000 0 -0.39 235 235
RAF1/14-3-3 E -0.096 0.17 0.34 1 -0.4 66 67
BAD/14-3-3 -0.12 0.16 0.32 1 -0.41 69 70
PRKCZ -0.16 0.19 0.22 1 -0.34 223 224
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.17 -10000 0 -0.41 73 73
PTPN1 0.036 0.028 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.19 0.23 -10000 0 -0.41 244 244
BCAR1 0.029 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.095 0.19 -10000 0 -0.33 174 174
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.15 0.21 -10000 0 -0.34 255 255
GRB10 0.029 0.051 -10000 0 -0.54 4 4
PTPN11 -0.17 0.2 -10000 0 -0.34 256 256
IRS1 -0.18 0.22 -10000 0 -0.37 257 257
IRS2 -0.23 0.26 -10000 0 -0.43 277 277
IGF-1R heterotetramer/IGF1 -0.2 0.26 -10000 0 -0.45 249 249
GRB2 0.033 0.017 -10000 0 -10000 0 0
PDPK1 -0.16 0.21 -10000 0 -0.36 223 223
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PRKD1 -0.22 0.28 -10000 0 -0.47 241 241
SHC1 0.027 0.014 -10000 0 -10000 0 0
FOXM1 transcription factor 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
NFATC3 0.56 0.46 1.1 112 -1 2 114
PLK1 0.22 0.2 0.65 39 -10000 0 39
BIRC5 0.36 0.25 0.69 110 -0.66 3 113
HSPA1B 0.56 0.46 1.1 137 -0.95 3 140
MAP2K1 0.17 0.13 0.34 131 -10000 0 131
BRCA2 0.59 0.49 1.2 121 -1.3 1 122
FOXM1 0.6 0.61 1.3 142 -1.2 3 145
XRCC1 0.56 0.47 1.1 112 -1.1 2 114
FOXM1B/p19 0.074 0.29 0.98 5 -1.1 3 8
Cyclin D1/CDK4 0.48 0.46 1 104 -0.9 9 113
CDC2 0.61 0.52 1.2 142 -1 3 145
TGFA 0.44 0.52 1 125 -0.94 20 145
SKP2 0.57 0.47 1.1 120 -1.1 2 122
CCNE1 0.085 0.062 0.23 26 -10000 0 26
CKS1B 0.61 0.5 1.2 146 -1.1 2 148
RB1 0.27 0.35 0.75 113 -0.77 8 121
FOXM1C/SP1 0.5 0.45 1 97 -1 7 104
AURKB 0.2 0.31 0.64 68 -0.79 23 91
CENPF 0.68 0.53 1.3 164 -1.3 1 165
CDK4 0.091 0.06 0.24 15 -10000 0 15
MYC 0.31 0.44 0.96 85 -0.87 10 95
CHEK2 0.16 0.13 0.34 128 -10000 0 128
ONECUT1 0.49 0.48 1.1 126 -0.9 6 132
CDKN2A -0.016 0.077 -10000 0 -0.22 17 17
LAMA4 0.55 0.48 1.1 119 -1.1 4 123
FOXM1B/HNF6 0.49 0.5 1.1 109 -1.1 6 115
FOS -0.13 0.65 1.1 48 -1 80 128
SP1 0.031 0.033 -10000 0 -0.21 5 5
CDC25B 0.57 0.47 1.2 115 -1.1 2 117
response to radiation 0.11 0.093 0.24 127 -10000 0 127
CENPB 0.56 0.46 1.1 120 -1.1 2 122
CENPA 0.63 0.51 1.2 138 -1.3 1 139
NEK2 0.69 0.52 1.2 167 -1.2 1 168
HIST1H2BA 0.56 0.46 1.1 109 -1.1 2 111
CCNA2 0.11 0.075 0.24 17 -10000 0 17
EP300 0.032 0.008 -10000 0 -10000 0 0
CCNB1/CDK1 0.59 0.52 1.2 122 -1.3 2 124
CCNB2 0.62 0.51 1.2 149 -1.1 2 151
CCNB1 0.63 0.54 1.3 136 -1.1 2 138
ETV5 0.53 0.52 1.1 122 -1.1 11 133
ESR1 0.37 0.61 1.1 110 -0.96 17 127
CCND1 0.5 0.51 1.1 136 -0.92 9 145
GSK3A 0.14 0.1 0.31 73 -10000 0 73
Cyclin A-E1/CDK1-2 0.2 0.13 0.38 120 -10000 0 120
CDK2 0.07 0.036 0.22 9 -10000 0 9
G2/M transition of mitotic cell cycle 0.14 0.12 0.28 169 -10000 0 169
FOXM1B/Cbp/p300 0.3 0.38 0.87 15 -1 3 18
GAS1 0.27 0.71 1.1 103 -1.1 56 159
MMP2 0.55 0.48 1.1 111 -1.2 6 117
RB1/FOXM1C 0.45 0.46 0.99 120 -1 6 126
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Arf6 signaling events

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
CENTA1/KIF3B 0.018 0.018 -10000 0 -0.34 1 1
ARNO/beta Arrestin1-2 -0.11 0.14 -10000 0 -0.26 236 236
EGFR -0.27 0.29 -10000 0 -0.54 264 264
EPHA2 0.026 0.063 -10000 0 -0.54 6 6
USP6 0.032 0.018 -10000 0 -10000 0 0
IQSEC1 0.033 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.31 0.26 -10000 0 -0.46 357 357
ARRB2 0.015 0.029 -10000 0 -0.33 3 3
mol:GTP 0.013 0.029 0.12 26 -10000 0 26
ARRB1 0.03 0.028 -10000 0 -0.54 1 1
FBXO8 0.033 0.007 -10000 0 -10000 0 0
TSHR 0.029 0.045 -10000 0 -0.54 3 3
EGF -0.15 0.27 -10000 0 -0.54 162 162
somatostatin receptor activity 0 0 -10000 0 -0.001 213 213
ARAP2 0 0 -10000 0 0 211 211
mol:GDP -0.14 0.14 -10000 0 -0.27 210 210
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 210 210
ITGA2B 0.034 0.013 -10000 0 -10000 0 0
ARF6 0.033 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.058 -10000 0 -0.32 6 6
ADAP1 0 0 -10000 0 0 131 131
KIF13B 0.027 0.029 -10000 0 -0.54 1 1
HGF/MET 0.005 0.14 -10000 0 -0.4 51 51
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.14 0.12 -10000 0 -0.26 211 211
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.26 0.24 -10000 0 -0.41 344 344
ADRB2 -0.26 0.29 -10000 0 -0.54 259 259
receptor agonist activity 0 0 -10000 0 0 207 207
actin filament binding 0 0 -10000 0 0 240 240
SRC 0.032 0.008 -10000 0 -10000 0 0
ITGB3 0.035 0.018 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -0.001 141 141
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 136 136
ARF6/GDP -0.03 0.084 0.18 1 -0.27 28 29
ARF6/GDP/GULP/ACAP1 -0.16 0.18 -10000 0 -0.35 197 197
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.031 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 -10000 0 0
ACAP2 0 0 -10000 0 0 230 230
LHCGR/beta Arrestin2 0.022 0.048 -10000 0 -0.47 3 3
EFNA1 0.028 0.015 -10000 0 -10000 0 0
HGF 0.034 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 204 204
CYTH2 -0.002 0.002 -10000 0 -0.004 240 240
NCK1 0.034 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 137 137
endosomal lumen acidification 0 0 0.001 4 0 144 148
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.069 0.22 -10000 0 -0.54 91 91
GNAQ/ARNO -0.003 0.003 -10000 0 -0.007 136 136
mol:Phosphatidic acid 0 0 -10000 0 0 230 230
PIP3-E 0 0 -10000 0 0 310 310
MET -0.023 0.17 -10000 0 -0.54 50 50
GNA14 0.042 0.067 -10000 0 -0.54 4 4
GNA15 0.035 0.019 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -0.001 167 167
GNA11 0.033 0.006 -10000 0 -10000 0 0
LHCGR 0.031 0.046 -10000 0 -0.54 3 3
AGTR1 -0.19 0.3 -10000 0 -0.54 206 206
desensitization of G-protein coupled receptor protein signaling pathway 0.022 0.048 -10000 0 -0.46 3 3
IPCEF1/ARNO -0.21 0.18 -10000 0 -0.31 354 354
alphaIIb/beta3 Integrin 0.05 0.019 -10000 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.006 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.01 0.13 -10000 0 -0.32 66 66
regulation of S phase of mitotic cell cycle -0.045 0.13 -10000 0 -0.3 90 90
GNAO1 0.029 0.012 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
SHBG/T-DHT 0.021 0.007 -10000 0 -10000 0 0
PELP1 0.029 0.01 -10000 0 -10000 0 0
AKT1 0.011 0.014 0.14 6 -10000 0 6
MAP2K1 -0.11 0.11 -10000 0 -0.36 61 61
T-DHT/AR -0.033 0.14 -10000 0 -0.4 67 67
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.003 -10000 0 -0.007 361 361
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.033 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
mol:GDP -0.079 0.17 -10000 0 -0.39 95 95
cell proliferation -0.3 0.21 -10000 0 -0.43 331 331
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
FOS -0.57 0.37 -10000 0 -0.8 362 362
mol:Ca2+ -0.038 0.037 -10000 0 -0.075 229 229
MAPK3 -0.21 0.16 -10000 0 -0.37 166 166
MAPK1 -0.16 0.16 -10000 0 -0.39 83 83
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 -0.003 0.002 -10000 0 -0.004 351 351
cAMP biosynthetic process 0.018 0.027 -10000 0 -10000 0 0
GNG2 0.032 0.026 -10000 0 -0.54 1 1
potassium channel inhibitor activity -0.003 0.002 -10000 0 -0.004 351 351
HRAS/GTP -0.059 0.12 -10000 0 -0.33 64 64
actin cytoskeleton reorganization 0.016 0.094 -10000 0 -0.28 42 42
SRC 0.03 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.003 0.002 -10000 0 -0.004 351 351
PI3K 0.008 0.11 -10000 0 -0.34 42 42
apoptosis 0.3 0.22 0.43 357 -10000 0 357
T-DHT/AR/PELP1 -0.015 0.13 -10000 0 -0.35 67 67
HRAS/GDP -0.069 0.17 -10000 0 -0.46 66 66
CREB1 -0.32 0.23 -10000 0 -0.46 357 357
RAC1-CDC42/GTP 0.025 0.099 -10000 0 -0.29 42 42
AR -0.044 0.2 -10000 0 -0.55 66 66
GNB1 0.034 0.011 -10000 0 -10000 0 0
RAF1 -0.086 0.11 -10000 0 -0.34 61 61
RAC1-CDC42/GDP -0.033 0.17 -10000 0 -0.44 66 66
T-DHT/AR/PELP1/Src -0.005 0.13 -10000 0 -0.33 65 65
MAP2K2 -0.12 0.11 -10000 0 -0.36 61 61
T-DHT/AR/PELP1/Src/PI3K -0.045 0.13 -10000 0 -0.3 90 90
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
SHBG 0.03 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.11 0.19 -10000 0 -0.48 76 76
mol:T-DHT -0.001 0.002 -10000 0 -0.004 90 90
RAC1 0.034 0.005 -10000 0 -10000 0 0
GNRH1 -0.001 0.057 0.14 1 -0.4 10 11
Gi family/GTP -0.11 0.14 -10000 0 -0.26 186 186
CDC42 0.033 0.007 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.11 0.11 0.52 5 -10000 0 5
SMARCC2 0.034 0.004 -10000 0 -10000 0 0
SMARCC1 0.035 0.019 -10000 0 -10000 0 0
TBX21 -0.12 0.22 0.4 1 -0.82 32 33
SUMO2 0.001 0.025 -10000 0 -10000 0 0
STAT1 (dimer) 0.071 0.067 0.28 25 -10000 0 25
FKBP4 0.036 0.024 -10000 0 -10000 0 0
FKBP5 0.024 0.082 -10000 0 -0.54 10 10
GR alpha/HSP90/FKBP51/HSP90 0.13 0.14 0.31 67 -0.34 5 72
PRL -0.06 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.51 184 -10000 0 184
RELA -0.095 0.12 0.27 3 -0.26 30 33
FGG 0.23 0.23 0.45 217 -10000 0 217
GR beta/TIF2 0.11 0.14 0.29 117 -0.33 4 121
IFNG -0.39 0.34 -10000 0 -0.69 226 226
apoptosis -0.25 0.18 -10000 0 -0.53 49 49
CREB1 0.057 0.041 -10000 0 -10000 0 0
histone acetylation 0.036 0.14 0.4 36 -0.33 9 45
BGLAP -0.093 0.14 -10000 0 -0.5 6 6
GR/PKAc 0.15 0.14 0.34 47 -0.31 3 50
NF kappa B1 p50/RelA -0.16 0.2 0.47 3 -0.33 157 160
SMARCD1 0.034 0.004 -10000 0 -10000 0 0
MDM2 0.12 0.099 0.22 181 -10000 0 181
GATA3 0.039 0.17 -10000 0 -0.54 34 34
AKT1 0.028 0.024 -10000 0 -10000 0 0
CSF2 -0.007 0.11 -10000 0 -10000 0 0
GSK3B 0.001 0.027 -10000 0 -10000 0 0
NR1I3 -0.19 0.17 -10000 0 -0.54 11 11
CSN2 0.19 0.19 0.38 200 -10000 0 200
BRG1/BAF155/BAF170/BAF60A 0.084 0.026 -10000 0 -10000 0 0
NFATC1 0.037 0.038 -10000 0 -0.54 2 2
POU2F1 0.033 0.015 -10000 0 -10000 0 0
CDKN1A 0.023 0.12 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.011 0.006 -10000 0 -10000 0 0
SFN 0.033 0.04 -10000 0 -0.54 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.14 0.14 0.34 40 -0.33 4 44
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.65 0.33 -10000 0 -0.8 421 421
JUN -0.21 0.24 0.38 2 -0.48 160 162
IL4 -0.12 0.15 -10000 0 -0.46 18 18
CDK5R1 0.027 0.014 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.35 0.24 -10000 0 -0.49 326 326
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.15 0.14 0.34 40 -0.35 3 43
cortisol/GR alpha (monomer) 0.29 0.31 0.57 231 -10000 0 231
NCOA2 0.028 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.42 0.26 -10000 0 -0.58 358 358
AP-1/NFAT1-c-4 -0.58 0.41 -10000 0 -0.82 340 340
AFP -0.17 0.2 -10000 0 -0.57 31 31
SUV420H1 0.031 0.01 -10000 0 -10000 0 0
IRF1 0.2 0.18 0.49 58 -10000 0 58
TP53 0.046 0.034 -10000 0 -0.51 1 1
PPP5C 0.036 0.016 -10000 0 -10000 0 0
KRT17 -0.89 0.65 -10000 0 -1.4 321 321
KRT14 -0.82 0.63 -10000 0 -1.3 320 320
TBP 0.039 0.011 -10000 0 -10000 0 0
CREBBP 0.18 0.15 0.3 281 -0.28 1 282
HDAC1 0.029 0.01 -10000 0 -10000 0 0
HDAC2 0.029 0.021 -10000 0 -10000 0 0
AP-1 -0.58 0.41 -10000 0 -0.83 340 340
MAPK14 0.01 0.023 -10000 0 -10000 0 0
MAPK10 -0.011 0.082 -10000 0 -0.55 10 10
MAPK11 0 0.025 -10000 0 -10000 0 0
KRT5 -0.95 0.63 -10000 0 -1.4 351 351
interleukin-1 receptor activity -0.003 0.006 -10000 0 -10000 0 0
NCOA1 0.036 0.027 -10000 0 -0.54 1 1
STAT1 0.071 0.068 0.28 25 -10000 0 25
CGA -0.085 0.16 0.42 1 -0.49 10 11
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.19 0.37 92 -10000 0 92
MAPK3 -0.001 0.024 -10000 0 -10000 0 0
MAPK1 0.009 0.023 -10000 0 -10000 0 0
ICAM1 -0.26 0.25 0.5 4 -0.51 169 173
NFKB1 -0.095 0.11 0.32 1 -0.26 26 27
MAPK8 -0.15 0.19 0.57 1 -0.36 142 143
MAPK9 0.009 0.024 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.19 -10000 0 -0.55 51 51
BAX 0.029 0.074 -10000 0 -10000 0 0
POMC -0.14 0.19 -10000 0 -1.2 3 3
EP300 0.18 0.14 0.29 275 -10000 0 275
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.52 193 -10000 0 193
proteasomal ubiquitin-dependent protein catabolic process 0.091 0.11 0.3 61 -10000 0 61
SGK1 0.23 0.17 0.36 299 -0.43 1 300
IL13 -0.3 0.25 -10000 0 -0.69 62 62
IL6 -0.75 0.48 0.61 1 -1 371 372
PRKACG 0.032 0.026 -10000 0 -0.54 1 1
IL5 -0.25 0.2 -10000 0 -0.66 29 29
IL2 -0.42 0.32 -10000 0 -0.7 238 238
CDK5 0.031 0.022 -10000 0 -10000 0 0
PRKACB 0.035 0.082 -10000 0 -0.54 8 8
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
IL8 -0.24 0.26 0.49 5 -0.5 180 185
CDK5R1/CDK5 0.036 0.021 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.095 0.18 0.42 3 -0.4 29 32
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.5 218 -10000 0 218
SMARCA4 0.035 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.17 0.16 0.34 182 -10000 0 182
NF kappa B1 p50/RelA/Cbp -0.003 0.2 0.48 26 -0.35 5 31
JUN (dimer) -0.21 0.24 0.38 2 -0.48 160 162
YWHAH 0.033 0.014 -10000 0 -10000 0 0
VIPR1 -0.11 0.16 -10000 0 -0.52 30 30
NR3C1 0.19 0.2 0.38 194 -0.42 6 200
NR4A1 0.014 0.12 -10000 0 -0.55 23 23
TIF2/SUV420H1 0.038 0.022 -10000 0 -10000 0 0
MAPKKK cascade -0.25 0.18 -10000 0 -0.53 49 49
cortisol/GR alpha (dimer)/Src-1 0.27 0.26 0.51 230 -10000 0 230
PBX1 0.042 0.041 -10000 0 -10000 0 0
POU1F1 0.038 0.026 -10000 0 -0.54 1 1
SELE -0.26 0.35 0.59 2 -0.71 118 120
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.16 0.34 184 -10000 0 184
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.5 218 -10000 0 218
mol:cortisol 0.18 0.17 0.33 237 -10000 0 237
MMP1 -0.022 0.34 0.42 4 -0.95 51 55
Signaling events mediated by PTP1B

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
PDGFRB 0.033 0.006 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.24 0.21 -10000 0 -0.41 237 237
PTP1B/AKT1 -0.16 0.15 0.25 1 -0.29 218 219
FYN 0.029 0.037 -10000 0 -0.54 2 2
p210 bcr-abl/PTP1B -0.19 0.16 0.25 1 -0.31 262 263
EGFR -0.28 0.28 -10000 0 -0.56 264 264
EGF/EGFR -0.35 0.26 -10000 0 -0.5 356 356
CSF1 0.034 0.008 -10000 0 -10000 0 0
AKT1 0.035 0.016 -10000 0 -10000 0 0
INSR 0.033 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.16 0.17 0.34 1 -0.31 195 196
Insulin Receptor/Insulin -0.11 0.13 -10000 0 -0.34 46 46
HCK 0.036 0.022 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
TYK2 -0.18 0.16 0.33 2 -0.31 218 220
EGF -0.18 0.26 -10000 0 -0.56 162 162
YES1 0.031 0.027 -10000 0 -0.54 1 1
CAV1 -0.37 0.23 -10000 0 -0.49 365 365
TXN 0.028 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.19 0.18 -10000 0 -0.34 230 230
cell migration 0.19 0.16 0.31 262 -0.25 1 263
STAT3 0.031 0.007 -10000 0 -10000 0 0
PRLR 0.073 0.062 -10000 0 -10000 0 0
ITGA2B 0.032 0.013 -10000 0 -10000 0 0
CSF1R 0.033 0.006 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.081 0.048 -10000 0 -10000 0 0
FGR 0.033 0.007 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.17 0.16 0.24 1 -0.3 236 237
Crk/p130 Cas -0.16 0.16 -10000 0 -0.31 204 204
DOK1 -0.15 0.14 0.27 1 -0.42 48 49
JAK2 -0.081 0.14 -10000 0 -0.53 31 31
Jak2/Leptin Receptor/Leptin -0.25 0.2 -10000 0 -0.44 205 205
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
PTPN1 -0.19 0.16 0.25 1 -0.31 263 264
LYN 0.03 0.015 -10000 0 -10000 0 0
CDH2 0.057 0.054 -10000 0 -10000 0 0
SRC -0.051 0.12 -10000 0 -0.67 15 15
ITGB3 0.033 0.018 -10000 0 -10000 0 0
CAT1/PTP1B -0.14 0.18 0.36 1 -0.42 88 89
CAPN1 0.031 0.013 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -10000 0 0
PI3K -0.12 0.16 -10000 0 -0.4 65 65
mol:H2O2 -0.005 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.22 0.19 -10000 0 -0.41 193 193
negative regulation of transcription -0.08 0.14 -10000 0 -0.52 31 31
FCGR2A 0.03 0.025 -10000 0 -10000 0 0
FER 0.027 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.045 0.018 -10000 0 -10000 0 0
BLK 0.039 0.043 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.051 0.03 -10000 0 -10000 0 0
RHOA 0.029 0.007 -10000 0 -10000 0 0
LEPR -0.33 0.28 -10000 0 -0.54 317 317
BCAR1 0.029 0.012 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.033 0.017 -10000 0 -10000 0 0
mol:NADPH -0.006 0.004 -10000 0 -10000 0 0
TRPV6 -0.005 0.15 0.42 2 -0.4 40 42
PRL 0.037 0.009 -10000 0 -10000 0 0
SOCS3 0.001 0.25 -10000 0 -1.3 16 16
SPRY2 -0.32 0.28 -10000 0 -0.55 298 298
Insulin Receptor/Insulin/IRS1 0.014 0.13 -10000 0 -0.35 59 59
CSF1/CSF1R -0.16 0.16 -10000 0 -0.31 206 206
Ras protein signal transduction 0.089 0.17 0.65 38 -10000 0 38
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
INS 0.033 0.007 -10000 0 -10000 0 0
LEP -0.24 0.29 -10000 0 -0.55 235 235
STAT5B -0.14 0.16 0.26 1 -0.36 95 96
STAT5A -0.14 0.16 0.26 1 -0.36 96 97
GRB2 0.033 0.017 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.18 0.16 0.24 1 -0.31 219 220
CSN2 0.079 0.062 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
LAT -0.035 0.077 -10000 0 -0.64 3 3
YBX1 0.044 0.027 -10000 0 -10000 0 0
LCK 0.048 0.043 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
NOX4 0.051 0.053 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.008 0.058 0.26 9 -0.35 2 11
NFATC2 0.01 0.054 0.26 9 -0.34 1 10
NFATC3 0.012 0.052 0.26 9 -10000 0 9
CD40LG -0.22 0.29 0.6 15 -0.51 186 201
PTGS2 -0.32 0.36 0.57 15 -0.62 260 275
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.032 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.032 -10000 0 -10000 0 0
CALM1 0.033 0.018 -10000 0 -10000 0 0
JUN -0.064 0.22 -10000 0 -0.54 86 86
mol:Ca2+ -0.003 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.012 -10000 0 -10000 0 0
FOSL1 0.034 0.01 -10000 0 -10000 0 0
CREM 0.033 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.031 0.17 0.45 15 -0.35 56 71
FOS -0.36 0.27 -10000 0 -0.54 342 342
IFNG -0.19 0.31 0.64 18 -0.51 184 202
AP-1/NFAT1-c-4 -0.25 0.34 0.7 11 -0.59 191 202
FASLG -0.19 0.29 0.64 17 -0.48 177 194
NFAT1-c-4/ICER1 0.016 0.098 0.4 9 -0.28 1 10
IL2RA -0.21 0.3 0.62 16 -0.51 183 199
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSF2 -0.22 0.3 0.61 16 -0.51 187 203
JunB/Fra1/NFAT1-c-4 0.039 0.11 0.41 9 -0.32 4 13
IL4 -0.22 0.29 0.58 15 -0.51 189 204
IL2 -0.009 0.15 -10000 0 -0.97 11 11
IL3 -0.009 0.13 -10000 0 -0.77 11 11
FKBP1A 0.033 0.012 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.033 0.015 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 0.007 0.43 0.81 1 -0.72 76 77
HDAC7 0.007 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.005 0.37 0.82 4 -0.69 50 54
SMAD4 0.032 0.027 -10000 0 -0.54 1 1
ID2 0.005 0.42 -10000 0 -0.7 81 81
AP1 -0.33 0.27 -10000 0 -0.48 351 351
ABCG2 -0.011 0.44 -10000 0 -0.72 86 86
HIF1A 0.023 0.13 0.32 4 -0.29 15 19
TFF3 -0.047 0.44 -10000 0 -0.7 100 100
GATA2 0.021 0.048 -10000 0 -10000 0 0
AKT1 0.021 0.13 0.33 3 -0.19 26 29
response to hypoxia -0.003 0.11 0.25 13 -0.16 65 78
MCL1 -0.027 0.39 -10000 0 -0.72 74 74
NDRG1 -0.014 0.4 0.88 1 -0.71 73 74
SERPINE1 0.014 0.44 0.84 7 -0.7 81 88
FECH 0.001 0.42 -10000 0 -0.7 81 81
FURIN 0.009 0.43 -10000 0 -0.71 81 81
NCOA2 0.034 0.023 -10000 0 -10000 0 0
EP300 0.035 0.17 0.45 15 -0.29 32 47
HMOX1 0.012 0.44 0.86 4 -0.71 80 84
BHLHE40 -0.051 0.39 0.72 3 -0.72 76 79
BHLHE41 -0.051 0.39 0.72 3 -0.72 76 79
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.043 0.16 -10000 0 -0.39 3 3
ENG 0.046 0.14 0.46 1 -0.41 2 3
JUN -0.072 0.22 -10000 0 -0.55 86 86
RORA -0.004 0.43 -10000 0 -0.7 88 88
ABCB1 -0.29 0.47 -10000 0 -0.94 160 160
TFRC 0.009 0.43 0.86 5 -0.7 81 86
CXCR4 0.013 0.43 0.86 1 -0.72 76 77
TF -0.004 0.44 -10000 0 -0.73 83 83
CITED2 -0.003 0.43 -10000 0 -0.7 87 87
HIF1A/ARNT -0.068 0.44 0.9 3 -0.83 68 71
LDHA -0.011 0.13 -10000 0 -0.74 13 13
ETS1 0.001 0.42 -10000 0 -0.72 76 76
PGK1 0.009 0.43 0.83 3 -0.7 83 86
NOS2 -0.051 0.39 0.72 3 -0.72 76 79
ITGB2 0.009 0.43 0.85 4 -0.7 83 87
ALDOA 0.007 0.42 -10000 0 -0.7 81 81
Cbp/p300/CITED2 -0.008 0.42 0.81 2 -0.77 66 68
FOS -0.36 0.27 -10000 0 -0.55 342 342
HK2 0.006 0.43 -10000 0 -0.71 81 81
SP1 -0.018 0.094 -10000 0 -0.22 49 49
GCK 0.067 0.22 0.69 1 -0.52 2 3
HK1 0.007 0.43 -10000 0 -0.7 84 84
NPM1 0.003 0.42 -10000 0 -0.71 80 80
EGLN1 -0.021 0.4 -10000 0 -0.71 76 76
CREB1 0.04 0.01 -10000 0 -10000 0 0
PGM1 0.003 0.43 -10000 0 -0.7 82 82
SMAD3 0.034 0.007 -10000 0 -10000 0 0
EDN1 -0.39 0.59 0.62 1 -1.2 157 158
IGFBP1 0.005 0.43 -10000 0 -0.72 78 78
VEGFA 0.071 0.36 0.8 19 -0.59 47 66
HIF1A/JAB1 0.041 0.1 0.3 6 -0.41 4 10
CP -0.061 0.51 0.84 5 -0.79 117 122
CXCL12 -0.084 0.48 -10000 0 -0.78 118 118
COPS5 0.033 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4 0.047 0.028 -10000 0 -0.25 3 3
BNIP3 0.002 0.43 0.85 1 -0.7 84 85
EGLN3 0.024 0.44 0.85 8 -0.71 79 87
CA9 0.017 0.44 0.85 6 -0.7 83 89
TERT -0.009 0.42 -10000 0 -0.71 78 78
ENO1 0.006 0.43 -10000 0 -0.7 81 81
PFKL 0.004 0.42 -10000 0 -0.71 79 79
NCOA1 0.035 0.027 -10000 0 -0.54 1 1
ADM -0.1 0.5 -10000 0 -0.76 133 133
ARNT 0.021 0.098 -10000 0 -0.16 1 1
HNF4A 0.036 0.009 -10000 0 -10000 0 0
ADFP -0.051 0.39 0.72 3 -0.72 76 79
SLC2A1 0.072 0.36 0.81 16 -0.58 49 65
LEP -0.14 0.48 -10000 0 -0.79 132 132
HIF1A/ARNT/Cbp/p300 -0.017 0.36 0.81 2 -0.7 52 54
EPO 0.071 0.32 0.79 13 -0.6 25 38
CREBBP 0.042 0.16 0.45 15 -0.28 13 28
HIF1A/ARNT/Cbp/p300/HDAC7 -0.01 0.35 0.79 5 -0.67 49 54
PFKFB3 -0.003 0.42 -10000 0 -0.71 80 80
NT5E -0.002 0.44 -10000 0 -0.72 83 83
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.05 0.037 -10000 0 -10000 0 0
PDGFRB 0.029 0.007 -10000 0 -10000 0 0
SPHK1 -0.041 0.13 -10000 0 -0.9 10 10
mol:S1P -0.043 0.13 0.3 1 -0.83 10 11
S1P1/S1P/Gi -0.28 0.29 0.34 4 -0.5 286 290
GNAO1 0.004 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.25 0.26 0.41 3 -0.52 194 197
PLCG1 -0.26 0.27 0.34 5 -0.47 281 286
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.007 -10000 0 -10000 0 0
GNAI2 0.005 0.029 -10000 0 -10000 0 0
GNAI3 0.005 0.029 -10000 0 -10000 0 0
GNAI1 -0.19 0.27 -10000 0 -0.56 181 181
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.004 0.04 -10000 0 -10000 0 0
S1P1/S1P -0.064 0.13 0.29 6 -0.66 10 16
negative regulation of cAMP metabolic process -0.28 0.28 0.33 5 -0.49 286 291
MAPK3 -0.37 0.35 0.37 7 -0.64 303 310
calcium-dependent phospholipase C activity -0.005 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
KDR 0.028 0.011 -10000 0 -10000 0 0
PLCB2 -0.053 0.12 0.32 6 -0.58 10 16
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.063 0.1 -10000 0 -0.55 10 10
receptor internalization -0.063 0.11 0.24 5 -0.61 10 15
PTGS2 -0.62 0.53 0.45 2 -1 308 310
Rac1/GTP -0.063 0.1 -10000 0 -0.55 10 10
RHOA 0.033 0.007 -10000 0 -10000 0 0
VEGFA 0.045 0.047 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.28 0.28 0.33 5 -0.49 286 291
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.002 0.067 -10000 0 -0.56 6 6
MAPK1 -0.4 0.38 0.36 5 -0.68 308 313
S1P1/S1P/PDGFB-D/PDGFRB -0.078 0.14 0.34 8 -0.64 10 18
ABCC1 0.031 0.023 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.11 0.078 -10000 0 -0.3 3 3
SMAD6-7/SMURF1 0.063 0.02 -10000 0 -10000 0 0
NOG 0.031 0.03 -10000 0 -0.54 1 1
SMAD9 -0.088 0.24 -10000 0 -0.68 62 62
SMAD4 0.032 0.027 -10000 0 -0.54 1 1
SMAD5 -0.1 0.19 -10000 0 -0.44 81 81
BMP7/USAG1 -0.23 0.2 -10000 0 -0.36 356 356
SMAD5/SKI -0.094 0.19 -10000 0 -0.44 74 74
SMAD1 0.004 0.09 -10000 0 -0.44 10 10
BMP2 -0.23 0.29 -10000 0 -0.54 227 227
SMAD1/SMAD1/SMAD4 0.029 0.088 -10000 0 -0.43 6 6
BMPR1A 0.03 0.045 -10000 0 -0.54 3 3
BMPR1B 0.086 0.069 -10000 0 -10000 0 0
BMPR1A-1B/BAMBI 0.079 0.12 0.25 23 -0.3 38 61
AHSG 0.033 0.006 -10000 0 -10000 0 0
CER1 0.032 0.011 -10000 0 -10000 0 0
BMP2-4/CER1 -0.16 0.23 -10000 0 -0.38 257 257
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.18 -10000 0 -0.39 97 97
BMP2-4 (homodimer) -0.21 0.25 -10000 0 -0.43 273 273
RGMB 0.033 0.007 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.022 0.19 -10000 0 -0.28 167 167
RGMA -0.049 0.2 -10000 0 -0.54 72 72
SMURF1 0.034 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.18 -10000 0 -0.4 110 110
BMP2-4/USAG1 -0.4 0.27 -10000 0 -0.51 401 401
SMAD6/SMURF1/SMAD5 -0.095 0.19 -10000 0 -0.44 76 76
SOSTDC1 -0.37 0.26 -10000 0 -0.54 352 352
BMP7/BMPR2/BMPR1A-1B 0.1 0.071 -10000 0 -0.32 3 3
SKI 0.033 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) -0.16 0.27 -10000 0 -0.54 167 167
HFE2 0.031 0.038 -10000 0 -0.54 2 2
ZFYVE16 0.033 0.007 -10000 0 -10000 0 0
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
BMP2-4/CHRD -0.16 0.23 -10000 0 -0.38 258 258
SMAD5/SMAD5/SMAD4 -0.096 0.19 -10000 0 -0.44 76 76
MAPK1 0.032 0.008 -10000 0 -10000 0 0
TAK1/TAB family -0.088 0.17 -10000 0 -0.36 100 100
BMP7 (homodimer) 0.042 0.042 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
BMP6/FETUA -0.098 0.21 -10000 0 -0.39 170 170
SMAD1/SKI 0.015 0.096 -10000 0 -0.41 10 10
SMAD6 0.033 0.007 -10000 0 -10000 0 0
CTDSP2 0.033 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA -0.17 0.23 -10000 0 -0.38 257 257
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.048 0.045 -10000 0 -10000 0 0
BMPR2 (homodimer) 0.034 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.06 0.037 -10000 0 -0.34 2 2
BMPR1A-1B (homodimer) 0.082 0.063 -10000 0 -0.4 3 3
CHRDL1 -0.31 0.28 -10000 0 -0.54 299 299
ENDOFIN/SMAD1 0.014 0.098 -10000 0 -0.42 10 10
SMAD6-7/SMURF1/SMAD1 0.047 0.1 -10000 0 -0.47 6 6
SMAD6/SMURF1 0.034 0.005 -10000 0 -10000 0 0
BAMBI 0.016 0.16 -10000 0 -0.54 36 36
SMURF2 0.031 0.013 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.36 0.31 -10000 0 -0.54 350 350
BMP2-4/GREM1 -0.16 0.23 -10000 0 -0.37 262 262
SMAD7 0.033 0.007 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.078 0.23 -10000 0 -0.63 65 65
SMAD1/SMAD6 0.014 0.098 -10000 0 -0.42 11 11
TAK1/SMAD6 0.047 0.015 -10000 0 -10000 0 0
BMP7 0.042 0.042 -10000 0 -10000 0 0
BMP6 -0.16 0.27 -10000 0 -0.54 167 167
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.19 -10000 0 -0.4 110 110
PPM1A 0.033 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.012 0.093 -10000 0 -0.46 8 8
SMAD7/SMURF1 0.048 0.013 -10000 0 -10000 0 0
CTDSPL 0.031 0.037 -10000 0 -0.54 2 2
PPP1CA 0.034 0.02 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.034 0.005 -10000 0 -10000 0 0
PPP1R15A 0.032 0.036 -10000 0 -0.54 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.11 0.18 -10000 0 -0.38 112 112
CHRD 0.036 0.021 -10000 0 -10000 0 0
BMPR2 0.034 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.21 -10000 0 -0.45 112 112
BMP4 -0.038 0.19 -10000 0 -0.54 65 65
FST 0.032 0.04 -10000 0 -0.54 2 2
BMP2-4/NOG -0.16 0.22 -10000 0 -0.38 242 242
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.11 0.074 -10000 0 -0.3 3 3
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.091 0.18 -10000 0 -0.58 61 61
PDGF/PDGFRA/CRKL -0.055 0.14 -10000 0 -0.42 60 60
positive regulation of JUN kinase activity 0.015 0.12 -10000 0 -0.32 44 44
CRKL 0.032 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.056 0.14 -10000 0 -0.42 61 61
AP1 -0.7 0.45 -10000 0 -0.97 363 363
mol:IP3 -0.085 0.14 -10000 0 -0.45 56 56
PLCG1 -0.085 0.14 -10000 0 -0.45 56 56
PDGF/PDGFRA/alphaV Integrin -0.056 0.14 -10000 0 -0.42 63 63
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.085 0.14 -10000 0 -0.45 56 56
CAV3 0.031 0.037 -10000 0 -0.54 2 2
CAV1 -0.38 0.26 -10000 0 -0.54 360 360
SHC/Grb2/SOS1 0.016 0.12 -10000 0 -0.33 44 44
PDGF/PDGFRA/Shf -0.054 0.14 -10000 0 -0.42 60 60
FOS -0.69 0.44 -10000 0 -0.95 363 363
JUN -0.13 0.15 -10000 0 -0.46 84 84
oligodendrocyte development -0.056 0.14 -10000 0 -0.41 63 63
GRB2 0.033 0.017 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:DAG -0.085 0.14 -10000 0 -0.45 56 56
PDGF/PDGFRA -0.091 0.18 -10000 0 -0.58 61 61
actin cytoskeleton reorganization -0.053 0.14 -10000 0 -0.42 59 59
SRF 0.031 0.014 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
PI3K -0.028 0.18 -10000 0 -0.42 81 81
PDGF/PDGFRA/Crk/C3G 0.001 0.14 -10000 0 -0.36 61 61
JAK1 -0.065 0.13 -10000 0 -0.42 59 59
ELK1/SRF -0.065 0.12 0.33 1 -0.36 55 56
SHB 0.035 0.018 -10000 0 -10000 0 0
SHF 0.034 0.013 -10000 0 -10000 0 0
CSNK2A1 0.063 0.025 -10000 0 -10000 0 0
GO:0007205 -0.093 0.14 -10000 0 -0.46 61 61
SOS1 0.034 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.015 0.12 -10000 0 -0.32 44 44
PDGF/PDGFRA/SHB -0.053 0.14 -10000 0 -0.42 59 59
PDGF/PDGFRA/Caveolin-1 -0.34 0.24 -10000 0 -0.47 362 362
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
ELK1 -0.11 0.13 0.23 2 -0.44 60 62
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.055 0.14 -10000 0 -0.42 61 61
JAK-STAT cascade -0.065 0.13 -10000 0 -0.42 59 59
cell proliferation -0.054 0.14 -10000 0 -0.42 60 60
Ephrin B reverse 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
EFNB2 0.026 0.058 -10000 0 -0.54 5 5
EPHB2 0.042 0.036 -10000 0 -10000 0 0
EFNB1 0.016 0.02 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.048 0.18 -10000 0 -0.28 177 177
Ephrin B2/EPHB1-2 -0.075 0.19 -10000 0 -0.31 188 188
neuron projection morphogenesis -0.06 0.16 -10000 0 -0.27 177 177
Ephrin B1/EPHB1-2/Tiam1 -0.059 0.18 -10000 0 -0.3 180 180
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.057 0.18 -10000 0 -0.57 55 55
YES1 -0.068 0.26 -10000 0 -0.79 55 55
Ephrin B1/EPHB1-2/NCK2 -0.059 0.18 -10000 0 -0.3 179 179
PI3K -0.044 0.22 -10000 0 -0.52 77 77
mol:GDP -0.059 0.18 -10000 0 -0.29 180 180
ITGA2B 0.034 0.013 -10000 0 -10000 0 0
endothelial cell proliferation 0.038 0.046 -10000 0 -0.31 7 7
FYN -0.071 0.25 -10000 0 -0.79 55 55
MAP3K7 -0.058 0.19 -10000 0 -0.6 55 55
FGR -0.064 0.25 -10000 0 -0.79 55 55
TIAM1 0.035 0.012 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
RGS3 0.034 0.005 -10000 0 -10000 0 0
cell adhesion -0.045 0.2 -10000 0 -0.56 54 54
LYN -0.065 0.25 -10000 0 -0.78 55 55
Ephrin B1/EPHB1-2/Src Family Kinases -0.07 0.24 -10000 0 -0.73 56 56
Ephrin B1/EPHB1-2 -0.061 0.2 -10000 0 -0.64 55 55
SRC -0.064 0.25 -10000 0 -0.78 56 56
ITGB3 0.035 0.018 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 189 189
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
RAC1 0.034 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.038 0.046 -10000 0 -0.31 7 7
alphaIIb/beta3 Integrin 0.05 0.019 -10000 0 -10000 0 0
BLK -0.076 0.26 -10000 0 -0.8 55 55
HCK -0.064 0.25 -10000 0 -0.78 55 55
regulation of stress fiber formation 0.06 0.18 0.3 179 -10000 0 179
MAPK8 -0.055 0.18 -10000 0 -0.55 55 55
Ephrin B1/EPHB1-2/RGS3 -0.06 0.18 -10000 0 -0.3 180 180
endothelial cell migration -0.05 0.17 0.26 1 -0.5 58 59
NCK2 0.034 0.007 -10000 0 -10000 0 0
PTPN13 -0.027 0.2 -10000 0 -0.65 46 46
regulation of focal adhesion formation 0.06 0.18 0.3 179 -10000 0 179
chemotaxis 0.06 0.18 0.3 180 -10000 0 180
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.054 0.17 -10000 0 -0.28 177 177
angiogenesis -0.06 0.2 -10000 0 -0.64 55 55
LCK -0.06 0.26 -10000 0 -0.78 56 56
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.2 0.19 -9999 0 -0.35 217 217
MAP3K8 -0.048 0.19 -9999 0 -0.55 64 64
FOS -0.099 0.12 -9999 0 -0.36 28 28
PRKCA -0.006 0.028 -9999 0 -10000 0 0
PTPN7 -0.002 0.044 -9999 0 -10000 0 0
HRAS 0.032 0.013 -9999 0 -10000 0 0
PRKCB -0.013 0.009 -9999 0 -0.018 361 361
NRAS 0.033 0.016 -9999 0 -10000 0 0
RAS family/GTP 0.029 0.038 -9999 0 -10000 0 0
MAPK3 -0.03 0.075 -9999 0 -0.61 3 3
MAP2K1 -0.055 0.088 -9999 0 -0.32 20 20
ELK1 -0.015 0.037 -9999 0 -10000 0 0
BRAF -0.016 0.038 -9999 0 -0.25 6 6
mol:GTP -0.004 0.003 -9999 0 -0.006 362 362
MAPK1 -0.052 0.12 -9999 0 -0.45 28 28
RAF1 -0.017 0.035 -9999 0 -0.25 5 5
KRAS 0.032 0.017 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.008 0.16 -10000 0 -0.3 104 104
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.44 158 158
AKT1 -0.18 0.37 -10000 0 -0.77 134 134
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.18 0.38 -10000 0 -0.8 131 131
mol:Ca2+ -0.032 0.12 0.26 3 -0.31 46 49
IGF1R 0.01 0.12 -10000 0 -0.54 21 21
E2/ER alpha (dimer)/Striatin -0.019 0.17 0.23 1 -0.33 111 112
SHC1 0.027 0.014 -10000 0 -10000 0 0
apoptosis 0.17 0.35 0.74 134 -10000 0 134
RhoA/GTP -0.024 0.12 -10000 0 -0.27 81 81
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.13 0.23 0.31 1 -0.45 137 138
regulation of stress fiber formation 0.017 0.12 -10000 0 -0.25 19 19
E2/ERA-ERB (dimer) -0.023 0.17 -10000 0 -0.33 110 110
KRAS 0.034 0.017 -10000 0 -10000 0 0
G13/GTP -0.019 0.15 -10000 0 -0.29 109 109
pseudopodium formation -0.017 0.12 0.25 19 -10000 0 19
E2/ER alpha (dimer)/PELP1 -0.025 0.17 -10000 0 -0.33 110 110
GRB2 0.033 0.017 -10000 0 -10000 0 0
GNG2 0.032 0.026 -10000 0 -0.54 1 1
GNAO1 0.03 0.012 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.25 -10000 0 -0.5 143 143
E2/ER beta (dimer) 0.024 0.005 -10000 0 -10000 0 0
mol:GDP -0.046 0.18 0.23 12 -0.39 105 117
mol:NADP -0.14 0.25 -10000 0 -0.5 143 143
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 -0.036 0.12 0.26 3 -0.32 49 52
IGF-1R heterotetramer 0.01 0.12 -10000 0 -0.54 21 21
PLCB1 -0.036 0.13 -10000 0 -0.3 68 68
PLCB2 0.001 0.087 -10000 0 -0.46 8 8
IGF1 -0.25 0.29 -10000 0 -0.54 250 250
mol:L-citrulline -0.14 0.25 -10000 0 -0.5 143 143
RHOA 0.033 0.007 -10000 0 -10000 0 0
Gai/GDP -0.14 0.28 -10000 0 -0.73 79 79
JNK cascade 0.024 0.005 -10000 0 -10000 0 0
BCAR1 0.029 0.012 -10000 0 -10000 0 0
ESR2 0.033 0.007 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.06 0.26 0.18 103 -0.54 106 209
Gq family/GDP/Gbeta gamma 0.009 0.15 -10000 0 -0.83 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.03 0.14 -10000 0 -0.54 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.22 0.31 1 -0.45 108 109
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
E2/ER alpha (dimer) -0.046 0.19 -10000 0 -0.39 110 110
STRN 0.033 0.027 -10000 0 -0.54 1 1
GNAL 0.03 0.045 -10000 0 -0.54 3 3
PELP1 0.031 0.01 -10000 0 -10000 0 0
MAPK11 0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
HBEGF -0.11 0.23 0.37 7 -0.56 57 64
cAMP biosynthetic process -0.021 0.13 -10000 0 -0.28 102 102
SRC -0.14 0.23 0.3 4 -0.44 135 139
PI3K 0.006 0.12 -10000 0 -0.38 46 46
GNB1 0.034 0.011 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.18 -10000 0 -0.37 88 88
SOS1 0.034 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.21 0.21 -10000 0 -0.42 213 213
Gs family/GTP -0.012 0.14 -10000 0 -0.28 102 102
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.06 0.025 -10000 0 -10000 0 0
vasodilation -0.14 0.24 -10000 0 -0.47 143 143
mol:DAG -0.036 0.12 0.26 3 -0.32 49 52
Gs family/GDP/Gbeta gamma -0.04 0.16 -10000 0 -0.36 84 84
MSN -0.019 0.12 0.33 5 -10000 0 5
Gq family/GTP 0.002 0.093 -10000 0 -0.43 10 10
mol:PI-3-4-5-P3 -0.17 0.36 -10000 0 -0.76 131 131
NRAS 0.035 0.016 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.14 0.24 0.47 143 -10000 0 143
GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
RhoA/GDP -0.027 0.19 0.24 12 -0.37 105 117
NOS3 -0.15 0.26 -10000 0 -0.52 143 143
GNA11 0.033 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.13 0.27 -10000 0 -0.56 131 131
E2/ER alpha (dimer)/PELP1/Src -0.14 0.24 0.31 2 -0.47 138 140
ruffle organization -0.017 0.12 0.25 19 -10000 0 19
ROCK2 -0.017 0.13 0.35 5 -10000 0 5
GNA14 0.043 0.067 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MMP9 -0.098 0.22 0.4 7 -0.55 54 61
MMP2 -0.14 0.22 0.3 5 -0.55 59 64
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.62 0.93 3 -1.1 99 102
STAT6 (cleaved dimer) -0.23 0.54 -10000 0 -1.1 107 107
IGHG1 0.022 0.3 0.62 14 -0.66 8 22
IGHG3 -0.16 0.58 0.78 3 -1 113 116
AKT1 -0.028 0.35 0.65 1 -0.69 39 40
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.026 0.28 0.58 4 -0.85 13 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.028 0.37 0.64 6 -0.7 47 53
THY1 -0.15 0.62 1 5 -1.1 100 105
MYB -0.007 0.16 -10000 0 -0.54 40 40
HMGA1 0.037 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.007 0.4 0.73 12 -0.64 60 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.003 0.34 0.63 6 -0.67 30 36
SP1 0.057 0.044 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.008 0.057 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.17 0.59 0.84 1 -1.1 105 106
SOCS1 -0.064 0.41 0.76 1 -0.71 82 83
SOCS3 -0.017 0.38 -10000 0 -1.1 19 19
FCER2 -0.15 0.52 0.87 6 -0.86 90 96
PARP14 0.042 0.031 -10000 0 -10000 0 0
CCL17 -0.13 0.64 1 9 -1.1 96 105
GRB2 0.033 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.027 0.29 0.58 9 -0.69 14 23
T cell proliferation -0.19 0.62 -10000 0 -1.1 113 113
IL4R/JAK1 -0.16 0.61 -10000 0 -1.1 97 97
EGR2 -0.52 0.86 0.98 4 -1.3 255 259
JAK2 0.029 0.089 -10000 0 -10000 0 0
JAK3 0.035 0.019 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
JAK1 0.035 0.046 -10000 0 -10000 0 0
COL1A2 0.036 0.31 0.66 9 -1.1 10 19
CCL26 -0.14 0.62 1.1 4 -1.1 101 105
IL4R -0.14 0.68 1.1 6 -1.2 99 105
PTPN6 0.015 0.044 0.2 1 -10000 0 1
IL13RA2 -0.16 0.63 0.96 4 -1.1 105 109
IL13RA1 0.031 0.091 0.27 1 -10000 0 1
IRF4 0.061 0.21 0.67 4 -0.67 8 12
ARG1 0.046 0.26 0.73 3 -1.1 4 7
CBL -0.018 0.36 0.65 6 -0.6 60 66
GTF3A 0.1 0.065 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
IL13RA1/JAK2 0.049 0.13 0.37 4 -10000 0 4
IRF4/BCL6 0.027 0.21 0.53 1 -0.68 9 10
CD40LG 0.048 0.032 0.31 2 -10000 0 2
MAPK14 -0.017 0.38 0.67 4 -0.66 52 56
mitosis -0.023 0.34 0.62 2 -0.65 39 41
STAT6 -0.16 0.75 1.2 14 -1.3 106 120
SPI1 0.043 0.033 -10000 0 -0.24 1 1
RPS6KB1 -0.006 0.33 0.64 5 -0.67 29 34
STAT6 (dimer) -0.16 0.76 1.2 14 -1.3 106 120
STAT6 (dimer)/PARP14 -0.18 0.64 -10000 0 -1.2 108 108
mast cell activation -0.005 0.026 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.02 0.36 0.62 7 -0.7 44 51
FRAP1 -0.029 0.35 0.65 1 -0.69 39 40
LTA -0.15 0.62 0.96 1 -1.1 95 96
FES 0.031 0.037 -10000 0 -0.54 2 2
T-helper 1 cell differentiation 0.14 0.73 1.2 106 -1.2 14 120
CCL11 -0.11 0.61 0.9 4 -1.1 99 103
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.007 0.34 0.62 7 -0.81 20 27
IL2RG 0.044 0.041 0.21 10 -10000 0 10
IL10 -0.11 0.63 1 11 -1.1 97 108
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 118 118
IL4 0.041 0.3 0.72 11 -1 14 25
IL5 -0.15 0.62 1 3 -1.1 96 99
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.067 0.54 0.99 12 -0.86 96 108
COL1A1 0.11 0.4 0.76 37 -1 20 57
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.17 0.62 -10000 0 -1.2 94 94
IL2R gamma/JAK3 0.063 0.039 -10000 0 -10000 0 0
TFF3 -0.27 0.73 0.93 3 -1.2 143 146
ALOX15 -0.15 0.62 0.93 3 -1.1 98 101
MYBL1 0.048 0.053 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.1 0.54 0.81 7 -0.9 105 112
SHC1 0.027 0.014 -10000 0 -10000 0 0
CEBPB 0.035 0.034 -10000 0 -0.26 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.046 0.36 0.62 5 -0.64 56 61
mol:PI-3-4-5-P3 -0.028 0.35 0.65 1 -0.69 39 40
PI3K -0.035 0.37 0.66 1 -0.74 39 40
DOK2 0.025 0.039 -10000 0 -0.54 2 2
ETS1 0.002 0.059 0.19 1 -0.51 1 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.036 0.28 0.57 9 -0.62 14 23
ITGB3 -0.14 0.62 0.96 4 -1.1 100 104
PIGR -0.4 0.84 1 9 -1.3 204 213
IGHE -0.041 0.1 0.18 14 -0.26 25 39
MAPKKK cascade 0.037 0.27 0.57 9 -0.61 14 23
BCL6 -0.024 0.17 -10000 0 -0.54 49 49
OPRM1 -0.15 0.62 0.93 3 -1.1 101 104
RETNLB -0.15 0.62 0.93 3 -1.1 95 98
SELP -0.3 0.82 0.98 9 -1.4 160 169
AICDA -0.15 0.59 0.94 1 -1.1 101 102
IL6-mediated signaling events

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
BCL2L1 -0.024 0.3 0.66 3 -0.72 31 34
CRP 0 0.31 0.72 6 -0.74 28 34
cell cycle arrest -0.053 0.34 0.64 7 -0.74 53 60
TIMP1 -0.014 0.28 0.66 9 -0.62 32 41
IL6ST 0.037 0.084 -10000 0 -0.54 9 9
Rac1/GDP -0.089 0.22 0.42 7 -0.42 85 92
AP1 -0.16 0.24 0.49 4 -0.53 88 92
GAB2 0.033 0.015 -10000 0 -10000 0 0
TNFSF11 -0.007 0.32 0.7 7 -0.71 31 38
HSP90B1 0.042 0.14 -10000 0 -0.89 7 7
GAB1 0.035 0.028 -10000 0 -0.54 1 1
MAPK14 -0.13 0.2 -10000 0 -0.53 60 60
AKT1 0.033 0.09 0.34 1 -0.41 7 8
FOXO1 0.006 0.13 -10000 0 -0.43 16 16
MAP2K6 -0.12 0.2 0.35 3 -0.45 85 88
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.056 0.24 0.47 11 -0.48 67 78
MITF -0.11 0.21 0.36 5 -0.42 97 102
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.034 0.005 -10000 0 -10000 0 0
A2M -0.17 0.49 -10000 0 -1.3 74 74
CEBPB 0.038 0.03 -10000 0 -0.54 1 1
GRB2/SOS1/GAB family/SHP2 0 0.14 0.36 2 -0.45 24 26
STAT3 -0.072 0.36 0.65 7 -0.8 55 62
STAT1 0.034 0.12 -10000 0 -0.85 7 7
CEBPD -0.08 0.43 0.67 4 -1 70 74
PIK3CA 0.034 0.009 -10000 0 -10000 0 0
PI3K 0.008 0.13 -10000 0 -0.4 42 42
JUN -0.064 0.22 -10000 0 -0.54 86 86
PIAS3/MITF -0.1 0.2 0.38 2 -0.41 87 89
MAPK11 -0.12 0.2 -10000 0 -0.53 60 60
STAT3 (dimer)/FOXO1 -0.086 0.33 0.6 8 -0.66 74 82
GRB2/SOS1/GAB family -0.082 0.18 0.37 2 -0.44 46 48
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.19 0.34 3 -0.41 100 103
GRB2 0.036 0.018 -10000 0 -10000 0 0
JAK2 0.032 0.011 -10000 0 -10000 0 0
LBP 0.009 0.28 0.65 12 -0.62 23 35
PIK3R1 -0.017 0.16 -10000 0 -0.54 45 45
JAK1 0.037 0.013 -10000 0 -10000 0 0
MYC -0.016 0.38 0.7 11 -0.94 45 56
FGG -0.026 0.3 0.7 3 -0.72 33 36
macrophage differentiation -0.053 0.34 0.64 7 -0.74 53 60
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.19 -10000 0 -0.3 265 265
JUNB -0.032 0.3 0.64 3 -0.72 33 36
FOS -0.36 0.27 -10000 0 -0.54 342 342
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.37 8 -0.44 99 107
STAT1/PIAS1 -0.074 0.22 0.41 11 -0.43 78 89
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.094 -10000 0 -0.41 10 10
STAT3 (dimer) -0.069 0.35 0.65 7 -0.8 53 60
PRKCD -0.034 0.26 0.53 11 -0.53 54 65
IL6R 0.03 0.031 -10000 0 -0.55 1 1
SOCS3 -0.15 0.24 -10000 0 -0.9 26 26
gp130 (dimer)/JAK1/JAK1/LMO4 0.072 0.12 0.31 2 -0.32 31 33
Rac1/GTP -0.078 0.23 0.43 9 -0.43 85 94
HCK 0.036 0.022 -10000 0 -10000 0 0
MAPKKK cascade 0.023 0.16 0.4 1 -0.56 23 24
bone resorption -0.003 0.3 0.66 10 -0.67 31 41
IRF1 -0.024 0.3 0.71 4 -0.74 29 33
mol:GDP -0.1 0.21 0.39 9 -0.42 94 103
SOS1 0.037 0.009 -10000 0 -10000 0 0
VAV1 -0.1 0.22 0.4 9 -0.42 96 105
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.2 -10000 0 -0.57 59 59
PTPN11 0.021 0.094 -10000 0 -0.81 5 5
IL6/IL6RA -0.23 0.2 -10000 0 -0.38 295 295
gp130 (dimer)/TYK2/TYK2/LMO4 0.066 0.11 0.28 1 -0.33 27 28
gp130 (dimer)/JAK2/JAK2/LMO4 0.062 0.11 0.28 1 -0.32 30 31
IL6 -0.37 0.27 -10000 0 -0.54 361 361
PIAS3 0.032 0.008 -10000 0 -10000 0 0
PTPRE 0.004 0.043 -10000 0 -0.52 1 1
PIAS1 0.033 0.007 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.14 0.17 0.29 3 -0.31 180 183
LMO4 0.029 0.12 0.21 12 -0.54 21 33
STAT3 (dimer)/PIAS3 -0.067 0.33 0.62 6 -0.72 59 65
MCL1 0.07 0.12 0.52 2 -10000 0 2
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.059 0.034 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.23 0.18 -10000 0 -0.34 363 363
PTK2 -0.047 0.12 0.4 2 -0.47 7 9
IGF1R 0.01 0.12 -10000 0 -0.54 21 21
PI4KB 0.028 0.014 -10000 0 -10000 0 0
MFGE8 0.007 0.13 -10000 0 -0.54 25 25
SRC 0.032 0.008 -10000 0 -10000 0 0
CDKN1B -0.1 0.13 -10000 0 -0.57 27 27
VEGFA 0.05 0.046 -10000 0 -10000 0 0
ILK -0.087 0.096 -10000 0 -0.47 16 16
ROCK1 0.033 0.006 -10000 0 -10000 0 0
AKT1 -0.082 0.089 -10000 0 -0.45 15 15
PTK2B 0.028 0.051 0.3 6 -0.3 1 7
alphaV/beta3 Integrin/JAM-A -0.16 0.17 0.28 1 -0.3 272 273
CBL 0.03 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.064 0.03 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.25 -10000 0 -0.38 256 256
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.039 0.06 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Syndecan-1 0.088 0.052 0.25 3 -0.34 1 4
PI4KA 0.032 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.31 0.25 -10000 0 -0.49 271 271
PI4 Kinase 0.038 0.022 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.099 0.067 0.25 8 -0.34 4 12
RPS6KB1 -0.28 0.23 0.6 1 -0.49 222 223
TLN1 0.033 0.006 -10000 0 -10000 0 0
MAPK3 -0.36 0.29 -10000 0 -0.55 334 334
GPR124 0.008 0.1 -10000 0 -0.54 17 17
MAPK1 -0.38 0.29 -10000 0 -0.55 349 349
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
alphaV/beta3 Integrin/Tumstatin 0.065 0.029 -10000 0 -0.34 1 1
cell adhesion 0.034 0.092 -10000 0 -0.3 30 30
ANGPTL3 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.072 0.037 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.01 0.12 -10000 0 -0.54 21 21
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
TGFBR2 -0.005 0.14 -10000 0 -0.54 34 34
ITGB3 0.035 0.018 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 250 250
RAC1 0.034 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.039 0.08 -10000 0 -0.34 18 18
apoptosis 0.033 0.027 -10000 0 -0.54 1 1
CD47 0.023 0.076 -10000 0 -0.54 9 9
alphaV/beta3 Integrin/CD47 0.057 0.062 -10000 0 -0.34 10 10
VCL 0.034 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.055 0.096 0.25 2 -0.34 23 25
CSF1 0.034 0.008 -10000 0 -10000 0 0
PIK3C2A -0.084 0.091 -10000 0 -0.46 13 13
PI4 Kinase/Pyk2 -0.15 0.13 -10000 0 -0.27 241 241
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.088 0.045 -10000 0 -0.32 1 1
FAK1/Vinculin -0.032 0.11 0.41 2 -0.37 8 10
alphaV beta3/Integrin/ppsTEM5 0.04 0.081 -10000 0 -0.34 18 18
RHOA 0.033 0.007 -10000 0 -10000 0 0
VTN 0.032 0.011 -10000 0 -10000 0 0
BCAR1 0.029 0.012 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 375 375
F11R -0.23 0.2 -10000 0 -0.4 292 292
alphaV/beta3 Integrin/Lactadherin 0.047 0.09 0.25 1 -0.34 22 23
alphaV/beta3 Integrin/TGFBR2 0.039 0.1 0.25 1 -0.34 33 34
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.069 0.041 -10000 0 -0.32 1 1
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.061 0.028 -10000 0 -0.31 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.066 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.056 0.047 0.29 1 -0.3 1 2
SDC1 0.072 0.063 -10000 0 -10000 0 0
VAV3 0.012 0.071 -10000 0 -0.3 19 19
PTPN11 0.034 0.004 -10000 0 -10000 0 0
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
FAK1/Paxillin -0.032 0.12 0.36 4 -0.37 8 12
cell migration -0.032 0.1 0.36 3 -0.35 7 10
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PI3K -0.16 0.18 -10000 0 -0.31 267 267
SPP1 0.089 0.085 -10000 0 -0.54 3 3
KDR 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.033 0.028 -10000 0 -0.54 1 1
COL4A3 0.033 0.006 -10000 0 -10000 0 0
angiogenesis -0.37 0.28 -10000 0 -0.55 329 329
Rac1/GTP 0.03 0.068 -10000 0 -0.28 18 18
EDIL3 0.023 0.13 -10000 0 -0.54 22 22
cell proliferation 0.038 0.1 0.25 1 -0.34 33 34
FAS signaling pathway (CD95)

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
SPTAN1 0.017 0.09 0.21 73 -10000 0 73
RFC1 0.017 0.086 0.21 72 -10000 0 72
PRKDC 0.038 0.11 0.23 104 -10000 0 104
RIPK1 0.04 0.009 -10000 0 -10000 0 0
CASP7 -0.04 0.11 -10000 0 -0.75 9 9
FASLG/FAS/FADD/FAF1 -0.023 0.09 0.34 3 -0.32 15 18
MAP2K4 -0.18 0.19 -10000 0 -0.47 80 80
mol:ceramide -0.075 0.12 0.26 1 -0.39 26 27
GSN -0.059 0.17 0.22 54 -0.34 104 158
FASLG/FAS/FADD/FAF1/Caspase 8 -0.032 0.096 0.31 3 -0.33 13 16
FAS -0.046 0.14 -10000 0 -0.56 32 32
BID -0.022 0.021 -10000 0 -10000 0 0
MAP3K1 -0.092 0.14 0.28 1 -0.47 23 24
MAP3K7 0.025 0.01 -10000 0 -10000 0 0
RB1 0.018 0.083 0.21 67 -10000 0 67
CFLAR 0.04 0.026 -10000 0 -0.52 1 1
HGF/MET -0.01 0.17 -10000 0 -0.36 89 89
ARHGDIB 0.02 0.094 0.25 34 -10000 0 34
FADD -0.008 0.028 -10000 0 -10000 0 0
actin filament polymerization 0.057 0.17 0.34 105 -0.22 55 160
NFKB1 -0.1 0.12 -10000 0 -0.65 8 8
MAPK8 -0.31 0.25 -10000 0 -0.46 348 348
DFFA 0.016 0.085 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.02 0.09 0.21 70 -10000 0 70
FAS/FADD/MET -0.031 0.15 -10000 0 -0.39 64 64
CFLAR/RIP1 0.059 0.027 -10000 0 -0.37 1 1
FAIM3 0.034 0.029 -10000 0 -10000 0 0
FAF1 -0.016 0.032 -10000 0 -10000 0 0
PARP1 0.024 0.1 0.24 73 -10000 0 73
DFFB 0.015 0.086 0.21 70 -10000 0 70
CHUK -0.098 0.12 -10000 0 -0.61 8 8
FASLG 0.001 0.061 -10000 0 -0.55 1 1
FAS/FADD -0.032 0.1 -10000 0 -0.38 32 32
HGF 0.034 0.01 -10000 0 -10000 0 0
LMNA 0.023 0.1 0.42 15 -10000 0 15
CASP6 0.017 0.087 0.21 72 -10000 0 72
CASP10 -0.012 0.029 -10000 0 -10000 0 0
CASP3 0.021 0.1 0.26 68 -0.22 9 77
PTPN13 -0.019 0.17 -10000 0 -0.54 46 46
CASP8 -0.027 0.021 -10000 0 -10000 0 0
IL6 -0.88 0.56 -10000 0 -1.2 375 375
MET -0.023 0.17 -10000 0 -0.54 50 50
ICAD/CAD 0.011 0.076 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.077 0.12 0.26 1 -0.39 26 27
activation of caspase activity by cytochrome c -0.022 0.021 -10000 0 -10000 0 0
PAK2 0.017 0.1 0.23 74 -10000 0 74
BCL2 -0.073 0.22 -10000 0 -0.54 94 94
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.28 0.52 1 5 -1.2 60 65
IL23A -0.24 0.47 1 7 -1 49 56
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.46 0.76 2 -0.99 62 64
positive regulation of T cell mediated cytotoxicity -0.27 0.52 1.1 8 -1.1 59 67
ITGA3 -0.23 0.46 0.95 6 -1 52 58
IL17F -0.18 0.35 0.69 10 -0.66 66 76
IL12B 0.007 0.082 0.31 6 -10000 0 6
STAT1 (dimer) -0.25 0.5 0.91 5 -1.1 58 63
CD4 -0.24 0.46 0.99 4 -1 51 55
IL23 -0.24 0.45 0.95 5 -0.99 50 55
IL23R -0.019 0.21 0.81 3 -1.1 10 13
IL1B -0.25 0.48 1 8 -1 54 62
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.46 0.92 8 -0.98 53 61
TYK2 0.003 0.06 0.27 2 -10000 0 2
STAT4 0.027 0.069 -10000 0 -0.54 7 7
STAT3 0.033 0.008 -10000 0 -10000 0 0
IL18RAP -0.007 0.16 -10000 0 -0.54 42 42
IL12RB1 0.004 0.06 0.26 3 -10000 0 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.009 0.074 0.29 3 -10000 0 3
IL23R/JAK2 -0.024 0.22 0.69 3 -1 10 13
positive regulation of chronic inflammatory response -0.27 0.52 1.1 8 -1.1 59 67
natural killer cell activation 0.001 0.015 0.08 2 -0.061 6 8
JAK2 0.004 0.076 0.32 4 -10000 0 4
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
NFKB1 0.034 0.009 -10000 0 -10000 0 0
RELA 0.034 0.008 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.23 0.44 0.92 6 -0.94 50 56
ALOX12B -0.24 0.46 0.99 4 -1 53 57
CXCL1 -0.64 0.73 1.1 6 -1.2 291 297
T cell proliferation -0.27 0.52 1.1 8 -1.1 59 67
NFKBIA 0.033 0.01 -10000 0 -10000 0 0
IL17A -0.12 0.3 0.65 12 -0.53 49 61
PI3K -0.28 0.47 0.82 1 -1 73 74
IFNG 0.022 0.074 0.18 65 -0.12 6 71
STAT3 (dimer) -0.26 0.46 0.8 1 -0.98 70 71
IL18R1 0.04 0.03 0.2 2 -0.54 1 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.33 0.76 11 -0.67 36 47
IL18/IL18R 0.064 0.14 0.28 27 -0.34 42 69
macrophage activation -0.013 0.029 0.075 21 -0.043 38 59
TNF -0.25 0.48 1.1 5 -1.1 48 53
STAT3/STAT4 -0.26 0.47 0.81 2 -1 60 62
STAT4 (dimer) -0.27 0.49 0.88 5 -1.1 63 68
IL18 0.047 0.045 0.2 26 -10000 0 26
IL19 -0.2 0.47 0.93 8 -0.99 49 57
STAT5A (dimer) -0.27 0.49 0.88 4 -1.1 60 64
STAT1 0.058 0.054 -10000 0 -10000 0 0
SOCS3 0.019 0.084 -10000 0 -0.54 11 11
CXCL9 -0.22 0.5 1.1 6 -1.1 51 57
MPO -0.23 0.46 1 4 -1 51 55
positive regulation of humoral immune response -0.27 0.52 1.1 8 -1.1 59 67
IL23/IL23R/JAK2/TYK2 -0.28 0.54 1.1 8 -1.2 58 66
IL6 -0.79 0.68 0.96 5 -1.2 356 361
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
IL2 0.049 0.039 0.24 1 -0.52 1 2
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.015 0.08 2 -0.061 6 8
CD3E -0.24 0.46 0.98 5 -1 52 57
keratinocyte proliferation -0.27 0.52 1.1 8 -1.1 59 67
NOS2 -0.24 0.46 0.88 8 -0.96 61 69
EPHB forward signaling

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.048 0.033 0.23 2 -0.34 1 3
cell-cell adhesion 0.1 0.12 0.26 174 -10000 0 174
Ephrin B/EPHB2/RasGAP 0.081 0.065 -10000 0 -0.3 6 6
ITSN1 0.034 0.005 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.045 0.021 -10000 0 -0.34 1 1
Ephrin B1/EPHB1 -0.099 0.19 -10000 0 -0.34 188 188
HRAS/GDP -0.081 0.16 -10000 0 -0.38 41 41
Ephrin B/EPHB1/GRB7 -0.055 0.18 -10000 0 -0.31 157 157
Endophilin/SYNJ1 0.018 0.048 0.26 1 -0.28 6 7
KRAS 0.034 0.017 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.055 0.19 -10000 0 -0.31 170 170
endothelial cell migration 0.027 0.11 -10000 0 -0.3 45 45
GRB2 0.033 0.017 -10000 0 -10000 0 0
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.008 0.062 0.3 5 -0.29 4 9
HRAS 0.034 0.013 -10000 0 -10000 0 0
RRAS 0.018 0.048 0.26 1 -0.28 6 7
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.094 0.16 0.36 2 -0.29 187 189
lamellipodium assembly -0.1 0.12 -10000 0 -0.26 174 174
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.062 0.14 -10000 0 -0.41 35 35
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
EPHB2 0.042 0.036 -10000 0 -10000 0 0
EPHB3 0.035 0.015 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 189 189
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
mol:GDP -0.082 0.14 -10000 0 -0.38 44 44
Ephrin B/EPHB2 0.068 0.056 -10000 0 -0.3 6 6
Ephrin B/EPHB3 0.062 0.052 -10000 0 -0.3 6 6
JNK cascade -0.09 0.16 0.39 4 -0.3 180 184
Ephrin B/EPHB1 -0.07 0.18 -10000 0 -0.3 187 187
RAP1/GDP -0.059 0.14 -10000 0 -0.36 39 39
EFNB2 0.026 0.058 -10000 0 -0.54 5 5
EFNB3 0.03 0.011 -10000 0 -10000 0 0
EFNB1 0.033 0.026 -10000 0 -0.54 1 1
Ephrin B2/EPHB1-2 -0.076 0.19 -10000 0 -0.32 188 188
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.061 0.17 -10000 0 -0.34 42 42
Rap1/GTP -0.074 0.14 -10000 0 -0.27 143 143
axon guidance 0.047 0.032 0.22 2 -0.34 1 3
MAPK3 -0.047 0.14 0.26 1 -0.38 30 31
MAPK1 -0.053 0.14 -10000 0 -0.38 31 31
Rac1/GDP -0.073 0.14 -10000 0 -0.36 42 42
actin cytoskeleton reorganization -0.079 0.11 -10000 0 -0.32 26 26
CDC42/GDP -0.072 0.14 -10000 0 -0.37 40 40
PI3K 0.032 0.11 -10000 0 -0.31 45 45
EFNA5 0.032 0.029 -10000 0 -0.54 1 1
Ephrin B2/EPHB4 0.038 0.046 -10000 0 -0.31 7 7
Ephrin B/EPHB2/Intersectin/N-WASP 0.02 0.065 -10000 0 -0.28 7 7
CDC42 0.033 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.076 0.14 -10000 0 -0.46 6 6
PTK2 0.15 0.27 0.67 102 -10000 0 102
MAP4K4 -0.091 0.16 0.39 4 -0.3 180 184
SRC 0.032 0.008 -10000 0 -10000 0 0
KALRN 0.034 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.048 0.022 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.054 0.13 0.45 5 -0.34 12 17
MAP2K1 -0.059 0.13 -10000 0 -0.39 31 31
WASL 0.033 0.026 -10000 0 -0.54 1 1
Ephrin B1/EPHB1-2/NCK1 -0.061 0.2 -10000 0 -0.31 188 188
cell migration -0.064 0.16 0.32 5 -0.42 34 39
NRAS 0.035 0.016 -10000 0 -10000 0 0
SYNJ1 0.018 0.049 0.26 1 -0.28 6 7
PXN 0.034 0.003 -10000 0 -10000 0 0
TF -0.014 0.068 0.25 1 -0.28 21 22
HRAS/GTP -0.061 0.16 -10000 0 -0.28 175 175
Ephrin B1/EPHB1-2 -0.072 0.19 -10000 0 -0.31 188 188
cell adhesion mediated by integrin -0.009 0.048 0.27 6 -0.23 3 9
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.062 0.18 -10000 0 -0.29 178 178
RAC1-CDC42/GTP -0.087 0.14 -10000 0 -0.27 162 162
RASA1 0.033 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.062 0.14 -10000 0 -0.36 40 40
ruffle organization -0.096 0.14 0.41 3 -0.47 7 10
NCK1 0.034 0.005 -10000 0 -10000 0 0
receptor internalization -0.005 0.049 0.25 1 -0.27 6 7
Ephrin B/EPHB2/KALRN 0.082 0.064 -10000 0 -0.3 6 6
ROCK1 0.024 0.034 -10000 0 -0.31 1 1
RAS family/GDP -0.084 0.094 -10000 0 -0.31 25 25
Rac1/GTP -0.088 0.14 -10000 0 -0.28 174 174
Ephrin B/EPHB1/Src/Paxillin -0.086 0.16 -10000 0 -0.41 43 43
Visual signal transduction: Rods

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
mol:K + 0.033 0.006 -10000 0 -10000 0 0
GNAT1/GTP 0.024 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.057 0.04 -10000 0 -0.24 2 2
PDE6G/GNAT1/GTP 0.042 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.033 0.007 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.089 0.17 -10000 0 -0.29 202 202
mol:Na + -0.089 0.17 -10000 0 -0.28 211 211
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.048 0.1 -10000 0 -0.32 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.083 0.19 -10000 0 -0.29 193 193
CNGB1 0.029 0.012 -10000 0 -10000 0 0
RDH5 -0.43 0.23 -10000 0 -0.54 409 409
SAG 0.055 0.059 -10000 0 -0.54 1 1
mol:Ca2+ -0.12 0.15 0.36 6 -0.51 7 13
Na + (4 Units) -0.09 0.16 -10000 0 -0.27 190 190
RGS9 0.001 0.13 -10000 0 -0.54 27 27
GNB1/GNGT1 0.07 0.044 0.25 1 -10000 0 1
GNAT1/GDP 0.057 0.092 -10000 0 -0.27 28 28
GUCY2D 0.031 0.011 -10000 0 -10000 0 0
GNGT1 0.066 0.059 -10000 0 -10000 0 0
GUCY2F 0.033 0.038 -10000 0 -0.54 2 2
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.025 0.052 -10000 0 -0.3 11 11
mol:11-cis-retinal -0.43 0.23 -10000 0 -0.54 409 409
mol:cGMP 0.055 0.073 -10000 0 -0.34 13 13
GNB1 0.034 0.011 -10000 0 -10000 0 0
Rhodopsin -0.31 0.18 -10000 0 -0.39 414 414
SLC24A1 0.033 0.006 -10000 0 -10000 0 0
CNGA1 -0.21 0.29 -10000 0 -0.54 216 216
Metarhodopsin II 0.022 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.067 0.072 -10000 0 -0.34 12 12
RGS9BP 0.053 0.064 -10000 0 -0.54 2 2
Metarhodopsin II/Transducin 0.036 0.037 -10000 0 -0.18 6 6
GCAP Family/Ca ++ 0.054 0.064 -10000 0 -0.34 12 12
PDE6A/B 0.038 0.071 -10000 0 -0.37 14 14
mol:Pi 0.048 0.099 -10000 0 -0.32 28 28
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.078 0.042 0.24 1 -10000 0 1
PDE6B 0.02 0.089 -10000 0 -0.54 12 12
PDE6A 0.034 0.008 -10000 0 -10000 0 0
PDE6G 0.033 0.014 -10000 0 -10000 0 0
RHO 0.034 0.005 -10000 0 -10000 0 0
PDE6 0.065 0.11 -10000 0 -0.3 25 25
GUCA1A 0.024 0.077 -10000 0 -0.54 9 9
GC2/GCAP Family 0.073 0.076 -10000 0 -0.36 13 13
GUCA1C 0.031 0.046 -10000 0 -0.54 3 3
GUCA1B 0.033 0.027 -10000 0 -0.54 1 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.024 0.12 0.24 1 -0.33 44 45
adherens junction organization -0.024 0.12 0.23 1 -0.33 47 48
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 0.32 3 -0.38 99 102
FMN1 -0.024 0.11 -10000 0 -0.3 52 52
mol:IP3 -0.023 0.098 -10000 0 -0.28 41 41
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.022 0.12 -10000 0 -0.32 52 52
CTNNB1 0.031 0.045 -10000 0 -0.54 3 3
AKT1 -0.019 0.11 -10000 0 -0.28 45 45
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.026 0.17 -10000 0 -0.52 37 37
CTNND1 0.033 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.02 0.1 -10000 0 -0.38 21 21
VASP -0.02 0.12 0.24 1 -0.37 23 24
ZYX -0.025 0.11 -10000 0 -0.37 25 25
JUB -0.024 0.11 -10000 0 -0.3 52 52
EGFR(dimer) -0.16 0.19 -10000 0 -0.32 248 248
E-cadherin/beta catenin-gamma catenin 0.036 0.09 -10000 0 -0.32 24 24
mol:PI-3-4-5-P3 -0.006 0.12 -10000 0 -0.29 49 49
PIK3CA 0.032 0.01 -10000 0 -10000 0 0
PI3K -0.006 0.13 -10000 0 -0.3 49 49
FYN -0.024 0.11 0.24 1 -0.39 22 23
mol:Ca2+ -0.023 0.096 -10000 0 -0.28 41 41
JUP 0.034 0.011 -10000 0 -10000 0 0
PIK3R1 -0.017 0.16 -10000 0 -0.54 45 45
mol:DAG -0.023 0.098 -10000 0 -0.28 41 41
CDH1 0.006 0.12 -10000 0 -0.54 22 22
RhoA/GDP -0.14 0.18 0.32 3 -0.38 99 102
establishment of polarity of embryonic epithelium -0.019 0.11 0.24 1 -0.37 23 24
SRC 0.032 0.008 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 264 264
CASR -0.022 0.097 0.24 2 -0.27 41 43
RhoA/GTP -0.005 0.1 -10000 0 -0.26 41 41
AKT2 -0.021 0.11 -10000 0 -0.29 44 44
actin cable formation -0.02 0.11 0.25 3 -0.36 23 26
apoptosis 0.017 0.12 0.31 45 -0.26 4 49
CTNNA1 0.033 0.007 -10000 0 -10000 0 0
mol:GDP -0.16 0.18 -10000 0 -0.31 243 243
PIP5K1A -0.021 0.1 -10000 0 -0.38 21 21
PLCG1 -0.024 0.099 -10000 0 -0.29 41 41
Rac1/GTP -0.14 0.18 -10000 0 -0.39 112 112
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A -0.038 0.19 -10000 0 -0.54 62 62
LAT2 -0.03 0.13 -10000 0 -0.36 46 46
AP1 -0.19 0.23 -10000 0 -0.46 154 154
mol:PIP3 0.004 0.19 0.35 27 -0.42 46 73
IKBKB 0.02 0.14 0.29 40 -0.27 33 73
AKT1 -0.006 0.2 0.34 73 -0.46 28 101
IKBKG 0.003 0.13 0.26 26 -0.26 36 62
MS4A2 -0.058 0.21 -10000 0 -0.53 83 83
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
MAP3K1 0.01 0.15 0.35 12 -0.4 24 36
mol:Ca2+ 0.012 0.16 0.31 31 -0.32 46 77
LYN 0.032 0.018 -10000 0 -10000 0 0
CBLB -0.03 0.13 -10000 0 -0.35 48 48
SHC1 0.027 0.014 -10000 0 -10000 0 0
RasGAP/p62DOK -0.093 0.18 -10000 0 -0.31 205 205
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.012 0.2 0.34 64 -0.34 90 154
PTPN13 -0.039 0.19 -10000 0 -0.59 27 27
PTPN11 0.033 0.022 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.002 0.16 0.36 18 -0.35 27 45
SYK 0.04 0.027 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.039 0.15 -10000 0 -0.42 49 49
LAT -0.026 0.12 0.21 2 -0.35 45 47
PAK2 0.008 0.16 0.37 10 -0.43 26 36
NFATC2 -0.012 0.057 -10000 0 -0.69 1 1
HRAS 0.003 0.16 0.32 8 -0.45 28 36
GAB2 0.03 0.012 -10000 0 -10000 0 0
PLA2G1B 0.009 0.11 -10000 0 -0.83 7 7
Fc epsilon R1 -0.037 0.19 -10000 0 -0.41 94 94
Antigen/IgE/Fc epsilon R1 -0.032 0.18 -10000 0 -0.38 94 94
mol:GDP -0.024 0.15 0.28 2 -0.45 29 31
JUN -0.065 0.22 -10000 0 -0.54 86 86
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
FOS -0.36 0.27 -10000 0 -0.54 342 342
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.026 0.13 -10000 0 -0.35 52 52
CHUK 0.002 0.13 0.26 26 -0.26 37 63
KLRG1 -0.024 0.12 -10000 0 -0.36 30 30
VAV1 -0.029 0.13 0.22 1 -0.35 47 48
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.028 0.12 -10000 0 -0.35 47 47
negative regulation of mast cell degranulation -0.028 0.11 -10000 0 -0.35 28 28
BTK -0.024 0.15 -10000 0 -0.48 27 27
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.047 0.17 -10000 0 -0.37 92 92
GAB2/PI3K/SHP2 -0.061 0.15 -10000 0 -0.38 65 65
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.033 0.13 -10000 0 -0.35 52 52
RAF1 0.008 0.12 -10000 0 -0.9 7 7
Fc epsilon R1/FcgammaRIIB/SHIP -0.02 0.18 -10000 0 -0.36 94 94
FCER1G 0.031 0.021 -10000 0 -10000 0 0
FCER1A -0.045 0.19 -10000 0 -0.55 63 63
Antigen/IgE/Fc epsilon R1/Fyn -0.021 0.17 -10000 0 -0.35 92 92
MAPK3 0.01 0.11 -10000 0 -0.86 7 7
MAPK1 0.004 0.11 -10000 0 -0.83 7 7
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.016 0.2 -10000 0 -0.63 31 31
DUSP1 -0.2 0.28 -10000 0 -0.54 209 209
NF-kappa-B/RelA 0.012 0.081 0.19 10 -0.18 17 27
actin cytoskeleton reorganization -0.015 0.18 -10000 0 -0.58 22 22
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.012 0.17 -10000 0 -0.46 36 36
FER -0.029 0.13 -10000 0 -0.35 47 47
RELA 0.034 0.005 -10000 0 -10000 0 0
ITK -0.003 0.069 -10000 0 -0.34 14 14
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG1 -0.001 0.17 0.32 7 -0.46 27 34
cytokine secretion -0.006 0.047 -10000 0 -10000 0 0
SPHK1 -0.026 0.12 -10000 0 -0.36 41 41
PTK2 -0.017 0.18 -10000 0 -0.62 22 22
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.04 0.16 -10000 0 -0.44 50 50
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.032 0.22 0.35 18 -0.49 55 73
MAP2K2 0.004 0.11 -10000 0 -0.84 7 7
MAP2K1 0.004 0.11 -10000 0 -0.84 7 7
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.013 0.11 0.24 1 -0.37 23 24
MAP2K4 -0.073 0.32 -10000 0 -0.86 68 68
Fc epsilon R1/FcgammaRIIB -0.02 0.19 -10000 0 -0.38 94 94
mol:Choline -0.012 0.2 0.34 64 -0.34 90 154
SHC/Grb2/SOS1 0.009 0.14 -10000 0 -0.4 24 24
FYN 0.029 0.037 -10000 0 -0.54 2 2
DOK1 0.036 0.016 -10000 0 -10000 0 0
PXN -0.016 0.17 -10000 0 -0.56 21 21
HCLS1 -0.028 0.13 0.21 2 -0.35 47 49
PRKCB -0.005 0.16 0.3 25 -0.32 56 81
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
IGHE 0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.028 0.11 -10000 0 -0.36 28 28
LCP2 0.036 0.023 -10000 0 -10000 0 0
PLA2G4A -0.16 0.2 -10000 0 -0.35 216 216
RASA1 0.033 0.011 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.012 0.2 0.34 64 -0.34 90 154
IKK complex 0.021 0.12 0.28 36 -0.21 24 60
WIPF1 0.037 0.022 -10000 0 -10000 0 0
PLK1 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
regulation of centriole-centriole cohesion -0.036 0.043 0.13 3 -0.12 21 24
BUB1B 0.093 0.062 0.16 185 -0.14 1 186
PLK1 0.046 0.035 0.11 57 -10000 0 57
PLK1S1 0.023 0.019 0.059 49 -10000 0 49
KIF2A 0.038 0.037 0.27 4 -10000 0 4
regulation of mitotic centrosome separation 0.046 0.035 0.11 57 -10000 0 57
GOLGA2 0.034 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.1 0.061 0.16 196 -10000 0 196
WEE1 0.049 0.077 0.22 2 -0.31 16 18
cytokinesis 0.13 0.081 0.21 156 -0.39 1 157
PP2A-alpha B56 0.14 0.11 -10000 0 -0.46 6 6
AURKA 0.051 0.039 0.13 18 -0.16 2 20
PICH/PLK1 0.13 0.094 0.24 169 -10000 0 169
CENPE 0.084 0.066 0.16 170 -10000 0 170
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.039 0.037 0.27 4 -10000 0 4
PPP2CA 0.033 0.006 -10000 0 -10000 0 0
FZR1 0.034 0.009 -10000 0 -10000 0 0
TPX2 0.08 0.037 0.12 109 -10000 0 109
PAK1 0.043 0.043 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
CLSPN 0.043 0.053 0.15 10 -0.2 12 22
GORASP1 0.033 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 40 -10000 0 40
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.023 0.019 0.059 49 -10000 0 49
G2 phase of mitotic cell cycle 0.001 0.003 0.016 7 -10000 0 7
STAG2 0.034 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.021 0.092 -10000 0 -0.5 15 15
spindle elongation 0.046 0.035 0.11 57 -10000 0 57
ODF2 0.037 0.015 -10000 0 -10000 0 0
BUB1 0.12 0.11 -10000 0 -0.48 8 8
TPT1 0.014 0.059 0.12 2 -0.16 47 49
CDC25C 0.082 0.066 0.17 3 -0.22 10 13
CDC25B 0.048 0.04 -10000 0 -10000 0 0
SGOL1 0.036 0.043 0.12 21 -0.13 3 24
RHOA 0.033 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.09 0.066 0.24 27 -0.21 1 28
CDC14B -0.002 0.065 -10000 0 -0.4 13 13
CDC20 0.082 0.068 -10000 0 -10000 0 0
PLK1/PBIP1 0.073 0.054 0.14 154 -10000 0 154
mitosis -0.001 0.003 0.033 2 -10000 0 2
FBXO5 0.038 0.043 0.16 19 -10000 0 19
CDC2 0.005 0.004 0.015 32 -10000 0 32
NDC80 0.11 0.073 -10000 0 -10000 0 0
metaphase plate congression 0.028 0.055 -10000 0 -0.21 22 22
ERCC6L 0.12 0.094 0.23 159 -10000 0 159
NLP/gamma Tubulin 0.025 0.024 0.086 15 -0.085 3 18
microtubule cytoskeleton organization 0.014 0.059 0.12 2 -0.16 47 49
G2/M transition DNA damage checkpoint 0 0.003 0.013 11 -10000 0 11
PPP1R12A 0.035 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.013 11 -10000 0 11
PLK1/PRC1-2 0.17 0.097 0.27 217 -10000 0 217
GRASP65/GM130/RAB1/GTP/PLK1 0.083 0.032 -10000 0 -10000 0 0
RAB1A 0.034 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.04 0.032 0.096 68 -10000 0 68
mitotic prometaphase 0.001 0.005 0.021 23 -10000 0 23
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.045 -10000 0 -10000 0 0
microtubule-based process 0.12 0.064 0.18 228 -10000 0 228
Golgi organization 0.046 0.035 0.11 57 -10000 0 57
Cohesin/SA2 0.055 0.026 0.16 2 -10000 0 2
PPP1CB/MYPT1 0.05 0.009 -10000 0 -10000 0 0
KIF20A 0.12 0.069 -10000 0 -10000 0 0
APC/C/CDC20 0.093 0.065 0.18 161 -10000 0 161
PPP2R1A 0.034 0.005 -10000 0 -10000 0 0
chromosome segregation 0.073 0.054 0.14 154 -10000 0 154
PRC1 0.1 0.072 -10000 0 -10000 0 0
ECT2 0.072 0.073 0.18 117 -10000 0 117
C13orf34 0.039 0.03 0.093 63 -10000 0 63
NUDC 0.028 0.055 -10000 0 -0.21 22 22
regulation of attachment of spindle microtubules to kinetochore 0.093 0.062 0.15 186 -0.14 1 187
spindle assembly 0.036 0.029 0.1 34 -10000 0 34
spindle stabilization 0.023 0.019 0.059 49 -10000 0 49
APC/C/HCDH1 0.021 0.06 -10000 0 -0.34 13 13
MKLP2/PLK1 0.12 0.065 0.18 228 -10000 0 228
CCNB1 0.086 0.069 -10000 0 -10000 0 0
PPP1CB 0.035 0.004 -10000 0 -10000 0 0
BTRC 0.037 0.021 -10000 0 -10000 0 0
ROCK2 0.04 0.05 0.21 1 -0.29 6 7
TUBG1 0.027 0.039 0.12 5 -0.15 17 22
G2/M transition of mitotic cell cycle 0.061 0.064 0.21 26 -10000 0 26
MLF1IP 0.07 0.065 -10000 0 -10000 0 0
INCENP 0.047 0.039 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.049 0.077 0.25 33 -0.19 2 35
STMN1 0.054 0.083 0.28 45 -10000 0 45
Aurora B/RasGAP/Survivin 0.11 0.075 0.26 1 -10000 0 1
Chromosomal passenger complex/Cul3 protein complex -0.071 0.13 0.21 24 -0.33 26 50
BIRC5 0.12 0.074 -10000 0 -10000 0 0
DES -0.012 0.13 -10000 0 -0.55 27 27
Aurora C/Aurora B/INCENP 0.075 0.051 -10000 0 -10000 0 0
Aurora B/TACC1 0.025 0.087 -10000 0 -0.32 24 24
Aurora B/PP2A 0.058 0.041 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.02 0.022 0.14 3 -10000 0 3
mitotic metaphase/anaphase transition -0.002 0.004 -10000 0 -10000 0 0
NDC80 0.099 0.1 0.28 84 -10000 0 84
Cul3 protein complex -0.23 0.18 -10000 0 -0.35 358 358
KIF2C 0.13 0.1 0.23 246 -10000 0 246
PEBP1 0.039 0.027 -10000 0 -0.54 1 1
KIF20A 0.12 0.069 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.056 0.041 -10000 0 -10000 0 0
SEPT1 0.035 0.023 -10000 0 -10000 0 0
SMC2 0.04 0.03 -10000 0 -10000 0 0
SMC4 0.045 0.04 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.063 0.16 0.29 24 -0.39 42 66
PSMA3 0.033 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.005 -10000 0 -10000 0 0
H3F3B 0.031 0.036 -10000 0 -10000 0 0
AURKB 0.05 0.053 0.2 1 -10000 0 1
AURKC 0.035 0.019 -10000 0 -10000 0 0
CDCA8 0.11 0.073 -10000 0 -10000 0 0
cytokinesis 0.18 0.15 0.35 198 -10000 0 198
Aurora B/Septin1 0.18 0.15 0.37 129 -10000 0 129
AURKA 0.077 0.067 -10000 0 -10000 0 0
INCENP 0.053 0.04 -10000 0 -10000 0 0
KLHL13 -0.38 0.26 -10000 0 -0.54 364 364
BUB1 0.15 0.052 0.2 3 -10000 0 3
hSgo1/Aurora B/Survivin 0.12 0.097 0.31 63 -10000 0 63
EVI5 0.036 0.026 -10000 0 -0.53 1 1
RhoA/GTP 0.21 0.14 0.35 199 -10000 0 199
SGOL1 0.073 0.064 -10000 0 -10000 0 0
CENPA 0.14 0.12 0.28 178 -10000 0 178
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.057 0.041 -10000 0 -10000 0 0
NCAPD2 0.035 0.021 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.058 0.041 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
NCAPH 0.078 0.066 -10000 0 -10000 0 0
NPM1 0.025 0.11 -10000 0 -0.47 10 10
RASA1 0.033 0.011 -10000 0 -10000 0 0
KLHL9 0.032 0.009 -10000 0 -10000 0 0
mitotic prometaphase 0.005 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.041 -10000 0 -10000 0 0
PPP1CC 0.034 0.004 -10000 0 -10000 0 0
Centraspindlin 0.23 0.15 0.38 221 -10000 0 221
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
NSUN2 0.026 0.093 0.26 1 -0.32 17 18
MYLK -0.07 0.17 -10000 0 -0.34 137 137
KIF23 0.12 0.073 -10000 0 -10000 0 0
VIM -0.007 0.13 -10000 0 -0.39 47 47
RACGAP1 0.08 0.065 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.025 0.11 -10000 0 -0.4 17 17
Chromosomal passenger complex 0.16 0.13 0.28 238 -10000 0 238
Chromosomal passenger complex/EVI5 0.14 0.11 0.36 25 -10000 0 25
TACC1 0.001 0.12 -10000 0 -0.54 24 24
PPP2R5D 0.033 0.006 -10000 0 -10000 0 0
CUL3 0.031 0.037 -10000 0 -0.54 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.046 0.24 0.58 2 -0.56 73 75
IHH 0.021 0.075 -10000 0 -0.2 1 1
SHH Np/Cholesterol/GAS1 -0.067 0.15 -10000 0 -0.31 124 124
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.067 0.15 0.31 124 -10000 0 124
SMO/beta Arrestin2 -0.003 0.19 0.41 2 -0.48 30 32
SMO -0.017 0.18 0.44 2 -0.5 31 33
AKT1 -0.02 0.19 0.3 1 -0.58 38 39
ARRB2 0.031 0.01 -10000 0 -10000 0 0
BOC -0.09 0.24 -10000 0 -0.54 108 108
ADRBK1 0.031 0.01 -10000 0 -10000 0 0
heart looping -0.016 0.18 0.44 2 -0.49 31 33
STIL 0.041 0.15 0.34 32 -0.34 7 39
DHH N/PTCH2 0.049 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 0.005 0.16 0.38 2 -0.32 82 84
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
DHH 0.034 0.004 -10000 0 -10000 0 0
PTHLH -0.11 0.39 0.52 6 -0.9 94 100
determination of left/right symmetry -0.016 0.18 0.44 2 -0.49 31 33
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
skeletal system development -0.11 0.39 0.52 6 -0.89 94 100
IHH N/Hhip 0.038 0.053 -10000 0 -10000 0 0
DHH N/Hhip 0.05 0.012 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.016 0.18 0.44 2 -0.49 31 33
pancreas development 0.034 0.012 -10000 0 -10000 0 0
HHAT 0.023 0.06 -10000 0 -0.54 5 5
PI3K 0.006 0.12 -10000 0 -0.38 46 46
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.14 0.27 -10000 0 -0.54 155 155
somite specification -0.016 0.18 0.44 2 -0.49 31 33
SHH Np/Cholesterol/PTCH1 -0.01 0.12 -10000 0 -0.33 15 15
SHH Np/Cholesterol/PTCH2 0.024 0.037 -10000 0 -0.31 5 5
SHH Np/Cholesterol/Megalin -0.057 0.14 -10000 0 -0.32 110 110
SHH 0.01 0.043 -10000 0 -0.4 5 5
catabolic process -0.01 0.18 0.46 2 -0.36 86 88
SMO/Vitamin D3 0.009 0.17 0.4 16 -0.44 14 30
SHH Np/Cholesterol/Hhip 0.024 0.038 -10000 0 -0.31 5 5
LRP2 -0.12 0.26 -10000 0 -0.54 136 136
receptor-mediated endocytosis -0.063 0.2 0.35 9 -0.5 39 48
SHH Np/Cholesterol/BOC -0.037 0.13 -10000 0 -0.31 84 84
SHH Np/Cholesterol/CDO 0.018 0.051 -10000 0 -0.35 8 8
mesenchymal cell differentiation -0.024 0.038 0.31 5 -10000 0 5
mol:Vitamin D3 0.027 0.16 0.41 17 -0.34 13 30
IHH N/PTCH2 0.037 0.052 -10000 0 -10000 0 0
CDON 0.026 0.052 -10000 0 -0.54 4 4
IHH N/PTCH1 -0.002 0.18 0.46 2 -0.36 86 88
Megalin/LRPAP1 -0.073 0.2 -10000 0 -0.4 136 136
PTCH2 0.034 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.014 0.034 -10000 0 -0.31 5 5
PTCH1 -0.01 0.18 0.46 2 -0.36 86 88
HHIP 0.034 0.012 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.18 -10000 0 -0.35 322 322
fibroblast growth factor receptor signaling pathway -0.22 0.18 -10000 0 -0.35 322 322
LAMA1 0.033 0.01 -10000 0 -10000 0 0
PRNP 0.018 0.091 -10000 0 -0.54 13 13
GPC1/SLIT2 -0.009 0.15 -10000 0 -0.39 65 65
SMAD2 -0.001 0.085 0.28 1 -0.31 32 33
GPC1/PrPc/Cu2+ 0.034 0.062 -10000 0 -0.34 13 13
GPC1/Laminin alpha1 0.048 0.017 -10000 0 -10000 0 0
TDGF1 0.033 0.01 -10000 0 -10000 0 0
CRIPTO/GPC1 0.048 0.016 -10000 0 -10000 0 0
APP/GPC1 0.046 0.044 -10000 0 -0.4 4 4
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.019 0.019 -10000 0 -0.34 1 1
FLT1 0.032 0.013 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.039 0.1 -10000 0 -0.34 34 34
SERPINC1 0.031 0.024 -10000 0 -10000 0 0
FYN 0.018 0.025 -10000 0 -0.34 2 2
FGR 0.02 0.011 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.025 0.083 0.29 2 -0.37 9 11
SLIT2 -0.039 0.19 -10000 0 -0.54 63 63
GPC1/NRG -0.002 0.13 -10000 0 -0.34 60 60
NRG1 -0.02 0.16 -10000 0 -0.54 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.07 0.038 -10000 0 -10000 0 0
LYN 0.018 0.014 -10000 0 -10000 0 0
mol:Spermine 0.01 0.01 -10000 0 -10000 0 0
cell growth -0.22 0.18 -10000 0 -0.35 322 322
BMP signaling pathway -0.034 0.013 -10000 0 -10000 0 0
SRC 0.019 0.01 -10000 0 -10000 0 0
TGFBR1 0.035 0.016 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.034 0.2 -10000 0 -0.54 66 66
GPC1 0.034 0.013 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.035 0.016 -10000 0 -10000 0 0
VEGFA 0.05 0.046 -10000 0 -10000 0 0
BLK 0.025 0.032 -10000 0 -10000 0 0
HCK 0.022 0.018 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 375 375
FGFR1 0.018 0.077 -10000 0 -0.54 9 9
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
TGFBR2 -0.005 0.14 -10000 0 -0.54 34 34
cell death 0.046 0.044 -10000 0 -0.4 4 4
ATIII/GPC1 0.043 0.026 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.006 0.16 -10000 0 -0.4 66 66
LCK 0.031 0.033 -10000 0 -10000 0 0
neuron differentiation -0.002 0.13 -10000 0 -0.33 60 60
PrPc/Cu2+ 0.013 0.067 -10000 0 -0.4 13 13
APP 0.031 0.055 -10000 0 -0.54 4 4
TGFBR2 (dimer) -0.005 0.14 -10000 0 -0.54 34 34
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.034 0.11 0.29 27 -0.33 7 34
epithelial cell differentiation 0.086 0.091 -10000 0 -10000 0 0
ITCH 0.046 0.025 -10000 0 -10000 0 0
WWP1 0.049 0.15 0.52 28 -10000 0 28
FYN 0.029 0.037 -10000 0 -0.54 2 2
EGFR -0.27 0.29 -10000 0 -0.54 264 264
PRL 0.033 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis 0.027 0.12 0.37 10 -0.36 5 15
PTPRZ1 -0.36 0.27 -10000 0 -0.54 348 348
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.015 0.1 -10000 0 -0.38 6 6
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.012 0.11 0.27 8 -0.31 39 47
ADAM17 0.047 0.025 -10000 0 -10000 0 0
ErbB4/ErbB4 0.03 0.12 0.4 29 -0.33 5 34
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.035 0.11 0.3 27 -0.3 6 33
NCOR1 0.031 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.005 0.11 -10000 0 -0.3 34 34
GRIN2B -0.017 0.11 -10000 0 -0.37 8 8
ErbB4/ErbB2/betacellulin 0.027 0.096 -10000 0 -0.3 12 12
STAT1 0.058 0.054 -10000 0 -10000 0 0
HBEGF 0.029 0.051 -10000 0 -0.54 4 4
PRLR 0.07 0.063 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.006 0.14 0.29 13 -0.38 44 57
axon guidance 0.12 0.14 0.37 65 -10000 0 65
NEDD4 0.039 0.06 -10000 0 -0.51 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.073 0.046 -10000 0 -10000 0 0
CBFA2T3 -0.023 0.17 -10000 0 -0.54 47 47
ErbB4/ErbB2/HBEGF 0.036 0.085 0.26 4 -0.3 6 10
MAPK3 0.029 0.12 0.37 8 -0.36 6 14
STAT1 (dimer) 0.053 0.11 0.31 29 -0.32 4 33
MAPK1 0.034 0.12 0.39 11 -0.36 6 17
JAK2 0.032 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.002 0.11 0.25 1 -0.3 29 30
NRG1 -0.015 0.12 -10000 0 -0.4 41 41
NRG3 0.035 0.043 -10000 0 -0.54 2 2
NRG2 -0.35 0.27 -10000 0 -0.54 333 333
NRG4 0.034 0.012 -10000 0 -10000 0 0
heart development 0.12 0.14 0.37 65 -10000 0 65
neural crest cell migration 0.002 0.11 0.25 1 -0.3 29 30
ERBB2 0.021 0.028 0.3 1 -0.37 1 2
WWOX/E4ICDs 0.027 0.1 0.31 17 -0.32 4 21
SHC1 0.027 0.014 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.12 0.16 -10000 0 -0.29 192 192
apoptosis -0.036 0.094 0.31 4 -0.31 23 27
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.18 0.17 0.29 1 -0.32 267 268
ErbB4/ErbB2/epiregulin 0.045 0.093 0.32 9 -0.31 2 11
ErbB4/ErbB4/betacellulin/betacellulin 0.02 0.12 0.29 26 -0.34 20 46
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.086 0.12 0.38 9 -0.32 2 11
MDM2 0.028 0.11 0.32 39 -0.34 3 42
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.002 0.1 -10000 0 -0.3 36 36
STAT5A 0.11 0.12 0.39 36 -10000 0 36
ErbB4/EGFR/neuregulin 1 beta -0.15 0.18 -10000 0 -0.33 203 203
DLG4 0.03 0.011 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.025 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.023 0.09 0.25 20 -0.29 4 24
STAT5A (dimer) 0.14 0.12 0.4 24 -10000 0 24
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.12 0.12 0.4 30 -0.36 1 31
LRIG1 0.015 0.1 -10000 0 -0.54 16 16
EREG 0.044 0.048 -10000 0 -0.54 1 1
BTC 0.011 0.12 -10000 0 -0.54 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.11 0.13 0.39 51 -10000 0 51
ERBB4 0.03 0.12 0.4 29 -0.36 4 33
STAT5B 0.033 0.01 -10000 0 -10000 0 0
YAP1 -0.001 0.12 0.26 6 -0.38 37 43
GRB2 0.033 0.017 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.037 0.081 -10000 0 -0.27 2 2
glial cell differentiation -0.023 0.089 0.29 4 -0.25 20 24
WWOX 0.034 0.03 -10000 0 -10000 0 0
cell proliferation 0.051 0.14 0.38 18 -0.38 10 28
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.067 0.14 0.31 59 -10000 0 59
GNAI2 0.033 0.01 -10000 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.012 -10000 0 -10000 0 0
RhoA/GTP -0.067 0.14 -10000 0 -0.32 59 59
negative regulation of cAMP metabolic process -0.08 0.14 -10000 0 -0.25 184 184
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.081 0.14 -10000 0 -0.25 184 184
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.16 0.2 -10000 0 -0.32 281 281
TC10/GTP -0.13 0.16 -10000 0 -0.28 270 270
Insulin Receptor/Insulin/IRS1/Shp2 0.039 0.14 -10000 0 -0.32 59 59
HRAS 0.034 0.013 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.001 0.19 -10000 0 -0.54 52 52
FOXO3 -0.031 0.16 -10000 0 -0.6 33 33
AKT1 -0.046 0.16 0.33 8 -0.45 22 30
INSR 0.039 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.091 0.072 0.36 22 -10000 0 22
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.029 0.051 -10000 0 -0.54 4 4
SORBS1 -0.28 0.29 -10000 0 -0.54 275 275
CRK 0.031 0.01 -10000 0 -10000 0 0
PTPN1 0.019 0.053 0.28 18 -10000 0 18
CAV1 -0.23 0.18 -10000 0 -0.33 365 365
CBL/APS/CAP/Crk-II/C3G -0.13 0.18 -10000 0 -0.3 274 274
Insulin Receptor/Insulin/IRS1/NCK2 0.04 0.13 -10000 0 -0.32 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.15 -10000 0 -0.3 91 91
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.017 0.097 0.36 1 -0.4 6 7
RPS6KB1 -0.04 0.14 0.31 8 -0.4 21 29
PARD6A 0.031 0.019 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.055 -10000 0 -0.55 4 4
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.013 0.15 -10000 0 -0.42 20 20
HRAS/GTP -0.009 0.077 -10000 0 -0.26 37 37
Insulin Receptor 0.039 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.038 0.12 -10000 0 -0.3 42 42
PRKCI 0.011 0.084 -10000 0 -0.51 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.045 0.16 -10000 0 -0.31 112 112
SHC1 0.027 0.014 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.058 0.052 -10000 0 -0.47 4 4
PI3K 0.008 0.15 -10000 0 -0.3 91 91
NCK2 0.034 0.007 -10000 0 -10000 0 0
RHOQ 0.033 0.026 -10000 0 -0.54 1 1
mol:H2O2 0.001 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
AKT2 -0.047 0.16 0.33 7 -0.44 22 29
PRKCZ -0.007 0.079 -10000 0 -0.39 14 14
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.011 0.09 -10000 0 -0.28 45 45
F2RL2 0.046 0.065 -10000 0 -0.54 3 3
TRIP10 0.032 0.026 -10000 0 -0.54 1 1
Insulin Receptor/Insulin/Shc 0.055 0.036 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.043 0.026 -10000 0 -0.34 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.076 0.055 -10000 0 -10000 0 0
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.14 0.18 -10000 0 -0.31 275 275
TC10/GDP 0.024 0.019 -10000 0 -0.4 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.068 0.057 -10000 0 -0.32 4 4
INPP5D -0.037 0.096 -10000 0 -0.3 59 59
SOS1 0.034 0.004 -10000 0 -10000 0 0
SGK1 -0.009 0.013 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
p62DOK/RasGAP 0.058 0.053 -10000 0 -0.47 4 4
INS 0.039 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.037 0.095 -10000 0 -0.29 59 59
GRB2 0.033 0.017 -10000 0 -10000 0 0
EIF4EBP1 -0.044 0.14 0.31 5 -0.4 21 26
PTPRA 0.037 0.013 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.043 0.026 -10000 0 -0.34 2 2
PDPK1 0.031 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.001 0.087 -10000 0 -0.25 41 41
Insulin Receptor/Insulin/IRS1 0.022 0.13 -10000 0 -0.32 59 59
Insulin Receptor/Insulin/IRS3 0.056 0.024 -10000 0 -10000 0 0
Par3/Par6 0.072 0.058 -10000 0 -0.29 5 5
p75(NTR)-mediated 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
Sortilin/TRAF6 0.048 0.011 -10000 0 -10000 0 0
Necdin/E2F1 -0.044 0.18 -10000 0 -0.36 117 117
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.003 0.15 -10000 0 -0.31 89 89
NGF (dimer)/p75(NTR)/BEX1 -0.007 0.14 -10000 0 -0.33 75 75
NT-4/5 (dimer)/p75(NTR) -0.041 0.15 -10000 0 -0.38 79 79
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 -0.032 0.16 0.33 3 -0.32 96 99
IKBKG 0.034 0.003 -10000 0 -10000 0 0
BDNF 0.038 0.047 -10000 0 -0.54 2 2
MGDIs/NGR/p75(NTR)/LINGO1 0.013 0.15 0.25 4 -0.33 72 76
FURIN 0.036 0.023 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0 0.15 -10000 0 -0.34 75 75
LINGO1 0.054 0.051 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.033 0.029 -10000 0 -10000 0 0
proBDNF (dimer) 0.038 0.047 -10000 0 -0.54 2 2
NTRK1 0.03 0.021 -10000 0 -10000 0 0
RTN4R 0.041 0.034 -10000 0 -10000 0 0
neuron apoptosis -0.012 0.16 0.51 2 -0.48 14 16
IRAK1 0.035 0.014 -10000 0 -10000 0 0
SHC1 -0.024 0.11 -10000 0 -0.34 50 50
ARHGDIA 0.032 0.011 -10000 0 -10000 0 0
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
Gamma Secretase 0.074 0.054 -10000 0 -0.3 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.008 0.14 -10000 0 -0.33 82 82
MAGEH1 0.018 0.095 -10000 0 -0.54 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.078 0.2 -10000 0 -0.38 147 147
Mammalian IAPs/DIABLO 0.045 0.078 -10000 0 -0.31 17 17
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.044 0.035 -10000 0 -10000 0 0
APP 0.031 0.055 -10000 0 -0.54 4 4
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.033 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.011 0.12 -10000 0 -0.29 73 73
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.036 0.11 0.21 31 -0.27 74 105
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.016 0.095 -10000 0 -0.25 57 57
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.018 0.14 -10000 0 -0.33 79 79
NCSTN 0.028 0.014 -10000 0 -10000 0 0
mol:GTP -0.018 0.15 -10000 0 -0.35 78 78
PSENEN 0.035 0.015 -10000 0 -10000 0 0
mol:ceramide -0.022 0.13 -10000 0 -0.31 74 74
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.012 0.078 -10000 0 -0.21 56 56
p75(NTR)/beta APP -0.025 0.16 -10000 0 -0.4 76 76
BEX1 0.053 0.048 -10000 0 -10000 0 0
mol:GDP -0.053 0.12 -10000 0 -0.34 75 75
NGF (dimer) 0.004 0.13 -10000 0 -0.31 64 64
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.027 0.15 -10000 0 -0.31 70 70
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
RAC1/GTP -0.014 0.12 -10000 0 -0.29 74 74
MYD88 0.034 0.011 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.018 0.15 -10000 0 -0.36 78 78
RHOB 0.032 0.038 -10000 0 -0.54 2 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.057 0.035 -10000 0 -10000 0 0
NT3 (dimer) -0.11 0.25 -10000 0 -0.54 130 130
TP53 -0.028 0.13 0.37 8 -0.29 71 79
PRDM4 -0.018 0.13 -10000 0 -0.31 74 74
BDNF (dimer) 0.054 0.17 -10000 0 -0.31 69 69
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
SORT1 0.034 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.008 0.15 -10000 0 -0.31 89 89
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0 0.13 -10000 0 -0.31 74 74
RHOC 0.034 0.005 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.029 0.14 0.31 5 -0.33 67 72
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 -0.022 0.13 -10000 0 -0.31 74 74
APH1B 0.032 0.027 -10000 0 -0.54 1 1
APH1A 0.031 0.027 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.018 0.14 -10000 0 -0.34 74 74
PSEN1 0.033 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.048 0.011 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.13 0.23 -10000 0 -0.43 172 172
MAPK8 -0.025 0.14 0.3 7 -0.32 65 72
MAPK9 -0.025 0.13 0.28 6 -0.32 64 70
APAF1 0.034 0.003 -10000 0 -10000 0 0
NTF3 -0.11 0.25 -10000 0 -0.54 130 130
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.099 0.24 -10000 0 -0.54 115 115
RAC1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.008 0.14 -10000 0 -0.3 71 71
p75 CTF/Sortilin/TRAF6/NRIF 0.08 0.026 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.019 0.15 -10000 0 -0.35 78 78
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.026 0.14 -10000 0 -0.3 71 71
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.016 0.14 -10000 0 -0.31 75 75
PRKACB 0.035 0.082 -10000 0 -0.54 8 8
proBDNF (dimer)/p75 ECD 0.051 0.037 -10000 0 -0.4 2 2
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BIRC2 0.03 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.16 -10000 0 -0.4 98 98
BAD -0.025 0.15 0.41 8 -0.33 65 73
RIPK2 0.029 0.021 -10000 0 -10000 0 0
NGFR -0.055 0.2 -10000 0 -0.54 75 75
CYCS -0.009 0.13 0.26 7 -0.29 72 79
ADAM17 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.003 0.12 -10000 0 -0.31 61 61
BCL2L11 -0.025 0.15 0.4 9 -0.33 65 74
BDNF (dimer)/p75(NTR) -0.021 0.16 -10000 0 -0.39 76 76
PI3K -0.029 0.16 -10000 0 -0.34 97 97
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.001 0.13 -10000 0 -0.31 74 74
NDNL2 0.033 0.007 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PRKCI 0.034 0.017 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.041 0.15 -10000 0 -0.38 79 79
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.005 0.13 -10000 0 -0.3 74 74
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.031 0.027 -10000 0 -0.54 1 1
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.028 0.13 -10000 0 -0.33 74 74
SQSTM1 0.034 0.008 -10000 0 -10000 0 0
NGFRAP1 0.009 0.12 -10000 0 -0.54 22 22
CASP3 -0.023 0.14 0.39 9 -0.31 66 75
E2F1 0.049 0.046 -10000 0 -10000 0 0
CASP9 0.033 0.007 -10000 0 -10000 0 0
IKK complex 0.03 0.084 -10000 0 -0.3 1 1
NGF (dimer)/TRKA 0.022 0.015 -10000 0 -10000 0 0
MMP7 -0.041 0.19 -10000 0 -0.54 63 63
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.011 0.13 -10000 0 -0.3 73 73
MMP3 0.092 0.098 -10000 0 -0.54 5 5
APAF-1/Caspase 9 -0.033 0.1 -10000 0 -0.26 75 75
Nectin adhesion 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
PDGFRB 0.033 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
PTK2 -0.053 0.17 -10000 0 -0.44 67 67
positive regulation of JNK cascade -0.024 0.15 -10000 0 -0.33 69 69
CDC42/GDP -0.018 0.2 0.46 1 -0.43 83 84
Rac1/GDP -0.018 0.2 -10000 0 -0.42 83 83
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
CDC42/GTP -0.023 0.18 -10000 0 -0.4 69 69
nectin-3/I-afadin -0.024 0.17 -10000 0 -0.41 78 78
RAPGEF1 -0.042 0.2 0.47 1 -0.46 78 79
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.22 -10000 0 -0.52 79 79
PDGFB-D/PDGFRB 0.033 0.006 -10000 0 -10000 0 0
TLN1 -0.039 0.12 0.2 3 -0.48 21 24
Rap1/GTP -0.03 0.14 -10000 0 -0.33 76 76
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.054 0.041 -10000 0 -0.31 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.41 78 78
PVR 0.035 0.015 -10000 0 -10000 0 0
Necl-5(dimer) 0.035 0.015 -10000 0 -10000 0 0
mol:GDP -0.045 0.24 0.47 1 -0.52 84 85
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
PI3K -0.004 0.18 -10000 0 -0.34 102 102
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
positive regulation of lamellipodium assembly -0.02 0.16 -10000 0 -0.33 83 83
PVRL1 0.031 0.014 -10000 0 -10000 0 0
PVRL3 -0.053 0.21 -10000 0 -0.54 76 76
PVRL2 0.038 0.026 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
CDH1 0.006 0.12 -10000 0 -0.54 22 22
CLDN1 -0.004 0.16 -10000 0 -0.54 41 41
JAM-A/CLDN1 -0.007 0.17 -10000 0 -0.36 80 80
SRC -0.074 0.24 -10000 0 -0.57 80 80
ITGB3 0.035 0.018 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
FARP2 -0.044 0.24 0.47 1 -0.54 70 71
RAC1 0.034 0.005 -10000 0 -10000 0 0
CTNNA1 0.033 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.001 0.15 -10000 0 -0.35 78 78
nectin-1/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
nectin-2/I-afadin 0.045 0.048 -10000 0 -0.4 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.044 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.005 0.15 -10000 0 -0.35 78 78
CDC42/GTP/IQGAP1/filamentous actin 0.043 0.013 -10000 0 -10000 0 0
F11R 0.028 0.017 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.024 0.15 -10000 0 -0.33 69 69
alphaV/beta3 Integrin/Talin -0.005 0.13 0.3 1 -0.46 20 21
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.4 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.4 3 3
PIP5K1C -0.037 0.12 -10000 0 -0.49 23 23
VAV2 -0.042 0.24 0.46 1 -0.54 74 75
RAP1/GDP -0.014 0.19 -10000 0 -0.4 72 72
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.001 0.15 -10000 0 -0.34 78 78
nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.41 78 78
Rac1/GTP -0.022 0.19 -10000 0 -0.4 83 83
PTPRM -0.035 0.14 -10000 0 -0.29 82 82
E-cadherin/beta catenin/alpha catenin 0.052 0.1 -10000 0 -0.29 25 25
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.035 0.032 -10000 0 -10000 0 0
CDKN2C -0.024 0.15 -10000 0 -0.52 42 42
CDKN2A 0.057 0.054 -10000 0 -10000 0 0
CCND2 -0.007 0.06 0.17 28 -0.19 16 44
RB1 0.004 0.072 0.22 14 -0.2 31 45
CDK4 -0.003 0.074 0.21 35 -0.21 13 48
CDK6 -0.004 0.073 0.21 33 -0.22 16 49
G1/S progression 0.003 0.087 0.21 52 -0.23 15 67
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.036 0.085 -10000 0 -0.41 14 14
HDAC1 0.023 0.027 -10000 0 -10000 0 0
AES 0.033 0.008 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
DTX1 0.031 0.044 -10000 0 -0.54 3 3
LRP6/FZD1 0.046 0.024 -10000 0 -0.4 1 1
TLE1 0.016 0.098 -10000 0 -0.55 15 15
AP1 -0.22 0.19 -10000 0 -0.34 321 321
NCSTN 0.028 0.014 -10000 0 -10000 0 0
ADAM10 0.034 0.013 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.019 0.14 -10000 0 -0.73 9 9
NICD/RBPSUH 0.054 0.093 -10000 0 -0.41 14 14
WIF1 -0.38 0.26 -10000 0 -0.54 363 363
NOTCH1 0.019 0.072 -10000 0 -0.42 12 12
PSENEN 0.035 0.015 -10000 0 -10000 0 0
KREMEN2 0.1 0.074 -10000 0 -10000 0 0
DKK1 0.005 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.01 0.092 -10000 0 -0.43 8 8
APH1B 0.032 0.027 -10000 0 -0.54 1 1
APH1A 0.031 0.027 -10000 0 -10000 0 0
AXIN1 0.016 0.07 -10000 0 -0.6 4 4
CtBP/CBP/TCF1/TLE1/AES 0.002 0.08 0.28 3 -0.39 6 9
PSEN1 0.033 0.007 -10000 0 -10000 0 0
FOS -0.36 0.27 -10000 0 -0.54 342 342
JUN -0.065 0.22 -10000 0 -0.54 86 86
MAP3K7 0.03 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.089 -10000 0 -0.42 10 10
MAPK3 0.032 0.009 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.069 -10000 0 -0.31 3 3
HNF1A 0.034 0.014 -10000 0 -10000 0 0
CTBP1 0.032 0.009 -10000 0 -10000 0 0
MYC -0.053 0.32 -10000 0 -1.3 31 31
NKD1 0.031 0.021 -10000 0 -10000 0 0
FZD1 0.033 0.026 -10000 0 -0.54 1 1
NOTCH1 precursor/Deltex homolog 1 0.055 0.095 -10000 0 -0.41 14 14
apoptosis -0.22 0.19 -10000 0 -0.34 321 321
Delta 1/NOTCHprecursor 0.053 0.092 -10000 0 -0.41 13 13
DLL1 0.032 0.009 -10000 0 -10000 0 0
PPARD 0.025 0.1 -10000 0 -0.81 6 6
Gamma Secretase 0.075 0.054 -10000 0 -0.3 1 1
APC 0.005 0.1 -10000 0 -0.51 14 14
DVL1 -0.039 0.094 -10000 0 -0.37 27 27
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.079 0.13 -10000 0 -0.29 42 42
LRP6 0.032 0.008 -10000 0 -10000 0 0
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
NLK 0.015 0.025 -10000 0 -10000 0 0
CCND1 0.034 0.23 -10000 0 -1.3 12 12
WNT1 0.034 0.004 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.019 0.12 0.34 2 -0.48 13 15
DKK2 0.031 0.054 -10000 0 -0.54 4 4
NOTCH1 precursor/DVL1 -0.014 0.12 -10000 0 -0.65 12 12
GSK3B 0.034 0.008 -10000 0 -10000 0 0
FRAT1 0.033 0.008 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.036 0.088 -10000 0 -0.41 14 14
PPP2R5D -0.003 0.065 -10000 0 -0.37 11 11
MAPK1 0.032 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.2 0.18 -10000 0 -0.31 350 350
RBPJ 0.033 0.008 -10000 0 -10000 0 0
CREBBP 0.033 0.03 -10000 0 -0.55 1 1
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.09 -10000 0 -0.25 45 45
epithelial cell differentiation 0.04 0.085 -10000 0 -0.29 25 25
CYFIP2 0.049 0.045 -10000 0 -10000 0 0
ENAH -0.007 0.071 0.28 5 -0.32 1 6
EGFR -0.27 0.29 -10000 0 -0.54 264 264
EPHA2 0.026 0.063 -10000 0 -0.54 6 6
MYO6 0.001 0.073 -10000 0 -0.28 24 24
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
ABI1/Sra1/Nap1 0.073 0.034 -10000 0 -10000 0 0
AQP5 -0.14 0.24 -10000 0 -0.49 149 149
CTNND1 0.033 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.071 -10000 0 -0.28 24 24
regulation of calcium-dependent cell-cell adhesion -0.023 0.1 -10000 0 -0.29 62 62
EGF -0.15 0.27 -10000 0 -0.54 162 162
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
AQP3 -0.052 0.18 -10000 0 -0.49 62 62
cortical microtubule organization 0.04 0.085 -10000 0 -0.29 25 25
GO:0000145 -0.021 0.063 -10000 0 -0.27 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.088 -10000 0 -0.29 25 25
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GDP -0.029 0.057 -10000 0 -0.42 1 1
ARF6 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.058 -10000 0 -0.32 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.001 0.069 -10000 0 -0.26 23 23
PVRL2 0.038 0.026 -10000 0 -10000 0 0
ZYX -0.002 0.072 -10000 0 -0.28 25 25
ARF6/GTP 0.062 0.061 -10000 0 -0.3 6 6
CDH1 0.006 0.12 -10000 0 -0.54 22 22
EGFR/EGFR/EGF/EGF -0.23 0.2 -10000 0 -0.35 352 352
RhoA/GDP 0.041 0.083 -10000 0 -0.28 25 25
actin cytoskeleton organization -0.021 0.067 -10000 0 -0.28 23 23
IGF-1R heterotetramer 0.01 0.12 -10000 0 -0.54 21 21
GIT1 0.032 0.011 -10000 0 -10000 0 0
IGF1R 0.01 0.12 -10000 0 -0.54 21 21
IGF1 -0.25 0.29 -10000 0 -0.54 250 250
DIAPH1 0.056 0.12 -10000 0 -0.56 7 7
Wnt receptor signaling pathway -0.04 0.085 0.29 25 -10000 0 25
RHOA 0.033 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.029 0.058 -10000 0 -0.42 1 1
CTNNA1 0.033 0.006 -10000 0 -10000 0 0
VCL -0.021 0.068 -10000 0 -0.28 23 23
EFNA1 0.028 0.015 -10000 0 -10000 0 0
LPP -0.023 0.065 -10000 0 -0.27 24 24
Ephrin A1/EPHA2 0.023 0.082 -10000 0 -0.29 25 25
SEC6/SEC8 -0.007 0.067 -10000 0 -0.27 22 22
MGAT3 -0.024 0.11 -10000 0 -0.29 62 62
HGF/MET 0.004 0.13 -10000 0 -0.29 72 72
HGF 0.034 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.091 -10000 0 -0.26 45 45
actin cable formation 0.054 0.11 0.32 21 -0.29 1 22
KIAA1543 -0.021 0.064 -10000 0 -0.27 24 24
KIFC3 0.001 0.069 -10000 0 -0.28 24 24
NCK1 0.034 0.005 -10000 0 -10000 0 0
EXOC3 0.032 0.008 -10000 0 -10000 0 0
ACTN1 -0.001 0.071 -10000 0 -0.28 24 24
NCK1/GIT1 0.046 0.016 -10000 0 -10000 0 0
mol:GDP 0.04 0.085 -10000 0 -0.29 25 25
EXOC4 0.034 0.005 -10000 0 -10000 0 0
STX4 -0.002 0.07 -10000 0 -0.28 24 24
PIP5K1C -0.001 0.072 -10000 0 -0.28 24 24
LIMA1 0.012 0.11 -10000 0 -0.54 19 19
ABI1 0.033 0.006 -10000 0 -10000 0 0
ROCK1 0.014 0.1 0.3 13 -0.38 1 14
adherens junction assembly -0.03 0.13 0.3 1 -0.6 13 14
IGF-1R heterotetramer/IGF1 -0.13 0.18 -10000 0 -0.3 247 247
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.4 3 3
MET -0.023 0.17 -10000 0 -0.54 50 50
PLEKHA7 -0.001 0.071 -10000 0 -0.28 24 24
mol:GTP 0.055 0.057 -10000 0 -0.31 6 6
establishment of epithelial cell apical/basal polarity -0.013 0.086 0.36 5 -0.35 1 6
cortical actin cytoskeleton stabilization -0.01 0.09 -10000 0 -0.25 45 45
regulation of cell-cell adhesion -0.021 0.067 -10000 0 -0.28 23 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.091 -10000 0 -0.26 45 45
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.005 0.13 -10000 0 -0.38 52 52
CRKL -0.002 0.11 0.37 1 -0.39 17 18
mol:PIP3 0.009 0.064 0.49 7 -10000 0 7
AKT1 0.021 0.08 0.43 7 -10000 0 7
PTK2B 0.027 0.014 -10000 0 -10000 0 0
RAPGEF1 -0.003 0.11 0.35 1 -0.43 10 11
RANBP10 0.03 0.012 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.022 0.12 -10000 0 -0.34 50 50
MAP3K5 -0.012 0.13 0.37 1 -0.41 23 24
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.12 -10000 0 -0.31 51 51
AP1 -0.29 0.24 -10000 0 -0.43 343 343
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
apoptosis -0.54 0.38 -10000 0 -0.77 364 364
STAT3 (dimer) -0.007 0.11 -10000 0 -0.42 16 16
GAB1/CRKL/SHP2/PI3K 0.011 0.14 -10000 0 -0.44 15 15
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.014 0.11 0.36 1 -0.42 10 11
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.032 0.008 -10000 0 -10000 0 0
PTEN 0.025 0.068 -10000 0 -0.54 7 7
ELK1 -0.019 0.085 0.26 14 -0.21 8 22
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.007 0.063 -10000 0 -0.26 5 5
PAK1 0.046 0.099 0.44 12 -10000 0 12
HGF/MET/RANBP10 0.021 0.12 -10000 0 -0.34 50 50
HRAS -0.033 0.2 -10000 0 -0.58 58 58
DOCK1 -0.004 0.11 0.43 2 -0.44 10 12
GAB1 -0.004 0.12 -10000 0 -0.38 22 22
CRK -0.003 0.11 0.37 1 -0.39 17 18
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.023 0.18 -10000 0 -0.53 56 56
JUN -0.065 0.22 -10000 0 -0.54 86 86
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.013 0.088 -10000 0 -0.27 51 51
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
cell morphogenesis -0.017 0.15 0.41 6 -0.44 18 24
GRB2/SHC 0.019 0.081 -10000 0 -0.25 31 31
FOS -0.36 0.27 -10000 0 -0.54 342 342
GLMN 0.004 0.004 -10000 0 -10000 0 0
cell motility -0.019 0.084 0.26 14 -0.21 8 22
HGF/MET/MUC20 0.007 0.12 -10000 0 -0.34 51 51
cell migration 0.019 0.08 -10000 0 -0.24 31 31
GRB2 0.033 0.017 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
MET/RANBP10 0 0.13 -10000 0 -0.39 51 51
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.012 0.097 -10000 0 -0.29 41 41
MET/MUC20 -0.017 0.13 -10000 0 -0.39 52 52
RAP1B 0.002 0.11 0.32 2 -0.41 9 11
RAP1A -0.004 0.1 0.51 1 -0.42 9 10
HGF/MET/RANBP9 0.026 0.12 -10000 0 -0.34 48 48
RAF1 -0.026 0.19 -10000 0 -0.55 58 58
STAT3 -0.007 0.11 -10000 0 -0.42 16 16
cell proliferation 0.025 0.15 0.33 11 -0.38 35 46
RPS6KB1 0.001 0.061 -10000 0 -0.38 7 7
MAPK3 -0.037 0.081 0.62 3 -10000 0 3
MAPK1 -0.004 0.17 0.65 29 -10000 0 29
RANBP9 0.033 0.009 -10000 0 -10000 0 0
MAPK8 -0.004 0.12 0.45 1 -0.43 11 12
SRC -0.007 0.097 -10000 0 -0.36 14 14
PI3K -0.009 0.13 -10000 0 -0.28 84 84
MET/Glomulin -0.013 0.11 -10000 0 -0.35 50 50
SOS1 0.034 0.004 -10000 0 -10000 0 0
MAP2K1 -0.022 0.18 0.48 1 -0.52 55 56
MET -0.023 0.17 -10000 0 -0.54 50 50
MAP4K1 0.002 0.12 0.39 1 -0.43 16 17
PTK2 0.027 0.014 -10000 0 -10000 0 0
MAP2K2 -0.023 0.18 0.48 1 -0.51 58 59
BAD 0.018 0.074 0.41 5 -10000 0 5
MAP2K4 -0.012 0.12 0.35 1 -0.39 21 22
SHP2/GRB2/SOS1/GAB1 0.019 0.14 -10000 0 -0.36 51 51
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
SH3KBP1 0.033 0.027 -10000 0 -0.54 1 1
HGS -0.015 0.077 -10000 0 -0.25 44 44
PLCgamma1/PKC 0.024 0.006 -10000 0 -10000 0 0
HGF 0.034 0.01 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
PTPRJ 0.035 0.016 -10000 0 -10000 0 0
NCK/PLCgamma1 0.025 0.094 -10000 0 -0.24 48 48
PDPK1 0.024 0.087 0.47 8 -10000 0 8
HGF/MET/SHIP 0.007 0.12 -10000 0 -0.34 51 51
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.012 -10000 0 -10000 0 0
CDC42/GTP -0.067 0.14 -10000 0 -0.32 58 58
PLCG1 -0.073 0.13 -10000 0 -0.33 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.045 0.017 -10000 0 -10000 0 0
cell migration -0.067 0.14 -10000 0 -0.31 59 59
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.07 0.13 -10000 0 -0.34 49 49
MAPK1 -0.077 0.13 -10000 0 -0.33 56 56
S1P/S1P5/Gi -0.081 0.14 -10000 0 -0.25 184 184
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
CDC42/GDP 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.033 0.05 0.2 3 -10000 0 3
S1P/S1P4/Gi -0.081 0.14 -10000 0 -0.25 184 184
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
S1P/S1P4/G12/G13 0.039 0.014 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.047 0.035 -10000 0 -0.3 3 3
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.061 0.28 3 -0.26 1 4
AP1 -0.21 0.19 -10000 0 -0.33 341 341
mol:PIP3 -0.15 0.16 -10000 0 -0.28 271 271
AKT1 0.005 0.09 -10000 0 -0.33 7 7
PTK2B -0.015 0.08 -10000 0 -0.18 81 81
RHOA 0.009 0.066 -10000 0 -0.26 20 20
PIK3CB 0.033 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0.058 0.19 44 -0.27 1 45
MAGI3 0.04 0.041 -10000 0 -0.54 1 1
RELA 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.017 0.022 -10000 0 -0.19 5 5
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.014 0.078 0.22 6 -0.3 5 11
NF kappa B1 p50/RelA 0.021 0.04 -10000 0 -0.31 1 1
endothelial cell migration 0.016 0.053 0.27 2 -0.47 5 7
ADCY4 -0.048 0.096 -10000 0 -0.3 15 15
ADCY5 -0.047 0.094 -10000 0 -0.29 12 12
ADCY6 -0.047 0.094 -10000 0 -0.29 12 12
ADCY7 -0.037 0.091 -10000 0 -0.3 13 13
ADCY1 -0.046 0.094 -10000 0 -0.28 14 14
ADCY2 -0.048 0.098 -10000 0 -0.31 17 17
ADCY3 -0.046 0.094 -10000 0 -0.29 12 12
ADCY8 -0.041 0.087 -10000 0 -0.31 10 10
ADCY9 -0.043 0.091 -10000 0 -0.23 32 32
GSK3B -0.014 0.079 0.25 4 -0.22 17 21
arachidonic acid secretion -0.053 0.1 -10000 0 -0.25 54 54
GNG2 0.032 0.026 -10000 0 -0.54 1 1
TRIP6 0.023 0.021 -10000 0 -0.39 1 1
GNAO1 0.019 0.021 -10000 0 -0.26 2 2
HRAS 0.034 0.013 -10000 0 -10000 0 0
NFKBIA 0.026 0.061 0.27 3 -0.25 3 6
GAB1 0.033 0.027 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.051 0.1 -10000 0 -0.86 6 6
JUN -0.065 0.22 -10000 0 -0.54 86 86
LPA/LPA2/NHERF2 0.023 0.016 -10000 0 -10000 0 0
TIAM1 0.033 0.12 -10000 0 -1 6 6
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 0.026 0.056 0.2 44 -10000 0 44
PLCB3 0.036 0.05 0.19 41 -10000 0 41
FOS -0.36 0.27 -10000 0 -0.54 342 342
positive regulation of mitosis -0.053 0.1 -10000 0 -0.25 54 54
LPA/LPA1-2-3 0.007 0.02 -10000 0 -0.18 5 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.029 0.012 -10000 0 -10000 0 0
stress fiber formation 0.016 0.058 -10000 0 -0.27 7 7
GNAZ 0.015 0.045 -10000 0 -0.28 10 10
EGFR/PI3K-beta/Gab1 -0.15 0.17 -10000 0 -0.3 271 271
positive regulation of dendritic cell cytokine production 0.007 0.02 -10000 0 -0.18 5 5
LPA/LPA2/MAGI-3 0.029 0.03 -10000 0 -0.2 3 3
ARHGEF1 0.037 0.054 -10000 0 -0.22 2 2
GNAI2 0.02 0.025 -10000 0 -0.21 5 5
GNAI3 0.02 0.023 -10000 0 -0.22 4 4
GNAI1 -0.11 0.17 -10000 0 -0.34 182 182
LPA/LPA3 0.002 0.01 -10000 0 -0.093 5 5
LPA/LPA2 0.002 0.01 -10000 0 -0.093 5 5
LPA/LPA1 0.007 0.026 -10000 0 -0.25 5 5
HB-EGF/EGFR -0.12 0.2 -10000 0 -0.31 244 244
HBEGF 0.065 0.076 -10000 0 -0.4 4 4
mol:DAG 0.026 0.056 0.2 44 -10000 0 44
cAMP biosynthetic process -0.055 0.1 0.24 1 -0.3 21 22
NFKB1 0.034 0.005 -10000 0 -10000 0 0
SRC 0.032 0.008 -10000 0 -10000 0 0
GNB1 0.033 0.011 -10000 0 -10000 0 0
LYN 0.04 0.069 0.27 19 -0.28 1 20
GNAQ 0.003 0.009 0.057 2 -0.075 5 7
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 0.003 0.016 0.074 2 -0.15 5 7
IL8 -0.19 0.22 0.34 13 -0.38 260 273
PTK2 0.02 0.021 -10000 0 -0.16 4 4
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
CASP3 0.017 0.022 -10000 0 -0.19 5 5
EGFR -0.27 0.29 -10000 0 -0.54 264 264
PLCG1 0.017 0.018 -10000 0 -0.1 3 3
PLD2 0.022 0.025 -10000 0 -0.2 5 5
G12/G13 0.044 0.03 -10000 0 -0.19 5 5
PI3K-beta -0.009 0.088 -10000 0 -0.38 7 7
cell migration 0.028 0.042 -10000 0 -0.25 6 6
SLC9A3R2 0.032 0.015 -10000 0 -10000 0 0
PXN 0.015 0.059 -10000 0 -0.28 7 7
HRAS/GTP -0.054 0.1 -10000 0 -0.25 57 57
RAC1 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.092 0.072 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
PRKCD 0.024 0.058 0.22 8 -0.26 1 9
Gi(beta/gamma) -0.05 0.11 -10000 0 -0.3 30 30
mol:LPA 0.003 0.016 0.074 2 -0.15 5 7
TRIP6/p130 Cas/FAK1/Paxillin 0.03 0.052 -10000 0 -0.24 3 3
MAPKKK cascade -0.053 0.1 -10000 0 -0.25 54 54
contractile ring contraction involved in cytokinesis 0.008 0.068 -10000 0 -0.26 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.021 0.039 -10000 0 -0.31 4 4
GNA15 0.016 0.014 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MAPT -0.014 0.079 0.22 6 -0.29 6 12
GNA11 0.015 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.053 0.11 -10000 0 -0.92 6 6
MMP2 0.016 0.053 0.27 2 -0.47 5 7
ErbB2/ErbB3 signaling events

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.005 0.015 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.1 -10000 0 -0.31 6 6
NFATC4 -0.028 0.081 0.28 3 -0.24 16 19
ERBB2IP 0.034 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.033 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.036 0.087 -10000 0 -0.3 28 28
JUN -0.055 0.071 -10000 0 -10000 0 0
HRAS 0.033 0.013 -10000 0 -10000 0 0
DOCK7 -0.036 0.09 0.26 2 -0.29 28 30
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.019 0.097 -10000 0 -0.3 25 25
AKT1 0.007 0.016 0.13 6 -10000 0 6
BAD -0.005 0.014 -10000 0 -10000 0 0
MAPK10 -0.022 0.071 0.26 4 -0.26 7 11
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.037 0.094 -10000 0 -0.32 28 28
RAF1 -0.038 0.095 -10000 0 -0.34 6 6
ErbB2/ErbB3/neuregulin 2 -0.18 0.17 -10000 0 -0.33 267 267
STAT3 0.01 0.16 -10000 0 -0.84 18 18
cell migration -0.014 0.072 0.27 6 -0.26 3 9
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.26 0.27 -10000 0 -0.66 115 115
FOS -0.34 0.26 -10000 0 -0.49 363 363
NRAS 0.034 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.087 -10000 0 -0.3 28 28
MAPK3 -0.16 0.21 -10000 0 -0.51 86 86
MAPK1 -0.18 0.24 -10000 0 -0.56 102 102
JAK2 -0.033 0.09 0.26 2 -0.29 28 30
NF2 0.004 0.061 -10000 0 -0.67 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.081 -10000 0 -0.28 24 24
NRG1 -0.021 0.16 -10000 0 -0.55 43 43
GRB2/SOS1 0.046 0.018 -10000 0 -10000 0 0
MAPK8 -0.038 0.1 -10000 0 -0.29 31 31
MAPK9 -0.019 0.065 0.26 3 -10000 0 3
ERBB2 -0.022 0.013 -10000 0 -10000 0 0
ERBB3 0.036 0.025 -10000 0 -10000 0 0
SHC1 0.026 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.019 0.026 -10000 0 -0.18 2 2
STAT3 (dimer) 0.011 0.16 -10000 0 -0.82 18 18
RNF41 -0.009 0.014 -10000 0 -10000 0 0
FRAP1 -0.002 0.013 0.11 6 -10000 0 6
RAC1-CDC42/GTP -0.037 0.06 -10000 0 -0.22 28 28
ErbB2/ErbB2/HSP90 (dimer) -0.008 0.023 -10000 0 -10000 0 0
CHRNA1 -0.12 0.16 -10000 0 -0.4 64 64
myelination -0.021 0.089 0.33 6 -10000 0 6
PPP3CB -0.033 0.086 0.25 2 -0.27 27 29
KRAS 0.033 0.017 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.035 0.1 -10000 0 -0.26 16 16
NRG2 -0.35 0.27 -10000 0 -0.54 333 333
mol:GDP 0 0.08 -10000 0 -0.28 24 24
SOS1 0.033 0.004 -10000 0 -10000 0 0
MAP2K2 -0.054 0.1 -10000 0 -0.35 11 11
SRC 0.032 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.033 0.092 0.27 2 -0.29 28 30
MAP2K1 -0.17 0.21 -10000 0 -0.59 52 52
heart morphogenesis -0.036 0.087 -10000 0 -0.3 28 28
RAS family/GDP 0.029 0.11 -10000 0 -0.3 5 5
GRB2 0.032 0.017 -10000 0 -10000 0 0
PRKACA 0.006 0.075 -10000 0 -0.67 6 6
CHRNE -0.006 0.018 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.016 -10000 0 -0.13 6 6
nervous system development -0.036 0.087 -10000 0 -0.3 28 28
CDC42 0.033 0.007 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.032 0.008 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.027 0.094 -10000 0 -0.27 17 17
NT3 (dimer)/TRKC -0.08 0.21 -10000 0 -0.4 142 142
NT3 (dimer)/TRKB -0.24 0.29 -10000 0 -0.48 276 276
SHC/Grb2/SOS1/GAB1/PI3K 0.003 0.073 -10000 0 -10000 0 0
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
BDNF 0.038 0.047 -10000 0 -0.54 2 2
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
DYNLT1 0.032 0.009 -10000 0 -10000 0 0
NTRK1 0.03 0.021 -10000 0 -10000 0 0
NTRK2 -0.23 0.29 -10000 0 -0.54 234 234
NTRK3 0.015 0.1 -10000 0 -0.54 16 16
NT-4/5 (dimer)/TRKB -0.17 0.23 -10000 0 -0.41 220 220
neuron apoptosis 0.12 0.21 0.44 111 -10000 0 111
SHC 2-3/Grb2 -0.13 0.23 -10000 0 -0.49 111 111
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 -0.14 0.24 -10000 0 -0.52 117 117
SHC3 -0.12 0.21 -10000 0 -0.5 90 90
STAT3 (dimer) 0.053 0.076 -10000 0 -0.36 10 10
NT3 (dimer)/TRKA -0.083 0.2 -10000 0 -0.38 132 132
RIN/GDP 0.006 0.11 0.26 3 -0.28 17 20
GIPC1 0.034 0.01 -10000 0 -10000 0 0
KRAS 0.034 0.017 -10000 0 -10000 0 0
DNAJA3 -0.054 0.13 -10000 0 -0.34 69 69
RIN/GTP 0.023 0.019 -10000 0 -0.4 1 1
CCND1 0.014 0.12 -10000 0 -0.78 10 10
MAGED1 0.044 0.035 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.033 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.04 0.026 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.032 0.067 -10000 0 -0.4 9 9
ELMO1 0.034 0.004 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.042 0.032 -10000 0 -0.29 4 4
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
DOCK1 0.03 0.045 -10000 0 -0.54 3 3
GAB2 0.03 0.012 -10000 0 -10000 0 0
RIT2 0.032 0.027 -10000 0 -0.54 1 1
RIT1 0.028 0.013 -10000 0 -10000 0 0
FRS2 0.032 0.029 -10000 0 -0.54 1 1
DNM1 0.034 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.035 0.15 -10000 0 -0.34 75 75
mol:GDP -0.008 0.15 0.33 6 -0.42 19 25
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.025 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.004 0.096 0.24 1 -0.28 16 17
TIAM1 0.035 0.012 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
BDNF (dimer)/TRKB -0.12 0.2 -10000 0 -0.34 231 231
KIDINS220/CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.039 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2 0.064 0.028 -10000 0 -0.34 1 1
SHC/GRB2/SOS1/GAB1 0.063 0.043 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.01 -10000 0 -10000 0 0
NT3 (dimer) -0.11 0.25 -10000 0 -0.54 130 130
RAP1/GDP 0.002 0.089 -10000 0 -0.25 14 14
KIDINS220/CRKL 0.032 0.008 -10000 0 -10000 0 0
BDNF (dimer) 0.038 0.047 -10000 0 -0.54 2 2
ubiquitin-dependent protein catabolic process 0.029 0.057 -10000 0 -0.34 9 9
Schwann cell development -0.037 0.032 -10000 0 -10000 0 0
EHD4 0.033 0.007 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.075 0.038 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.027 0.066 -10000 0 -0.3 6 6
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.22 -10000 0 -0.35 266 266
ABL1 0.034 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
Rap1/GTP -0.041 0.12 -10000 0 -0.43 23 23
STAT3 0.053 0.076 -10000 0 -0.36 10 10
axon guidance -0.16 0.2 -10000 0 -0.34 266 266
MAPK3 0.048 0.066 0.28 4 -10000 0 4
MAPK1 0.051 0.069 0.28 5 -10000 0 5
CDC42/GDP 0.008 0.11 0.28 6 -0.28 16 22
NTF3 -0.11 0.25 -10000 0 -0.54 130 130
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.038 0.022 -10000 0 -10000 0 0
PI3K 0.006 0.12 -10000 0 -0.38 46 46
FRS3 0.033 0.006 -10000 0 -10000 0 0
FAIM 0.033 0.006 -10000 0 -10000 0 0
GAB1 0.033 0.027 -10000 0 -0.54 1 1
RASGRF1 -0.052 0.14 -10000 0 -0.34 76 76
SOS1 0.034 0.004 -10000 0 -10000 0 0
MCF2L -0.081 0.17 -10000 0 -0.35 136 136
RGS19 0.034 0.021 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.099 0.36 1 -0.43 5 6
Rac1/GDP 0.007 0.11 0.26 5 -0.28 17 22
NGF (dimer)/TRKA/GRIT 0.02 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis -0.027 0.22 0.42 1 -0.73 28 29
NGF (dimer)/TRKA/NEDD4-2 0.029 0.058 -10000 0 -0.34 9 9
MAP2K1 0.064 0.087 0.36 13 -10000 0 13
NGFR -0.055 0.2 -10000 0 -0.54 75 75
NGF (dimer)/TRKA/GIPC/GAIP 0.024 0.025 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0 0.084 -10000 0 -0.26 38 38
FRS2 family/SHP2/GRB2/SOS1 0.087 0.043 -10000 0 -0.3 1 1
NRAS 0.035 0.016 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
PRKCI 0.034 0.017 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.018 0.072 -10000 0 -0.56 4 4
RASA1 0.033 0.011 -10000 0 -10000 0 0
TRKA/c-Abl 0.042 0.023 -10000 0 -10000 0 0
SQSTM1 0.034 0.008 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.099 0.2 -10000 0 -0.31 229 229
NGF (dimer)/TRKA/p62/Atypical PKCs 0.049 0.029 -10000 0 -10000 0 0
MATK 0.038 0.027 -10000 0 -10000 0 0
NEDD4L 0.018 0.095 -10000 0 -0.54 14 14
RAS family/GDP -0.033 0.057 -10000 0 -0.22 17 17
NGF (dimer)/TRKA -0.059 0.14 -10000 0 -0.36 78 78
Rac1/GTP -0.05 0.098 -10000 0 -0.28 40 40
FRS2 family/SHP2/CRK family 0.082 0.046 -10000 0 -0.3 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.027 0.081 -10000 0 -0.43 10 10
Crk/p130 Cas/Paxillin -0.083 0.14 -10000 0 -0.39 66 66
JUN -0.002 0.15 0.28 3 -0.43 21 24
HRAS 0.034 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.11 0.17 -10000 0 -0.3 60 60
RAP1A 0.034 0.005 -10000 0 -10000 0 0
FRS2 0.032 0.029 -10000 0 -0.54 1 1
RAP1A/GDP 0.025 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.11 0.17 0.35 3 -0.3 58 61
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.053 0.14 -10000 0 -0.31 61 61
RHOA 0.033 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.074 0.15 -10000 0 -0.28 47 47
GRB7 0.029 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.11 0.17 -10000 0 -0.3 59 59
MAPKKK cascade 0.056 0.14 0.24 7 -0.29 42 49
BCAR1 0.029 0.012 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.013 0.2 -10000 0 -0.38 93 93
lamellipodium assembly -0.045 0.16 -10000 0 -0.35 72 72
RET51/GFRalpha1/GDNF/SHC 0.089 0.16 -10000 0 -0.3 45 45
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.042 0.13 -10000 0 -0.31 46 46
RET9/GFRalpha1/GDNF/Shank3 0.047 0.14 -10000 0 -0.31 62 62
MAPK3 0.041 0.13 0.26 9 -0.28 46 55
DOK1 0.036 0.016 -10000 0 -10000 0 0
DOK6 0.031 0.055 -10000 0 -0.54 4 4
PXN 0.034 0.003 -10000 0 -10000 0 0
neurite development 0.042 0.13 0.33 1 -0.34 3 4
DOK5 0.012 0.11 -10000 0 -0.54 18 18
GFRA1 0.025 0.23 -10000 0 -0.54 65 65
MAPK8 0.052 0.12 0.27 4 -0.37 8 12
HRAS/GTP 0.09 0.16 0.3 4 -0.32 44 48
tube development 0.054 0.14 0.31 12 -0.3 58 70
MAPK1 0.043 0.13 0.28 9 -0.28 46 55
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.019 0.11 -10000 0 -0.26 59 59
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC 0.032 0.008 -10000 0 -10000 0 0
PDLIM7 0.033 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.11 0.17 0.35 2 -0.31 44 46
SHC1 0.027 0.014 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.088 0.17 -10000 0 -0.3 60 60
RET51/GFRalpha1/GDNF/Dok5 0.084 0.18 -10000 0 -0.3 65 65
PRKCA 0.031 0.013 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
CREB1 0.041 0.12 -10000 0 -0.28 33 33
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.017 0.097 -10000 0 -0.25 41 41
RET51/GFRalpha1/GDNF/Grb7 0.096 0.16 -10000 0 -0.3 45 45
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.071 -10000 0 -10000 0 0
DOK4 0.03 0.012 -10000 0 -10000 0 0
JNK cascade -0.001 0.15 0.28 3 -0.42 21 24
RET9/GFRalpha1/GDNF/FRS2 0.048 0.15 -10000 0 -0.31 63 63
SHANK3 0.032 0.009 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.018 0.099 -10000 0 -0.25 41 41
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.052 0.13 0.26 6 -0.39 5 11
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.059 0.13 0.24 4 -0.39 8 12
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.046 0.11 0.24 5 -0.26 33 38
PI3K -0.042 0.26 0.3 7 -0.55 72 79
SOS1 0.034 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.056 0.14 -10000 0 -0.3 58 58
GRB10 0.029 0.051 -10000 0 -0.54 4 4
activation of MAPKK activity 0.055 0.12 0.26 6 -0.38 2 8
RET51/GFRalpha1/GDNF/FRS2 0.1 0.17 0.35 1 -0.3 61 62
GAB1 0.033 0.027 -10000 0 -0.54 1 1
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 118 118
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.045 0.11 0.24 5 -0.35 3 8
RET51/GFRalpha1/GDNF/PKC alpha 0.095 0.17 -10000 0 -0.3 57 57
GRB2 0.033 0.017 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GDNF 0.033 0.009 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.068 0.23 -10000 0 -0.38 87 87
Rac1/GTP -0.034 0.2 0.25 3 -0.42 72 75
RET9/GFRalpha1/GDNF 0.036 0.15 -10000 0 -0.34 62 62
GFRalpha1/GDNF 0.037 0.17 -10000 0 -0.4 62 62
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.013 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.13 0.17 -9999 0 -0.56 19 19
Syndecan-3/Neurocan 0.043 0.1 -9999 0 -0.47 16 16
POMC 0.035 0.031 -9999 0 -0.54 1 1
EGFR -0.27 0.29 -9999 0 -0.54 264 264
Syndecan-3/EGFR -0.12 0.18 -9999 0 -0.3 188 188
AGRP 0.03 0.015 -9999 0 -10000 0 0
NCSTN 0.028 0.014 -9999 0 -10000 0 0
PSENEN 0.035 0.015 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.032 0.027 -9999 0 -0.54 1 1
APH1A 0.031 0.027 -9999 0 -10000 0 0
NCAN 0.039 0.027 -9999 0 -10000 0 0
long-term memory 0.041 0.096 -9999 0 -0.45 13 13
Syndecan-3/IL8 0.048 0.11 -9999 0 -0.46 16 16
PSEN1 0.033 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.04 0.021 -9999 0 -10000 0 0
FYN 0.029 0.037 -9999 0 -0.54 2 2
limb bud formation -0.002 0.09 -9999 0 -0.48 16 16
MC4R 0.034 0.013 -9999 0 -10000 0 0
SRC 0.032 0.008 -9999 0 -10000 0 0
PTN -0.36 0.27 -9999 0 -0.54 348 348
FGFR/FGF/Syndecan-3 -0.002 0.09 -9999 0 -0.49 16 16
neuron projection morphogenesis -0.12 0.16 -9999 0 -0.55 19 19
Syndecan-3/AgRP 0.034 0.1 -9999 0 -0.47 16 16
Syndecan-3/AgRP/MC4R 0.05 0.1 -9999 0 -0.46 15 15
Fyn/Cortactin 0.038 0.03 -9999 0 -0.4 1 1
SDC3 -0.002 0.091 -9999 0 -0.49 16 16
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.048 0.11 -9999 0 -0.46 16 16
IL8 0.047 0.052 -9999 0 -0.54 1 1
Syndecan-3/Fyn/Cortactin 0.043 0.099 -9999 0 -0.46 13 13
Syndecan-3/CASK -0.003 0.087 -9999 0 -0.47 16 16
alpha-MSH/MC4R 0.049 0.027 -9999 0 -0.4 1 1
Gamma Secretase 0.074 0.054 -9999 0 -0.3 1 1
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.041 0.009 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response -0.011 0.22 0.73 21 -0.52 8 29
IL27/IL27R/JAK1 0.033 0.28 0.7 13 -1.1 17 30
TBX21 0.025 0.26 0.54 37 -0.59 37 74
IL12B 0.042 0.027 -10000 0 -10000 0 0
IL12A 0.005 0.062 0.15 3 -0.4 11 14
IL6ST 0.033 0.079 0.24 1 -0.54 8 9
IL27RA/JAK1 0.004 0.23 0.53 3 -1.2 17 20
IL27 -0.021 0.18 0.33 1 -0.54 52 53
TYK2 0.043 0.025 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.19 0.14 -10000 0 -0.78 2 2
T-helper 2 cell differentiation -0.011 0.22 0.73 21 -0.52 8 29
T cell proliferation during immune response -0.011 0.22 0.73 21 -0.52 8 29
MAPKKK cascade 0.011 0.22 0.52 8 -0.73 21 29
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT2 0.034 0.004 -10000 0 -10000 0 0
STAT1 0.06 0.056 0.22 2 -10000 0 2
IL12RB1 0.037 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.05 0.25 0.54 48 -0.63 22 70
IL27/IL27R/JAK2/TYK2 0.01 0.22 0.53 8 -0.76 20 28
positive regulation of T cell mediated cytotoxicity 0.011 0.22 0.52 8 -0.73 21 29
STAT1 (dimer) 0.039 0.32 0.79 24 -1 21 45
JAK2 0.039 0.022 0.23 1 -10000 0 1
JAK1 0.036 0.013 -10000 0 -10000 0 0
STAT2 (dimer) 0.025 0.21 0.5 6 -0.72 20 26
T cell proliferation -0.18 0.25 0.6 3 -0.59 75 78
IL12/IL12R/TYK2/JAK2 0.067 0.19 0.52 2 -0.76 14 16
IL17A -0.19 0.14 -10000 0 -0.78 2 2
mast cell activation -0.011 0.22 0.73 21 -0.52 8 29
IFNG 0.033 0.065 0.14 102 -0.1 11 113
T cell differentiation 0 0.009 0.019 28 -0.024 18 46
STAT3 (dimer) 0.024 0.2 0.51 5 -0.74 18 23
STAT5A (dimer) 0.023 0.21 0.54 4 -0.73 19 23
STAT4 (dimer) 0.021 0.21 0.5 6 -0.72 21 27
STAT4 0.027 0.069 -10000 0 -0.54 7 7
T cell activation -0.005 0.027 0.12 16 -0.12 9 25
IL27R/JAK2/TYK2 0.053 0.24 0.59 2 -1.1 17 19
GATA3 -0.017 0.38 0.61 22 -1.3 34 56
IL18 0.019 0.036 0.14 41 -10000 0 41
positive regulation of mast cell cytokine production 0.024 0.2 0.5 5 -0.7 19 24
IL27/EBI3 0.014 0.14 0.34 3 -0.39 51 54
IL27RA -0.014 0.24 0.54 4 -1.3 17 21
IL6 -0.37 0.26 -10000 0 -0.54 361 361
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
monocyte differentiation 0.002 0.003 -10000 0 -10000 0 0
IL2 -0.009 0.11 0.48 8 -1.2 1 9
IL1B 0.009 0.04 0.14 10 -0.4 4 14
EBI3 0.041 0.026 0.22 2 -10000 0 2
TNF 0.013 0.02 0.14 4 -10000 0 4
TCGA08_rtk_signaling

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
PDGFRA -0.036 0.19 -10000 0 -0.54 61 61
HRAS 0.034 0.013 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 264 264
AKT -0.018 0.12 0.36 5 -0.25 51 56
FOXO3 0.031 0.01 -10000 0 -10000 0 0
AKT1 0.035 0.016 -10000 0 -10000 0 0
FOXO1 -0.023 0.17 -10000 0 -0.54 47 47
AKT3 0.028 0.019 -10000 0 -10000 0 0
FOXO4 0.034 0.002 -10000 0 -10000 0 0
MET -0.023 0.17 -10000 0 -0.54 50 50
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
PIK3CB 0.033 0.006 -10000 0 -10000 0 0
NRAS 0.035 0.016 -10000 0 -10000 0 0
PIK3CG 0.037 0.021 -10000 0 -10000 0 0
PIK3R3 0.042 0.034 -10000 0 -10000 0 0
PIK3R2 0.035 0.016 -10000 0 -10000 0 0
NF1 0.032 0.009 -10000 0 -10000 0 0
RAS -0.076 0.14 0.23 1 -0.33 85 86
ERBB2 0.028 0.029 -10000 0 -0.54 1 1
proliferation/survival/translation -0.016 0.096 0.3 24 -0.28 2 26
PI3K -0.068 0.16 0.32 9 -0.32 97 106
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
KRAS 0.034 0.017 -10000 0 -10000 0 0
FOXO 0.034 0.081 0.29 10 -0.17 10 20
AKT2 0.033 0.006 -10000 0 -10000 0 0
PTEN 0.025 0.068 -10000 0 -0.54 7 7
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.016 0.18 -10000 0 -0.75 3 3
PCK1 -0.75 0.54 -10000 0 -1 384 384
HNF4A 0.031 0.2 0.71 2 -0.74 3 5
KCNJ11 0.036 0.24 0.74 3 -0.75 3 6
AKT1 0.01 0.15 -10000 0 -0.46 5 5
response to starvation 0.005 0.002 -10000 0 -10000 0 0
DLK1 0.026 0.22 0.87 1 -0.81 3 4
NKX2-1 0.033 0.12 0.64 1 -10000 0 1
ACADM 0.013 0.21 -10000 0 -0.86 8 8
TAT -0.055 0.19 -10000 0 -0.72 13 13
CEBPB 0.034 0.028 -10000 0 -0.54 1 1
CEBPA 0.035 0.045 -10000 0 -0.54 3 3
TTR -0.036 0.26 0.58 1 -0.62 53 54
PKLR 0.033 0.19 -10000 0 -0.79 2 2
APOA1 0.02 0.22 -10000 0 -0.88 3 3
CPT1C 0.026 0.2 0.71 1 -0.75 3 4
ALAS1 0.029 0.14 -10000 0 -10000 0 0
TFRC -0.018 0.2 0.67 3 -0.52 2 5
FOXF1 0.025 0.021 -10000 0 -10000 0 0
NF1 0.037 0.01 -10000 0 -10000 0 0
HNF1A (dimer) 0.051 0.022 -10000 0 -10000 0 0
CPT1A 0.023 0.21 0.69 4 -0.7 3 7
HMGCS1 0.021 0.2 0.74 2 -0.75 3 5
NR3C1 0.001 0.16 -10000 0 -0.52 41 41
CPT1B 0.015 0.19 -10000 0 -0.75 3 3
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.016 -10000 0 -10000 0 0
GCK 0.021 0.19 -10000 0 -0.75 3 3
CREB1 -0.18 0.14 -10000 0 -0.27 331 331
IGFBP1 0.015 0.14 -10000 0 -0.66 4 4
PDX1 0.041 0.16 -10000 0 -1.1 2 2
UCP2 0.024 0.2 0.65 2 -0.7 3 5
ALDOB 0.021 0.22 -10000 0 -0.81 3 3
AFP -0.053 0.14 0.39 1 -0.37 39 40
BDH1 0.023 0.19 0.67 2 -0.75 3 5
HADH 0.016 0.23 -10000 0 -0.93 5 5
F2 0.036 0.22 -10000 0 -0.82 3 3
HNF1A 0.051 0.022 -10000 0 -10000 0 0
G6PC -0.098 0.12 -10000 0 -0.46 3 3
SLC2A2 0.046 0.16 -10000 0 -0.84 2 2
INS 0.022 0.015 0.25 1 -10000 0 1
FOXA1 -0.006 0.23 0.38 3 -0.53 74 77
FOXA3 -0.11 0.14 0.3 1 -0.26 123 124
FOXA2 0.028 0.27 -10000 0 -0.92 3 3
ABCC8 -0.07 0.43 0.9 1 -0.93 87 88
ALB -0.056 0.15 0.39 1 -0.39 47 48
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.09 0.16 0.33 72 -0.4 11 83
FYN 0.062 0.16 0.41 25 -0.41 17 42
LAT/GRAP2/SLP76 0.071 0.16 0.43 26 -0.41 11 37
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 0.059 0.16 0.37 46 -0.31 27 73
B2M 0.036 0.011 -10000 0 -10000 0 0
IKBKG 0.034 0.07 0.19 49 -10000 0 49
MAP3K8 -0.039 0.19 -10000 0 -0.54 64 64
mol:Ca2+ -0.011 0.017 -10000 0 -0.089 12 12
integrin-mediated signaling pathway 0.037 0.022 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.053 0.18 0.49 22 -0.42 27 49
TRPV6 0.013 0.22 1.3 10 -0.54 17 27
CD28 0.027 0.085 -10000 0 -0.54 10 10
SHC1 0.073 0.18 0.34 79 -0.41 21 100
receptor internalization 0.025 0.18 0.35 26 -0.4 62 88
PRF1 0.038 0.16 0.54 9 -0.85 5 14
KRAS 0.034 0.017 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
COT/AKT1 0.036 0.16 0.34 42 -0.31 34 76
LAT 0.055 0.17 0.4 30 -0.44 16 46
EntrezGene:6955 0.002 0.004 -10000 0 -10000 0 0
CD3D 0.04 0.036 -10000 0 -10000 0 0
CD3E 0.034 0.016 -10000 0 -10000 0 0
CD3G 0.038 0.073 0.2 1 -0.54 5 6
RASGRP2 0.009 0.048 0.17 9 -0.16 27 36
RASGRP1 0.065 0.16 0.43 31 -0.33 15 46
HLA-A 0.041 0.025 -10000 0 -10000 0 0
RASSF5 0.029 0.022 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.037 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.067 0.097 0.22 88 -0.13 1 89
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.009 0.047 -10000 0 -0.17 19 19
PRKCA 0.042 0.1 0.3 29 -0.22 5 34
GRAP2 0.034 0.018 -10000 0 -10000 0 0
mol:IP3 0.003 0.09 0.29 10 -0.33 10 20
EntrezGene:6957 0.003 0.006 0.044 1 -10000 0 1
TCR/CD3/MHC I/CD8 0.025 0.13 0.31 22 -0.31 45 67
ORAI1 -0.02 0.17 -10000 0 -1.1 10 10
CSK 0.047 0.16 0.4 19 -0.44 15 34
B7 family/CD28 0.082 0.17 0.47 23 -0.44 13 36
CHUK 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.042 0.17 0.4 22 -0.4 33 55
PTPN6 0.045 0.15 0.37 25 -0.42 17 42
VAV1 0.044 0.16 0.44 19 -0.44 17 36
Monovalent TCR/CD3 0.023 0.1 0.28 21 -0.36 21 42
CBL 0.03 0.011 -10000 0 -10000 0 0
LCK 0.063 0.16 0.39 30 -0.41 14 44
PAG1 0.062 0.16 0.39 29 -0.46 13 42
RAP1A 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.041 0.17 0.36 27 -0.42 24 51
CD80 0.044 0.037 0.19 1 -10000 0 1
CD86 0.036 0.012 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 0.01 0.066 -10000 0 -0.21 16 16
HRAS 0.034 0.013 -10000 0 -10000 0 0
GO:0035030 0.042 0.14 0.38 27 -0.38 13 40
CD8A 0.003 0.006 0.044 3 -10000 0 3
CD8B 0.041 0.025 0.19 11 -10000 0 11
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDK1/PKC theta 0.071 0.18 0.42 55 -0.37 22 77
CSK/PAG1 0.065 0.16 0.39 28 -0.46 11 39
SOS1 0.034 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.056 0.024 -10000 0 -10000 0 0
GRAP2/SLP76 0.066 0.17 0.46 19 -0.42 16 35
STIM1 0.004 0.1 1.2 3 -10000 0 3
RAS family/GTP 0.076 0.11 0.28 53 -0.19 7 60
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.023 0.19 0.35 26 -0.41 62 88
mol:DAG -0.015 0.067 0.13 2 -0.28 12 14
RAP1A/GDP 0.035 0.048 0.13 56 -10000 0 56
PLCG1 0.032 0.008 -10000 0 -10000 0 0
CD247 0.022 0.11 -10000 0 -0.55 15 15
cytotoxic T cell degranulation 0.038 0.16 0.53 10 -0.75 6 16
RAP1A/GTP 0.002 0.016 -10000 0 -0.059 27 27
mol:PI-3-4-5-P3 0.055 0.17 0.46 24 -0.36 26 50
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.025 0.12 0.33 9 -0.41 10 19
NRAS 0.035 0.016 -10000 0 -10000 0 0
ZAP70 0.038 0.024 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.046 0.13 0.3 12 -0.4 11 23
MALT1 0.033 0.009 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
CD8 heterodimer 0.033 0.022 0.16 9 -10000 0 9
CARD11 0.038 0.026 -10000 0 -10000 0 0
PRKCB -0.012 0.05 0.15 5 -0.2 12 17
PRKCE 0.046 0.11 0.32 29 -0.22 8 37
PRKCQ 0.06 0.18 0.47 28 -0.4 23 51
LCP2 0.036 0.023 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.06 0.15 0.34 53 -0.27 27 80
IKK complex 0.056 0.092 0.23 71 -10000 0 71
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 0.029 0.13 0.3 43 -0.26 27 70
PDPK1 0.064 0.16 0.39 51 -0.3 24 75
TCR/CD3/MHC I/CD8/Fyn 0.015 0.17 0.38 16 -0.48 25 41
Regulation of nuclear SMAD2/3 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
EP300 0.035 0.016 -10000 0 -10000 0 0
HSPA8 0.029 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.075 0.19 0.33 1 -0.39 111 112
AKT1 0.038 0.02 -10000 0 -10000 0 0
GSC -0.096 0.4 -10000 0 -1.3 46 46
NKX2-5 0.045 0.049 -10000 0 -10000 0 0
muscle cell differentiation 0.001 0.13 0.46 18 -10000 0 18
SMAD2-3/SMAD4/SP1 0.053 0.12 -10000 0 -0.31 13 13
SMAD4 -0.028 0.084 -10000 0 -0.26 28 28
CBFB 0.03 0.014 -10000 0 -10000 0 0
SAP18 0.031 0.009 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.16 0.2 -10000 0 -0.34 273 273
SMAD3/SMAD4/VDR 0.052 0.095 -10000 0 -0.35 6 6
MYC -0.007 0.12 -10000 0 -0.55 25 25
CDKN2B -0.049 0.2 -10000 0 -0.8 16 16
AP1 -0.26 0.29 -10000 0 -0.62 139 139
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.1 -10000 0 -0.39 19 19
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.009 0.11 0.25 1 -0.35 24 25
SP3 0.035 0.008 -10000 0 -10000 0 0
CREB1 0.033 0.006 -10000 0 -10000 0 0
FOXH1 0.018 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.045 0.14 -10000 0 -0.38 53 53
GATA3 0.034 0.16 -10000 0 -0.53 34 34
SKI/SIN3/HDAC complex/NCoR1 0.017 0.084 -10000 0 -0.38 15 15
MEF2C/TIF2 0.007 0.15 -10000 0 -0.54 25 25
endothelial cell migration -0.058 0.11 0.57 7 -10000 0 7
MAX 0.025 0.024 -10000 0 -10000 0 0
RBBP7 0.037 0.021 -10000 0 -10000 0 0
RBBP4 0.033 0.006 -10000 0 -10000 0 0
RUNX2 0.035 0.018 -10000 0 -10000 0 0
RUNX3 -0.005 0.15 -10000 0 -0.54 35 35
RUNX1 0.017 0.099 -10000 0 -0.54 15 15
CTBP1 0.033 0.008 -10000 0 -10000 0 0
NR3C1 -0.019 0.15 -10000 0 -0.55 39 39
VDR 0.032 0.037 -10000 0 -0.54 2 2
CDKN1A 0.005 0.11 -10000 0 -1.1 3 3
KAT2B 0.001 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.025 0.11 -10000 0 -0.32 32 32
DCP1A 0.033 0.008 -10000 0 -10000 0 0
SKI 0.033 0.007 -10000 0 -10000 0 0
SERPINE1 0.058 0.11 -10000 0 -0.57 7 7
SMAD3/SMAD4/ATF2 0.004 0.092 -10000 0 -0.27 14 14
SMAD3/SMAD4/ATF3 -0.09 0.2 -10000 0 -0.41 130 130
SAP30 0.033 0.009 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.063 0.04 -10000 0 -10000 0 0
JUN -0.26 0.28 -10000 0 -0.63 133 133
SMAD3/SMAD4/IRF7 0.021 0.094 -10000 0 -0.29 9 9
TFE3 0.03 0.045 -10000 0 -0.19 4 4
COL1A2 0.075 0.13 0.39 10 -0.71 5 15
mesenchymal cell differentiation -0.004 0.092 0.27 14 -10000 0 14
DLX1 0.043 0.035 -10000 0 -10000 0 0
TCF3 0.035 0.017 -10000 0 -10000 0 0
FOS -0.37 0.28 -10000 0 -0.56 342 342
SMAD3/SMAD4/Max -0.018 0.089 -10000 0 -0.28 11 11
Cbp/p300/SNIP1 0.061 0.032 -10000 0 -0.32 1 1
ZBTB17 0.027 0.021 -10000 0 -10000 0 0
LAMC1 -0.037 0.14 -10000 0 -0.59 27 27
TGIF2/HDAC complex/SMAD3/SMAD4 0.005 0.091 -10000 0 -0.28 10 10
IRF7 0.039 0.023 -10000 0 -10000 0 0
ESR1 -0.07 0.25 0.22 3 -0.55 106 109
HNF4A 0.032 0.008 -10000 0 -10000 0 0
MEF2C 0.014 0.17 0.44 7 -0.55 28 35
SMAD2-3/SMAD4 0.008 0.11 -10000 0 -0.29 25 25
Cbp/p300/Src-1 0.062 0.039 -10000 0 -0.32 2 2
IGHV3OR16-13 -0.007 0.071 -10000 0 -0.45 10 10
TGIF2/HDAC complex 0.033 0.01 -10000 0 -10000 0 0
CREBBP 0.032 0.028 -10000 0 -0.52 1 1
SKIL 0.044 0.04 -10000 0 -10000 0 0
HDAC1 0.033 0.005 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
SNIP1 0.033 0.006 -10000 0 -10000 0 0
GCN5L2 0.003 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.018 0.13 -10000 0 -0.38 30 30
MSG1/HSC70 -0.21 0.22 -10000 0 -0.4 294 294
SMAD2 0.019 0.053 -10000 0 -0.18 5 5
SMAD3 -0.015 0.063 -10000 0 -0.21 6 6
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.069 -10000 0 -0.29 8 8
SMAD2/SMAD2/SMAD4 0.01 0.053 0.22 6 -0.22 5 11
NCOR1 0.031 0.011 -10000 0 -10000 0 0
NCOA2 0.028 0.014 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
MYOD/E2A 0.048 0.035 -10000 0 -0.4 2 2
SMAD2-3/SMAD4/SP1/MIZ-1 0.074 0.12 -10000 0 -0.32 8 8
IFNB1 -0.012 0.071 0.33 1 -0.3 1 2
SMAD3/SMAD4/MEF2C 0.021 0.18 0.41 1 -0.56 29 30
CITED1 -0.3 0.29 -10000 0 -0.54 293 293
SMAD2-3/SMAD4/ARC105 0.024 0.11 -10000 0 -0.29 15 15
RBL1 0.04 0.031 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.002 0.11 -10000 0 -0.4 18 18
RUNX1-3/PEBPB2 0.021 0.12 -10000 0 -0.35 48 48
SMAD7 -0.18 0.22 -10000 0 -0.51 95 95
MYC/MIZ-1 0.008 0.098 -10000 0 -0.41 25 25
SMAD3/SMAD4 0.032 0.097 0.32 12 -0.38 3 15
IL10 -0.007 0.12 0.36 2 -0.37 30 32
PIASy/HDAC complex 0.026 0.028 -10000 0 -10000 0 0
PIAS3 0.034 0.009 -10000 0 -10000 0 0
CDK2 0.04 0.023 0.21 2 -10000 0 2
IL5 -0.004 0.12 0.4 1 -0.36 33 34
CDK4 0.036 0.011 -10000 0 -10000 0 0
PIAS4 0.026 0.028 -10000 0 -10000 0 0
ATF3 -0.12 0.25 -10000 0 -0.54 126 126
SMAD3/SMAD4/SP1 0.039 0.1 -10000 0 -0.3 11 11
FOXG1 0.042 0.036 -10000 0 -10000 0 0
FOXO3 0.021 0.02 -10000 0 -10000 0 0
FOXO1 -0.018 0.12 -10000 0 -0.39 47 47
FOXO4 0.022 0.019 -10000 0 -10000 0 0
heart looping 0.014 0.17 0.44 7 -0.55 28 35
CEBPB 0.031 0.029 -10000 0 -0.54 1 1
SMAD3/SMAD4/DLX1 0.012 0.093 -10000 0 -0.27 11 11
MYOD1 0.033 0.041 -10000 0 -0.54 2 2
SMAD3/SMAD4/HNF4 0.005 0.091 -10000 0 -0.26 15 15
SMAD3/SMAD4/GATA3 0.024 0.15 -10000 0 -0.4 35 35
SnoN/SIN3/HDAC complex/NCoR1 0.044 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.006 0.15 -10000 0 -0.36 49 49
SMAD3/SMAD4/SP1-3 0.061 0.11 -10000 0 -0.34 4 4
MED15 0.032 0.008 -10000 0 -10000 0 0
SP1 0.047 0.024 -10000 0 -10000 0 0
SIN3B 0.034 0.014 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.045 0.12 -10000 0 -0.36 26 26
ITGB5 -0.003 0.084 -10000 0 -0.53 2 2
TGIF/SIN3/HDAC complex/CtBP 0.024 0.07 -10000 0 -0.33 12 12
SMAD3/SMAD4/AR -0.045 0.16 -10000 0 -0.38 77 77
AR -0.04 0.2 -10000 0 -0.54 66 66
negative regulation of cell growth -0.023 0.12 -10000 0 -0.35 30 30
SMAD3/SMAD4/MYOD 0.004 0.095 -10000 0 -0.28 17 17
E2F5 0.035 0.035 -10000 0 -10000 0 0
E2F4 0.029 0.012 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.05 0.11 -10000 0 -0.35 11 11
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.11 -10000 0 -0.35 24 24
TFDP1 0.033 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.25 0.3 -10000 0 -0.64 134 134
SMAD3/SMAD4/RUNX2 0.005 0.093 -10000 0 -0.27 14 14
TGIF2 0.033 0.01 -10000 0 -10000 0 0
TGIF1 0.031 0.027 -10000 0 -0.54 1 1
ATF2 0.034 0.005 -10000 0 -10000 0 0
amb2 Integrin signaling

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.021 0.077 -10000 0 -0.28 5 5
alphaM/beta2 Integrin/GPIbA -0.016 0.078 0.26 3 -10000 0 3
alphaM/beta2 Integrin/proMMP-9 0.041 0.097 0.26 15 -10000 0 15
PLAUR 0.067 0.06 -10000 0 -10000 0 0
HMGB1 -0.029 0.045 -10000 0 -0.23 2 2
alphaM/beta2 Integrin/Talin -0.019 0.072 -10000 0 -10000 0 0
AGER -0.035 0.051 -10000 0 -0.59 1 1
RAP1A 0.034 0.005 -10000 0 -10000 0 0
SELPLG 0.034 0.028 -10000 0 -0.54 1 1
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.1 0.14 -10000 0 -0.38 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.092 0.072 -10000 0 -10000 0 0
CYR61 -0.13 0.26 -10000 0 -0.54 143 143
TLN1 0.033 0.006 -10000 0 -10000 0 0
Rap1/GTP 0.061 0.086 -10000 0 -0.34 8 8
RHOA 0.033 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.24 -10000 0 -0.54 118 118
MYH2 0.064 0.093 0.32 3 -0.45 5 8
MST1R 0.042 0.037 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.012 0.067 -10000 0 -10000 0 0
APOB 0.034 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.028 0.039 -10000 0 -0.54 2 2
JAM3 -0.009 0.14 -10000 0 -0.54 34 34
GP1BA 0.036 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.032 0.099 -10000 0 -0.37 20 20
alphaM/beta2 Integrin 0.049 0.082 0.24 3 -0.35 9 12
JAM3 homodimer -0.009 0.14 -10000 0 -0.54 34 34
ICAM2 0.02 0.077 -10000 0 -0.54 9 9
ICAM1 0.039 0.028 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor 0.046 0.086 0.24 3 -0.34 11 14
cell adhesion -0.016 0.078 0.26 3 -10000 0 3
NFKB1 -0.22 0.19 0.4 1 -0.36 297 298
THY1 0.034 0.025 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
Lipoprotein(a) 0.043 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.063 0.13 -10000 0 -0.33 75 75
IL6 -0.52 0.36 0.38 1 -0.74 369 370
ITGB2 -0.022 0.062 0.2 2 -10000 0 2
elevation of cytosolic calcium ion concentration 0.032 0.11 0.3 9 -10000 0 9
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.2 -10000 0 -0.42 123 123
JAM2 -0.12 0.25 -10000 0 -0.54 133 133
alphaM/beta2 Integrin/ICAM1 0.009 0.092 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA/Plg 0.011 0.09 -10000 0 -0.36 1 1
RhoA/GTP 0.044 0.1 -10000 0 -0.39 14 14
positive regulation of phagocytosis 0.037 0.083 0.28 3 -0.31 5 8
Ron/MSP 0.055 0.028 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.034 0.11 0.31 9 -10000 0 9
alphaM/beta2 Integrin/uPAR 0.01 0.095 0.26 12 -10000 0 12
PLAU 0.056 0.052 -10000 0 -10000 0 0
PLAT -0.068 0.21 -10000 0 -0.54 85 85
actin filament polymerization 0.064 0.097 0.31 8 -0.41 6 14
MST1 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.01 0.071 -10000 0 -10000 0 0
TNF -0.21 0.18 0.41 3 -0.6 6 9
RAP1B 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.003 0.085 -10000 0 -10000 0 0
fibrinolysis 0.009 0.088 -10000 0 -0.36 1 1
HCK 0.036 0.022 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation 0.046 0.086 0.24 3 -0.34 11 14
VTN 0.032 0.011 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.11 0.18 -10000 0 -0.37 138 138
LPA 0.032 0.009 -10000 0 -10000 0 0
LRP1 0.034 0.004 -10000 0 -10000 0 0
cell migration 0.029 0.091 0.27 2 -0.36 2 4
FN1 0.13 0.066 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.016 0.075 0.25 1 -10000 0 1
MPO 0.031 0.016 -10000 0 -10000 0 0
KNG1 0.033 0.007 -10000 0 -10000 0 0
RAP1/GDP 0.044 0.011 -10000 0 -10000 0 0
ROCK1 0.063 0.11 0.28 7 -0.39 12 19
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.031 0.027 -10000 0 -0.54 1 1
CTGF 0.011 0.11 -10000 0 -0.54 19 19
alphaM/beta2 Integrin/Hck -0.017 0.076 0.27 5 -10000 0 5
ITGAM -0.028 0.043 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.074 0.16 -10000 0 -0.36 100 100
HP 0.029 0.012 -10000 0 -10000 0 0
leukocyte adhesion -0.17 0.2 -10000 0 -0.47 121 121
SELP -0.11 0.24 -10000 0 -0.54 118 118
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.033 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.047 0.13 0.24 4 -0.3 93 97
FRAP1 -0.013 0.1 0.34 1 -0.48 17 18
AKT1 -0.04 0.12 0.25 5 -0.28 69 74
INSR 0.034 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.044 0.011 -10000 0 -10000 0 0
mol:GTP -0.003 0.11 0.27 3 -0.27 34 37
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.056 -10000 0 -0.22 8 8
TSC2 0.031 0.01 -10000 0 -10000 0 0
RHEB/GDP -0.012 0.092 -10000 0 -0.25 35 35
TSC1 0.034 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.019 0.13 -10000 0 -0.33 71 71
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.005 0.07 -10000 0 -0.25 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.033 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.008 0.1 0.3 4 -0.35 15 19
MAP3K5 -0.018 0.096 0.2 5 -0.29 49 54
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
apoptosis -0.018 0.096 0.2 5 -0.29 49 54
mol:LY294002 0 0.001 0.001 2 -0.002 61 63
EIF4B -0.008 0.094 0.28 4 -0.31 14 18
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.016 0.096 -10000 0 -0.29 12 12
eIF4E/eIF4G1/eIF4A1 -0.002 0.067 -10000 0 -0.29 17 17
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.025 0.15 -10000 0 -0.31 102 102
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.076 0.24 13 -0.2 11 24
FKBP1A 0.033 0.012 -10000 0 -10000 0 0
RHEB/GTP 0.005 0.1 0.25 3 -0.25 30 33
mol:Amino Acids 0 0.001 0.001 2 -0.002 61 63
FKBP12/Rapamycin 0.025 0.009 -10000 0 -10000 0 0
PDPK1 -0.051 0.12 0.22 7 -0.29 88 95
EIF4E 0.034 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.038 0.2 -10000 0 -0.57 59 59
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.049 -10000 0 -0.26 1 1
TSC1/TSC2 -0.002 0.12 0.29 3 -0.29 34 37
tumor necrosis factor receptor activity 0 0.001 0.002 61 -0.001 2 63
RPS6 0.032 0.027 -10000 0 -0.54 1 1
PPP5C 0.036 0.016 -10000 0 -10000 0 0
EIF4G1 0.033 0.006 -10000 0 -10000 0 0
IRS1 -0.041 0.13 -10000 0 -0.35 72 72
INS 0.033 0.007 -10000 0 -10000 0 0
PTEN 0.025 0.067 -10000 0 -0.54 7 7
PDK2 -0.045 0.12 0.24 5 -0.29 72 77
EIF4EBP1 -0.034 0.25 -10000 0 -1 29 29
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PPP2R5D -0.011 0.098 0.35 3 -0.43 17 20
peptide biosynthetic process 0.019 0.016 -10000 0 -10000 0 0
RHEB 0.034 0.008 -10000 0 -10000 0 0
EIF4A1 0.03 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.005 15 -0.003 5 20
EEF2 0.02 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.017 0.24 -10000 0 -0.97 29 29
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.038 0.11 1 1 -10000 0 1
VDR 0.032 0.037 -10000 0 -0.54 2 2
FAM120B 0.032 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.062 0.077 0.29 14 -10000 0 14
RXRs/LXRs/DNA/Oxysterols 0.089 0.089 -10000 0 -0.37 2 2
MED1 0.029 0.012 -10000 0 -10000 0 0
mol:9cRA 0.01 0.014 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.031 0.13 -10000 0 -0.63 8 8
RXRs/NUR77 0.07 0.092 -10000 0 -0.3 17 17
RXRs/PPAR -0.15 0.14 -10000 0 -0.26 259 259
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RARs/VDR/DNA/Vit D3 0.016 0.13 -10000 0 -0.3 72 72
RARA 0.031 0.012 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
VDR/VDR/DNA 0.032 0.037 -10000 0 -0.54 2 2
RARs/RARs/DNA/9cRA 0.007 0.12 -10000 0 -0.29 72 72
RARG 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 0.061 0.17 0.56 50 -10000 0 50
RARs/THRs/DNA/SMRT -0.03 0.13 -10000 0 -0.52 10 10
THRA -0.002 0.13 -10000 0 -0.54 28 28
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.075 0.069 -10000 0 -0.3 4 4
NR1H4 0.035 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.1 0.088 -10000 0 -0.28 5 5
NR1H2 0.043 0.015 -10000 0 -10000 0 0
NR1H3 0.043 0.031 -10000 0 -0.54 1 1
RXRs/VDR/DNA/Vit D3 0.077 0.062 -10000 0 -0.29 4 4
NR4A1 0.008 0.12 -10000 0 -0.54 23 23
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.057 0.057 -10000 0 -10000 0 0
RXRG 0.031 0.056 -10000 0 -0.54 4 4
RXR alpha/CCPG 0.052 0.02 -10000 0 -10000 0 0
RXRA 0.042 0.015 -10000 0 -10000 0 0
RXRB 0.044 0.016 -10000 0 -10000 0 0
THRB 0.028 0.057 -10000 0 -0.54 5 5
PPARG -0.38 0.26 -10000 0 -0.54 365 365
PPARD 0.034 0.01 -10000 0 -10000 0 0
TNF 0.082 0.089 -10000 0 -10000 0 0
mol:Oxysterols 0.009 0.013 -10000 0 -10000 0 0
cholesterol transport 0.089 0.089 -10000 0 -0.37 2 2
PPARA 0.031 0.027 -10000 0 -0.54 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.054 0.21 -10000 0 -0.54 77 77
RXRs/NUR77/BCL2 -0.028 0.12 -10000 0 -0.26 83 83
SREBF1 0.083 0.1 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.075 0.07 -10000 0 -0.3 4 4
ABCA1 0.077 0.11 -10000 0 -1 2 2
RARs/THRs 0.006 0.16 -10000 0 -0.32 95 95
RXRs/FXR 0.084 0.065 -10000 0 -0.31 4 4
BCL2 -0.074 0.22 -10000 0 -0.54 94 94
HIF-2-alpha transcription factor network

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
MMP14 0.036 0.1 0.48 1 -0.67 4 5
oxygen homeostasis 0.025 0.03 0.18 4 -10000 0 4
TCEB2 0.031 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.13 0.14 0.44 21 -0.32 5 26
EPO 0.22 0.25 0.68 57 -0.46 3 60
FIH (dimer) 0.056 0.031 0.26 1 -10000 0 1
APEX1 0.057 0.038 0.24 2 -10000 0 2
SERPINE1 0.26 0.24 0.71 45 -0.5 4 49
FLT1 -0.014 0.17 -10000 0 -0.69 18 18
ADORA2A 0.26 0.25 0.66 73 -0.48 4 77
germ cell development 0.25 0.23 0.69 38 -0.49 3 41
SLC11A2 0.26 0.24 0.7 41 -0.5 4 45
BHLHE40 0.18 0.23 0.67 37 -0.46 6 43
HIF1AN 0.056 0.031 0.26 1 -10000 0 1
HIF2A/ARNT/SIRT1 0.17 0.19 0.54 42 -0.36 5 47
ETS1 0.041 0.034 -10000 0 -0.54 1 1
CITED2 0.007 0.14 -10000 0 -0.79 12 12
KDR -0.004 0.15 -10000 0 -0.64 17 17
PGK1 0.26 0.24 0.7 44 -0.49 4 48
SIRT1 0.036 0.008 -10000 0 -10000 0 0
response to hypoxia 0.002 0.006 -10000 0 -10000 0 0
HIF2A/ARNT 0.23 0.26 0.77 23 -0.56 4 27
EPAS1 0.16 0.18 0.47 64 -0.32 10 74
SP1 0.047 0.029 -10000 0 -10000 0 0
ABCG2 0.24 0.26 0.69 39 -0.62 10 49
EFNA1 0.18 0.22 0.65 20 -0.5 4 24
FXN 0.25 0.24 0.65 56 -0.48 3 59
POU5F1 0.25 0.24 0.69 38 -0.51 3 41
neuron apoptosis -0.22 0.26 0.55 4 -0.74 26 30
EP300 0.032 0.008 -10000 0 -10000 0 0
EGLN3 0.081 0.068 0.22 55 -10000 0 55
EGLN2 0.059 0.035 0.22 3 -10000 0 3
EGLN1 0.045 0.034 0.26 1 -10000 0 1
VHL/Elongin B/Elongin C 0.053 0.033 -10000 0 -10000 0 0
VHL 0.035 0.018 0.18 7 -10000 0 7
ARNT 0.044 0.038 0.21 1 -10000 0 1
SLC2A1 0.25 0.24 0.64 69 -0.48 4 73
TWIST1 0.21 0.29 0.64 54 -0.54 32 86
ELK1 0.04 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.14 0.18 0.54 21 -0.36 5 26
VEGFA 0.26 0.25 0.72 45 -0.5 4 49
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.12 0.11 0.28 7 -0.63 4 11
Syndecan-4/Syndesmos 0.13 0.12 0.4 3 -0.72 4 7
positive regulation of JNK cascade 0.063 0.18 0.41 1 -0.7 5 6
Syndecan-4/ADAM12 0.15 0.13 0.42 4 -0.76 4 8
CCL5 0.028 0.06 -10000 0 -0.54 5 5
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DNM2 0.034 0.005 -10000 0 -10000 0 0
ITGA5 0.034 0.007 -10000 0 -10000 0 0
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
PLG 0.013 0.04 -10000 0 -0.54 1 1
ADAM12 0.056 0.06 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.032 0.012 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha 0.008 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.13 0.12 0.42 1 -0.72 4 5
Syndecan-4/CXCL12/CXCR4 0.066 0.19 0.42 1 -0.76 5 6
Syndecan-4/Laminin alpha3 0.055 0.16 0.41 2 -0.83 4 6
MDK 0.043 0.036 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.063 0.17 0.4 1 -0.76 4 5
Syndecan-4/Midkine 0.14 0.12 0.41 2 -0.7 4 6
FZD7 -0.13 0.26 -10000 0 -0.54 141 141
Syndecan-4/FGFR1/FGF -0.066 0.16 -10000 0 -0.61 8 8
THBS1 0.037 0.025 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.14 0.12 0.41 2 -0.72 4 6
positive regulation of MAPKKK cascade 0.063 0.18 0.41 1 -0.7 5 6
Syndecan-4/TACI 0.13 0.12 0.41 2 -0.76 4 6
CXCR4 0.044 0.037 -10000 0 -10000 0 0
cell adhesion 0.09 0.071 0.26 50 -10000 0 50
Syndecan-4/Dynamin 0.14 0.12 0.42 1 -0.76 4 5
Syndecan-4/TSP1 0.14 0.12 0.46 2 -0.76 4 6
Syndecan-4/GIPC 0.14 0.12 0.42 3 -0.76 4 7
Syndecan-4/RANTES 0.13 0.12 0.4 1 -0.76 4 5
ITGB1 0.033 0.006 -10000 0 -10000 0 0
LAMA1 0.033 0.01 -10000 0 -10000 0 0
LAMA3 -0.15 0.27 -10000 0 -0.54 158 158
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.028 0.22 0.71 47 -10000 0 47
Syndecan-4/alpha-Actinin 0.14 0.12 0.42 1 -0.76 4 5
TFPI -0.19 0.28 -10000 0 -0.54 196 196
F2 0.039 0.02 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.044 0.15 0.41 1 -0.76 4 5
ACTN1 0.033 0.007 -10000 0 -10000 0 0
TNC 0.037 0.036 -10000 0 -0.54 1 1
Syndecan-4/CXCL12 0.056 0.18 0.42 1 -0.8 5 6
FGF6 0.03 0.037 -10000 0 -0.54 2 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
CXCL12 -0.14 0.26 -10000 0 -0.54 148 148
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 375 375
FGFR1 0.018 0.077 -10000 0 -0.54 9 9
Syndecan-4/PI-4-5-P2 0.095 0.11 -10000 0 -0.76 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.074 0.18 295 -10000 0 295
cell migration -0.012 0.008 -10000 0 -10000 0 0
PRKCD 0.016 0.035 -10000 0 -10000 0 0
vasculogenesis 0.14 0.12 0.45 2 -0.72 4 6
SDC4 0.11 0.12 -10000 0 -0.81 4 4
Syndecan-4/Tenascin C 0.14 0.12 0.41 2 -0.76 4 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.12 0.12 0.4 1 -0.76 4 5
MMP9 0.092 0.077 -10000 0 -10000 0 0
Rac1/GTP 0.091 0.071 0.27 50 -10000 0 50
cytoskeleton organization 0.13 0.12 0.4 3 -0.69 4 7
GIPC1 0.034 0.01 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.036 0.19 0.42 1 -0.87 4 5
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.011 0.095 0.35 8 -0.31 8 16
TBX21 -0.13 0.37 0.71 6 -1.2 40 46
B2M 0.038 0.013 -10000 0 -10000 0 0
TYK2 0.017 0.036 -10000 0 -10000 0 0
IL12RB1 0.018 0.036 -10000 0 -10000 0 0
GADD45B -0.07 0.28 0.7 2 -0.81 35 37
IL12RB2 0.029 0.074 0.25 6 -0.55 1 7
GADD45G -0.06 0.26 0.69 3 -0.7 41 44
natural killer cell activation -0.007 0.022 -10000 0 -10000 0 0
RELB 0.036 0.019 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL18 0.045 0.045 0.21 12 -10000 0 12
IL2RA 0.04 0.034 -10000 0 -10000 0 0
IFNG 0.062 0.065 -10000 0 -0.54 1 1
STAT3 (dimer) -0.061 0.24 0.56 10 -0.59 47 57
HLA-DRB5 -0.008 0.032 -10000 0 -10000 0 0
FASLG -0.06 0.26 0.72 7 -0.83 15 22
NF kappa B2 p52/RelB -0.081 0.25 0.53 6 -0.59 60 66
CD4 -0.008 0.031 -10000 0 -10000 0 0
SOCS1 0.032 0.012 -10000 0 -10000 0 0
EntrezGene:6955 -0.014 0.015 -10000 0 -10000 0 0
CD3D 0.003 0.05 -10000 0 -10000 0 0
CD3E -0.001 0.033 -10000 0 -10000 0 0
CD3G 0.004 0.081 -10000 0 -0.56 5 5
IL12Rbeta2/JAK2 0.027 0.074 0.3 7 -0.41 1 8
CCL3 -0.085 0.25 0.7 2 -0.72 26 28
CCL4 -0.085 0.25 0.7 2 -0.78 20 22
HLA-A 0.042 0.026 -10000 0 -10000 0 0
IL18/IL18R 0.058 0.14 0.38 14 -0.36 42 56
NOS2 -0.085 0.25 0.59 9 -0.58 67 76
IL12/IL12R/TYK2/JAK2/SPHK2 0.009 0.098 0.35 8 -0.32 8 16
IL1R1 -0.17 0.43 0.7 2 -1.2 60 62
IL4 0.038 0.03 -10000 0 -0.17 1 1
JAK2 0.017 0.037 0.25 1 -10000 0 1
EntrezGene:6957 -0.011 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.002 0.15 0.34 22 -0.46 13 35
RAB7A -0.043 0.24 0.64 4 -0.71 24 28
lysosomal transport -0.04 0.23 0.63 4 -0.67 24 28
FOS -0.83 0.6 0.57 1 -1.2 364 365
STAT4 (dimer) -0.033 0.27 0.62 9 -0.67 41 50
STAT5A (dimer) -0.06 0.26 0.57 8 -0.6 56 64
GZMA -0.091 0.24 0.57 7 -0.59 63 70
GZMB -0.09 0.26 0.7 6 -0.77 25 31
HLX 0.025 0.038 -10000 0 -0.54 2 2
LCK -0.084 0.27 0.69 9 -0.63 60 69
TCR/CD3/MHC II/CD4 -0.12 0.16 0.28 5 -0.44 59 64
IL2/IL2R 0.087 0.056 0.37 4 -0.32 1 5
MAPK14 -0.057 0.28 0.63 8 -0.73 44 52
CCR5 -0.066 0.28 0.72 9 -0.75 38 47
IL1B 0.016 0.066 0.25 1 -0.55 4 5
STAT6 -0.039 0.18 0.39 7 -0.66 27 34
STAT4 0.027 0.069 -10000 0 -0.54 7 7
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT1 0.058 0.054 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
NFKB2 0.035 0.012 -10000 0 -10000 0 0
IL12B 0.01 0.047 0.25 2 -10000 0 2
CD8A 0.005 0.009 -10000 0 -10000 0 0
CD8B 0.042 0.026 0.2 10 -10000 0 10
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.012 0.094 0.3 8 -0.35 8 16
IL2RB 0.035 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.26 0.61 10 -0.62 40 50
IL2RG 0.043 0.034 -10000 0 -10000 0 0
IL12 0.007 0.089 0.29 2 -0.41 11 13
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
CD247 -0.004 0.11 -10000 0 -0.55 15 15
IL2 0.033 0.027 -10000 0 -0.54 1 1
SPHK2 0.034 0.005 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.093 -10000 0 -0.56 11 11
IL12/IL12R/TYK2/JAK2 -0.099 0.27 0.67 8 -0.66 61 69
MAP2K3 -0.069 0.29 0.62 8 -0.75 49 57
RIPK2 0.029 0.021 -10000 0 -10000 0 0
MAP2K6 -0.061 0.27 0.62 8 -0.71 45 53
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.012 0.033 -10000 0 -10000 0 0
IL18RAP -0.01 0.16 0.21 2 -0.55 42 44
IL12Rbeta1/TYK2 0.03 0.046 -10000 0 -10000 0 0
EOMES 0.042 0.1 -10000 0 -0.61 3 3
STAT1 (dimer) -0.013 0.26 0.67 15 -0.59 39 54
T cell proliferation -0.03 0.22 0.53 9 -0.54 42 51
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.037 0.031 0.21 1 -0.55 1 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.02 0.23 0.52 2 -0.62 38 40
ATF2 -0.055 0.26 0.59 8 -0.69 41 49
Syndecan-2-mediated signaling events

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.07 0.093 0.23 3 -0.32 16 19
EPHB2 0.042 0.036 -10000 0 -10000 0 0
Syndecan-2/TACI 0.016 0.066 -10000 0 -0.33 16 16
LAMA1 0.033 0.01 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.057 0.17 -10000 0 -0.32 134 134
HRAS 0.034 0.013 -10000 0 -10000 0 0
Syndecan-2/CASK -0.001 0.06 -10000 0 -0.33 16 16
ITGA5 0.034 0.007 -10000 0 -10000 0 0
BAX -0.001 0.064 0.49 2 -10000 0 2
EPB41 0.033 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.015 0.06 -10000 0 -0.3 16 16
LAMA3 -0.15 0.27 -10000 0 -0.54 158 158
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.32 0.28 -10000 0 -0.54 315 315
Syndecan-2/MMP2 0.013 0.073 -10000 0 -0.37 16 16
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.081 -10000 0 -0.37 18 18
dendrite morphogenesis 0.021 0.07 -10000 0 -0.33 16 16
Syndecan-2/GM-CSF 0.02 0.068 -10000 0 -0.33 16 16
determination of left/right symmetry 0 0.071 -10000 0 -0.39 16 16
Syndecan-2/PKC delta 0.017 0.066 -10000 0 -0.33 16 16
GNB2L1 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.041 0.093 0.26 4 -0.3 16 20
MAPK1 0.046 0.096 0.23 7 -0.3 16 23
Syndecan-2/RACK1 0.03 0.062 -10000 0 -0.28 16 16
NF1 0.032 0.009 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0 0.071 -10000 0 -0.39 16 16
ITGA2 0.014 0.1 -10000 0 -0.54 17 17
MAPK8 0.001 0.068 0.4 2 -0.33 17 19
Syndecan-2/alpha2/beta1 Integrin 0.034 0.091 -10000 0 -0.33 23 23
Syndecan-2/Kininogen 0.017 0.066 -10000 0 -0.33 16 16
ITGB1 0.033 0.006 -10000 0 -10000 0 0
SRC 0.041 0.089 0.3 6 -0.28 15 21
Syndecan-2/CASK/Protein 4.1 0.015 0.06 -10000 0 -0.3 16 16
extracellular matrix organization 0.017 0.066 -10000 0 -0.33 16 16
actin cytoskeleton reorganization 0.069 0.093 0.23 3 -0.32 16 19
Syndecan-2/Caveolin-2/Ras -0.15 0.18 -10000 0 -0.32 236 236
Syndecan-2/Laminin alpha3 -0.081 0.16 -10000 0 -0.35 130 130
Syndecan-2/RasGAP 0.042 0.066 -10000 0 -0.28 15 15
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
PRKCD 0.034 0.016 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.071 -10000 0 -0.33 16 16
GO:0007205 0.003 0.005 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.058 -10000 0 -0.27 15 15
RHOA 0.033 0.007 -10000 0 -10000 0 0
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.081 -10000 0 -0.37 18 18
Syndecan-2/Synbindin 0.015 0.065 -10000 0 -0.33 16 16
TGFB1 0.034 0.008 -10000 0 -10000 0 0
CASP3 0.041 0.095 0.28 4 -0.3 16 20
FN1 0.13 0.066 -10000 0 -10000 0 0
Syndecan-2/IL8 0.024 0.074 0.23 1 -0.33 16 17
SDC2 0 0.071 -10000 0 -0.39 16 16
KNG1 0.033 0.007 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.016 0.066 -10000 0 -0.33 16 16
TRAPPC4 0.03 0.011 -10000 0 -10000 0 0
CSF2 0.039 0.028 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.017 0.066 -10000 0 -0.33 16 16
Syndecan-2/Syntenin/PI-4-5-P2 0.015 0.06 -10000 0 -0.3 16 16
Syndecan-2/Ezrin 0.015 0.06 -10000 0 -0.3 16 16
PRKACA 0.043 0.096 0.23 4 -0.3 16 20
angiogenesis 0.024 0.074 0.23 1 -0.33 16 17
MMP2 0.028 0.039 -10000 0 -0.54 2 2
IL8 0.047 0.052 -10000 0 -0.54 1 1
calcineurin-NFAT signaling pathway 0.016 0.066 -10000 0 -0.33 16 16
Ceramide 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
SPHK2 -0.021 0.12 -10000 0 -0.4 45 45
MAP4K4 0.004 0.081 -10000 0 -0.39 6 6
BAG4 0.028 0.015 -10000 0 -10000 0 0
PKC zeta/ceramide -0.012 0.067 0.14 9 -0.28 8 17
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BAX 0.008 0.049 -10000 0 -0.35 5 5
RIPK1 0.033 0.006 -10000 0 -10000 0 0
AKT1 0.009 0.076 0.72 5 -10000 0 5
BAD -0.013 0.07 0.18 2 -0.34 5 7
SMPD1 0.019 0.063 0.24 6 -0.25 10 16
RB1 -0.012 0.067 0.16 2 -0.3 7 9
FADD/Caspase 8 0.032 0.12 0.29 10 -0.42 8 18
MAP2K4 -0.013 0.07 -10000 0 -0.35 6 6
NSMAF 0.028 0.028 -10000 0 -0.54 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.007 0.073 0.31 3 -0.35 4 7
EGF -0.15 0.27 -10000 0 -0.54 162 162
mol:ceramide -0.012 0.074 0.16 34 -0.29 8 42
MADD 0.034 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.023 0.12 -10000 0 -0.41 46 46
ASAH1 0.027 0.042 -10000 0 -0.54 2 2
negative regulation of cell cycle -0.014 0.067 0.16 2 -0.29 7 9
cell proliferation -0.11 0.14 -10000 0 -0.27 171 171
BID -0.015 0.19 -10000 0 -0.68 33 33
MAP3K1 -0.011 0.073 0.2 1 -0.32 7 8
EIF2A -0.004 0.073 0.27 7 -0.25 5 12
TRADD 0.029 0.012 -10000 0 -10000 0 0
CRADD 0.034 0.005 -10000 0 -10000 0 0
MAPK3 -0.003 0.072 0.27 5 -0.32 5 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.008 0.077 0.27 5 -0.36 4 9
Cathepsin D/ceramide 0.011 0.079 -10000 0 -0.27 7 7
FADD 0.029 0.1 0.28 2 -0.42 4 6
KSR1 -0.006 0.073 0.21 6 -0.36 4 10
MAPK8 -0.008 0.07 -10000 0 -0.27 10 10
PRKRA -0.012 0.07 0.2 1 -0.34 5 6
PDGFA -0.018 0.16 -10000 0 -0.54 45 45
TRAF2 0.034 0.012 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 250 250
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.012 0.073 0.16 34 -0.29 8 42
CTSD 0.046 0.042 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.049 0.01 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.11 0.15 -10000 0 -0.28 167 167
PRKCD 0.034 0.016 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.023 0.12 -10000 0 -0.41 46 46
RelA/NF kappa B1 0.049 0.01 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.034 0.03 -10000 0 -0.54 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.008 0.09 -10000 0 -0.32 18 18
TNFR1A/BAG4/TNF-alpha 0.053 0.034 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.021 0.12 -10000 0 -0.4 45 45
MAP2K1 -0.007 0.072 0.29 4 -0.34 4 8
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
CYCS 0.027 0.082 0.22 26 -0.25 6 32
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.023 -10000 0 -10000 0 0
EIF2AK2 -0.007 0.069 0.22 5 -0.3 5 10
TNF-alpha/TNFR1A/FAN 0.057 0.036 -10000 0 -0.33 1 1
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.023 0.092 -10000 0 -0.43 13 13
MAP2K2 -0.007 0.072 0.29 4 -0.33 4 8
SMPD3 -0.001 0.11 0.24 3 -0.3 54 57
TNF 0.038 0.023 -10000 0 -10000 0 0
PKC zeta/PAR4 0.025 0.021 -10000 0 -0.4 1 1
mol:PHOSPHOCHOLINE 0.083 0.12 0.24 171 -0.22 3 174
NF kappa B1/RelA/I kappa B alpha 0.075 0.031 -10000 0 -0.3 1 1
AIFM1 0.026 0.082 0.19 59 -0.24 7 66
BCL2 -0.074 0.22 -10000 0 -0.54 94 94
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.048 0.022 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 64 64
CRKL 0.032 0.008 -10000 0 -10000 0 0
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
FYN 0.029 0.037 -10000 0 -0.54 2 2
ITGA3 0.029 0.029 -10000 0 -0.54 1 1
RELN/VLDLR/Fyn -0.011 0.16 -10000 0 -0.36 81 81
MAPK8IP1/MKK7/MAP3K11/JNK1 0.078 0.046 -10000 0 -10000 0 0
AKT1 -0.055 0.14 -10000 0 -0.3 105 105
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
DAB1 0.033 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.07 0.084 -10000 0 -0.29 20 20
LRPAP1/LRP8 0.072 0.047 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.074 0.088 -10000 0 -0.28 22 22
DAB1/alpha3/beta1 Integrin 0.018 0.13 -10000 0 -0.3 56 56
long-term memory 0.08 0.11 -10000 0 -0.32 20 20
DAB1/LIS1 0.034 0.15 -10000 0 -0.3 63 63
DAB1/CRLK/C3G 0.019 0.14 -10000 0 -0.3 63 63
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
DAB1/NCK2 0.039 0.15 -10000 0 -0.31 63 63
ARHGEF2 0.03 0.022 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.032 0.012 -10000 0 -10000 0 0
CDK5R1 0.033 0.014 -10000 0 -10000 0 0
RELN 0.012 0.11 -10000 0 -0.54 20 20
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
RELN/LRP8/Fyn 0.065 0.095 -10000 0 -0.32 22 22
GRIN2A/RELN/LRP8/DAB1/Fyn 0.083 0.095 -10000 0 -0.3 14 14
MAPK8 0.032 0.026 -10000 0 -0.54 1 1
RELN/VLDLR/DAB1 -0.005 0.15 -10000 0 -0.33 79 79
ITGB1 0.033 0.006 -10000 0 -10000 0 0
MAP1B -0.039 0.16 0.24 5 -0.34 87 92
RELN/LRP8 0.069 0.091 -10000 0 -0.32 20 20
GRIN2B/RELN/LRP8/DAB1/Fyn 0.079 0.11 -10000 0 -0.33 23 23
PI3K 0.006 0.12 -10000 0 -0.38 46 46
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.043 0.027 -10000 0 -0.4 1 1
RAP1A -0.028 0.12 0.35 3 -0.48 5 8
PAFAH1B1 0.032 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.034 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.047 0.014 -10000 0 -10000 0 0
GRIN2B 0.021 0.085 -10000 0 -0.54 11 11
NCK2 0.034 0.007 -10000 0 -10000 0 0
neuron differentiation 0.049 0.069 0.24 3 -0.54 1 4
neuron adhesion -0.011 0.13 0.38 5 -0.46 4 9
LRP8 0.071 0.063 -10000 0 -10000 0 0
GSK3B -0.05 0.14 -10000 0 -0.5 23 23
RELN/VLDLR/DAB1/Fyn 0.005 0.15 -10000 0 -0.31 81 81
MAP3K11 0.034 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.054 0.16 -10000 0 -0.31 111 111
CDK5 0.037 0.021 -10000 0 -10000 0 0
MAPT 0.014 0.12 0.79 10 -0.49 3 13
neuron migration -0.027 0.15 0.38 4 -0.4 27 31
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.048 0.068 -10000 0 -0.55 1 1
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 79 79
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.025 0.004 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.033 0.014 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.1 -10000 0 -0.38 20 20
IRAK/TOLLIP 0.038 0.014 -10000 0 -10000 0 0
IKBKB 0.029 0.013 -10000 0 -10000 0 0
IKBKG 0.034 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.054 0.044 0.25 2 -0.4 3 5
IL1A 0.036 0.017 0.18 7 -10000 0 7
IL1B -0.017 0.12 -10000 0 -0.42 40 40
IRAK/TRAF6/p62/Atypical PKCs 0.064 0.027 -10000 0 -10000 0 0
IL1R2 0.038 0.055 -10000 0 -0.54 3 3
IL1R1 -0.028 0.18 -10000 0 -0.54 55 55
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.029 0.13 -10000 0 -0.42 32 32
TOLLIP 0.033 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.038 0.067 -10000 0 -0.35 1 1
JUN -0.05 0.1 -10000 0 -0.27 80 80
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.022 0.19 -10000 0 -0.37 108 108
IL1 alpha/IL1R1/IL1RAP/MYD88 0.041 0.13 -10000 0 -0.32 55 55
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.053 0.13 -10000 0 -0.3 55 55
IL1 beta fragment/IL1R1/IL1RAP -0.021 0.16 -10000 0 -0.35 87 87
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.01 0.05 0.18 4 -0.27 11 15
IRAK1 0.019 0.011 -10000 0 -10000 0 0
IL1RN/IL1R1 0.016 0.15 -10000 0 -0.39 55 55
IRAK4 0.034 0.005 -10000 0 -10000 0 0
PRKCI 0.034 0.017 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.006 0.12 -10000 0 -0.38 46 46
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.021 0.14 -10000 0 -0.41 33 33
CHUK 0.034 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.021 0.16 -10000 0 -0.35 87 87
IL1 beta/IL1R2 0.007 0.12 -10000 0 -0.36 43 43
IRAK/TRAF6/TAK1/TAB1/TAB2 0.045 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.032 0.18 -10000 0 -0.34 108 108
IRAK3 0.035 0.033 -10000 0 -0.54 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.006 0.15 -10000 0 -0.32 85 85
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.002 0.1 -10000 0 -0.27 54 54
IL1 alpha/IL1R1/IL1RAP 0.024 0.13 -10000 0 -0.34 55 55
RELA 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.034 0.008 -10000 0 -10000 0 0
MYD88 0.034 0.011 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.053 0.028 -10000 0 -10000 0 0
IL1RAP 0.033 0.006 -10000 0 -10000 0 0
UBE2N 0.034 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.021 0.12 -10000 0 -0.29 80 80
CASP1 -0.013 0.15 -10000 0 -0.54 38 38
IL1RN/IL1R2 0.067 0.056 0.25 7 -0.4 3 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.004 0.16 -10000 0 -0.34 87 87
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.004 0.13 -10000 0 -0.35 55 55
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
IL1RN 0.054 0.049 -10000 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.045 0.016 -10000 0 -10000 0 0
MAP2K6 0.014 0.053 0.36 1 -0.28 10 11
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.006 -10000 0 -10000 0 0
mol:S1P 0.001 0.003 0.03 6 -10000 0 6
S1P1/S1P/Gi -0.091 0.16 -10000 0 -0.28 185 185
GNAO1 0.031 0.013 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.041 0.016 -10000 0 -10000 0 0
AKT1 -0.01 0.1 -10000 0 -0.5 16 16
AKT3 -0.014 0.12 0.43 1 -0.56 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.033 0.006 -10000 0 -10000 0 0
GNAI2 0.035 0.011 -10000 0 -10000 0 0
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.002 0.004 0.035 6 -10000 0 6
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.07 0.14 0.25 1 -0.34 58 59
MAPK3 -0.062 0.13 0.23 1 -0.33 48 49
MAPK1 -0.068 0.13 0.23 1 -0.33 55 56
JAK2 -0.061 0.15 0.33 1 -0.34 59 60
CXCR4 -0.063 0.14 0.24 2 -0.33 52 54
FLT1 0.035 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC -0.065 0.13 0.31 2 -0.33 54 56
S1P/S1P3/Gi -0.07 0.15 0.25 1 -0.34 58 59
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.058 0.14 -10000 0 -0.31 58 58
VEGFA 0.052 0.046 0.22 1 -10000 0 1
S1P/S1P2/Gi -0.074 0.14 -10000 0 -0.34 58 58
VEGFR1 homodimer/VEGFA homodimer 0.062 0.039 0.26 1 -10000 0 1
RHOA 0.033 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.025 0.037 -10000 0 -0.27 5 5
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.063 -10000 0 -0.54 6 6
G12/G13 0.045 0.017 -10000 0 -10000 0 0
GNA14 0.043 0.067 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.033 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.059 0.14 -10000 0 -0.31 58 58
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.008 0.23 -10000 0 -0.9 24 24
NCK1/PAK1/Dok-R -0.033 0.094 -10000 0 -0.41 24 24
NCK1/Dok-R 0.017 0.24 -10000 0 -1 23 23
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
mol:beta2-estradiol -0.001 0.04 0.23 14 -10000 0 14
RELA 0.034 0.005 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
F2 0.018 0.047 0.27 13 -10000 0 13
TNIP2 0.033 0.013 -10000 0 -10000 0 0
NF kappa B/RelA 0.043 0.23 -10000 0 -0.94 23 23
FN1 0.13 0.066 -10000 0 -10000 0 0
PLD2 -0.004 0.23 -10000 0 -1 23 23
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB14 -0.001 0.19 -10000 0 -0.54 52 52
ELK1 0.005 0.22 -10000 0 -0.94 23 23
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.043 0.045 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.094 0.25 -10000 0 -0.96 23 23
CDKN1A -0.002 0.19 -10000 0 -0.67 20 20
ITGA5 0.034 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.016 0.24 -10000 0 -1 23 23
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:NO 0.017 0.18 -10000 0 -0.65 24 24
PLG -0.005 0.23 -10000 0 -1 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.002 0.21 -10000 0 -0.84 24 24
GRB2 0.033 0.017 -10000 0 -10000 0 0
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
ANGPT2 -0.074 0.23 -10000 0 -0.66 34 34
BMX -0.16 0.28 -10000 0 -1.3 23 23
ANGPT1 -0.013 0.21 -10000 0 -1.2 14 14
tube development -0.012 0.2 -10000 0 -0.73 21 21
ANGPT4 0.032 0.008 -10000 0 -10000 0 0
response to hypoxia -0.001 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.003 0.28 -10000 0 -1.1 23 23
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 375 375
STAT5A (dimer) -0.001 0.23 -10000 0 -0.84 21 21
mol:L-citrulline 0.017 0.18 -10000 0 -0.65 24 24
AGTR1 -0.18 0.3 -10000 0 -0.54 206 206
MAPK14 -0.003 0.26 -10000 0 -1 26 26
Tie2/SHP2 0.001 0.21 -10000 0 -1 15 15
TEK -0.004 0.22 -10000 0 -1.1 16 16
RPS6KB1 0.021 0.23 -10000 0 -0.86 24 24
Angiotensin II/AT1 -0.13 0.22 -10000 0 -0.39 208 208
Tie2/Ang1/GRB2 0.011 0.25 -10000 0 -1.1 23 23
MAPK3 0.004 0.22 -10000 0 -0.93 23 23
MAPK1 -0.005 0.22 -10000 0 -0.96 23 23
Tie2/Ang1/GRB7 0.005 0.24 -10000 0 -1.1 23 23
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.004 0.24 -10000 0 -1 23 23
PI3K -0.004 0.26 -10000 0 -1 24 24
FES -0.01 0.26 -10000 0 -1.1 26 26
Crk/Dok-R 0.017 0.24 -10000 0 -1 23 23
Tie2/Ang1/ABIN2 0.012 0.25 -10000 0 -1.1 23 23
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.013 0.21 -10000 0 -0.8 24 24
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.033 0.23 -10000 0 -0.82 24 24
Tie2/Ang2 -0.027 0.26 -10000 0 -1 21 21
Tie2/Ang1 0 0.25 -10000 0 -1.1 23 23
FOXO1 0.007 0.22 -10000 0 -0.81 25 25
ELF1 0.035 0.027 -10000 0 -10000 0 0
ELF2 0.001 0.23 -10000 0 -1 23 23
mol:Choline -0.002 0.22 -10000 0 -0.99 23 23
cell migration -0.015 0.053 -10000 0 -0.23 24 24
FYN -0.018 0.22 -10000 0 -0.84 21 21
DOK2 0.025 0.039 -10000 0 -0.54 2 2
negative regulation of cell cycle 0.002 0.17 -10000 0 -0.59 21 21
ETS1 0.031 0.056 -10000 0 -0.29 11 11
PXN 0.038 0.2 -10000 0 -0.68 24 24
ITGB1 0.033 0.006 -10000 0 -10000 0 0
NOS3 0.012 0.2 -10000 0 -0.74 24 24
RAC1 0.034 0.005 -10000 0 -10000 0 0
TNF 0.037 0.054 0.26 1 -0.25 13 14
MAPKKK cascade -0.002 0.22 -10000 0 -0.99 23 23
RASA1 0.033 0.011 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.003 0.24 -10000 0 -1 23 23
NCK1 0.034 0.005 -10000 0 -10000 0 0
vasculogenesis 0.02 0.16 -10000 0 -0.58 24 24
mol:Phosphatidic acid -0.002 0.22 -10000 0 -0.99 23 23
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.017 0.18 -10000 0 -0.65 24 24
Rac1/GTP 0.014 0.21 -10000 0 -0.8 24 24
MMP2 -0.004 0.24 -10000 0 -1 23 23
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.042 0.26 5 -10000 0 5
AES 0.026 0.035 0.22 4 -10000 0 4
FBXW11 0.033 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.048 0.024 -10000 0 -0.4 1 1
SMAD4 0.032 0.027 -10000 0 -0.54 1 1
DKK2 0.031 0.054 -10000 0 -0.54 4 4
TLE1 0.01 0.1 0.23 5 -0.55 15 20
MACF1 0.034 0.006 -10000 0 -10000 0 0
CTNNB1 0.15 0.11 0.35 30 -0.41 3 33
WIF1 -0.38 0.26 -10000 0 -0.54 363 363
beta catenin/RanBP3 0.042 0.15 0.5 41 -0.4 3 44
KREMEN2 0.1 0.074 -10000 0 -10000 0 0
DKK1 0.005 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.16 0.1 0.35 25 -0.41 2 27
FZD1 0.033 0.026 -10000 0 -0.54 1 1
AXIN2 0.027 0.28 0.64 46 -1.1 15 61
AXIN1 0.032 0.01 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.069 0.087 -10000 0 -0.54 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.091 0.15 0.41 4 -0.6 12 16
Axin1/APC/GSK3 0.065 0.059 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.06 0.076 0.37 1 -0.54 1 2
HNF1A 0.028 0.041 0.25 6 -10000 0 6
CTBP1 0.025 0.038 0.24 4 -10000 0 4
MYC 0.093 0.44 0.62 129 -1.3 29 158
RANBP3 0.033 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.099 0.069 -10000 0 -0.31 3 3
NKD1 0.031 0.021 -10000 0 -10000 0 0
TCF4 0.019 0.076 0.24 5 -0.54 7 12
TCF3 0.028 0.042 0.26 5 -10000 0 5
WNT1/LRP6/FZD1/Axin1 0.076 0.039 -10000 0 -0.32 1 1
Ran/GTP 0.025 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.003 0.21 0.53 35 -0.54 13 48
LEF1 0.054 0.067 0.26 8 -10000 0 8
DVL1 0.078 0.058 0.25 3 -10000 0 3
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.097 0.17 0.34 3 -0.6 14 17
DKK1/LRP6/Kremen 2 0.079 0.13 -10000 0 -0.29 42 42
LRP6 0.033 0.008 -10000 0 -10000 0 0
CSNK1A1 0.028 0.042 0.26 5 -10000 0 5
NLK 0.035 0.031 -10000 0 -10000 0 0
CCND1 0.11 0.38 0.74 95 -1.2 14 109
WNT1 0.035 0.005 -10000 0 -10000 0 0
GSK3A 0.035 0.005 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -10000 0 -10000 0 0
FRAT1 0.034 0.008 -10000 0 -10000 0 0
PPP2R5D 0.055 0.058 -10000 0 -0.39 3 3
APC 0.038 0.062 0.38 4 -0.3 1 5
WNT1/LRP6/FZD1 0.16 0.1 0.25 89 -0.29 1 90
CREBBP 0.023 0.044 0.25 3 -0.55 1 4
Coregulation of Androgen receptor activity

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
NRIP1 0.029 0.065 -10000 0 -0.54 6 6
SVIL 0.022 0.084 -10000 0 -0.54 11 11
ZNF318 0.03 0.008 -10000 0 -10000 0 0
JMJD2C 0.007 0.01 0.12 4 -10000 0 4
T-DHT/AR/Ubc9 -0.036 0.14 -10000 0 -0.32 78 78
CARM1 0.035 0.013 -10000 0 -10000 0 0
PRDX1 0.034 0.014 -10000 0 -10000 0 0
PELP1 0.031 0.01 -10000 0 -10000 0 0
CTNNB1 0.031 0.045 -10000 0 -0.54 3 3
AKT1 0.034 0.017 -10000 0 -10000 0 0
PTK2B 0.028 0.014 -10000 0 -10000 0 0
MED1 0.028 0.012 -10000 0 -10000 0 0
MAK 0.037 0.032 -10000 0 -10000 0 0
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.035 0.008 -10000 0 -10000 0 0
GSN -0.11 0.25 -10000 0 -0.54 129 129
NCOA2 0.028 0.014 -10000 0 -10000 0 0
NCOA6 0.034 0.008 -10000 0 -10000 0 0
DNA-PK 0.053 0.03 -10000 0 -10000 0 0
NCOA4 0.033 0.026 -10000 0 -0.54 1 1
PIAS3 0.033 0.008 -10000 0 -10000 0 0
cell proliferation 0 0.066 -10000 0 -0.45 5 5
XRCC5 0.033 0.006 -10000 0 -10000 0 0
UBE3A 0.034 0.009 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.052 0.13 -10000 0 -0.31 85 85
FHL2 -0.1 0.32 -10000 0 -0.98 55 55
RANBP9 0.035 0.009 -10000 0 -10000 0 0
JMJD1A -0.027 0.061 -10000 0 -0.14 119 119
CDK6 0.028 0.064 -10000 0 -0.54 6 6
TGFB1I1 0.029 0.045 -10000 0 -0.54 3 3
T-DHT/AR/CyclinD1 -0.037 0.16 -10000 0 -0.36 76 76
XRCC6 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.056 0.17 -10000 0 -0.36 81 81
CTDSP1 0.034 0.006 -10000 0 -10000 0 0
CTDSP2 0.031 0.008 -10000 0 -10000 0 0
BRCA1 0.037 0.021 -10000 0 -10000 0 0
TCF4 0.023 0.068 -10000 0 -0.54 7 7
CDKN2A 0.051 0.053 -10000 0 -10000 0 0
SRF 0.021 0.057 -10000 0 -10000 0 0
NKX3-1 -0.071 0.11 -10000 0 -0.22 171 171
KLK3 0.012 0.056 -10000 0 -10000 0 0
TMF1 0.033 0.007 -10000 0 -10000 0 0
HNRNPA1 0.033 0.006 -10000 0 -10000 0 0
AOF2 0.001 0.002 -10000 0 -10000 0 0
APPL1 0.015 0.014 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.04 0.14 -10000 0 -0.33 79 79
AR -0.069 0.2 -10000 0 -0.56 66 66
UBA3 0 0.001 -10000 0 -10000 0 0
PATZ1 0.031 0.009 -10000 0 -10000 0 0
PAWR 0.034 0.03 -10000 0 -0.54 1 1
PRKDC 0.03 0.019 -10000 0 -10000 0 0
PA2G4 0.032 0.006 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.032 0.13 -10000 0 -0.29 76 76
RPS6KA3 0.033 0.037 -10000 0 -0.54 2 2
T-DHT/AR/ARA70 -0.039 0.14 -10000 0 -0.33 74 74
LATS2 0.02 0.076 -10000 0 -0.54 9 9
T-DHT/AR/PRX1 -0.034 0.13 -10000 0 -0.3 79 79
Cyclin D3/CDK11 p58 0.024 0.004 -10000 0 -10000 0 0
VAV3 0.028 0.12 -10000 0 -0.54 19 19
KLK2 -0.017 0.069 0.3 1 -0.42 1 2
CASP8 0.033 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.019 0.13 -10000 0 -0.32 55 55
TMPRSS2 -0.22 0.41 -10000 0 -0.96 119 119
CCND1 0.023 0.088 -10000 0 -0.54 10 10
PIAS1 0.035 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.035 0.049 1 -0.071 137 138
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.037 0.016 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.043 0.14 -10000 0 -0.32 85 85
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.004 0.053 -10000 0 -10000 0 0
CCND3 0.033 0.006 -10000 0 -10000 0 0
TGIF1 0.03 0.027 -10000 0 -0.54 1 1
FKBP4 0.037 0.024 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer 0.098 0.076 0.31 7 -0.28 4 11
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.1 0.37 13 -10000 0 13
alphaV/beta3 Integrin/Osteopontin/Src 0.098 0.072 0.26 2 -0.39 4 6
AP1 -0.14 0.22 0.49 1 -0.46 89 90
ILK 0.076 0.073 0.32 4 -0.3 4 8
bone resorption 0.06 0.07 -10000 0 -10000 0 0
PTK2B 0.027 0.014 -10000 0 -10000 0 0
PYK2/p130Cas 0.1 0.089 0.33 1 -0.28 4 5
ITGAV 0.04 0.029 0.18 2 -0.54 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.048 0.024 -10000 0 -0.4 1 1
alphaV/beta3 Integrin/Osteopontin 0.12 0.077 0.32 3 -0.33 4 7
MAP3K1 0.078 0.078 0.3 10 -0.3 5 15
JUN -0.064 0.22 -10000 0 -0.54 86 86
MAPK3 0.078 0.095 0.34 17 -0.28 3 20
MAPK1 0.077 0.092 0.33 13 -0.28 4 17
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.063 0.077 0.3 8 -0.29 6 14
ITGB3 0.041 0.021 -10000 0 -10000 0 0
NFKBIA 0.076 0.098 0.34 21 -10000 0 21
FOS -0.36 0.27 -10000 0 -0.54 342 342
CD44 0.034 0.011 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
PLAU 0.083 0.15 0.51 6 -0.53 1 7
NF kappa B1 p50/RelA 0.14 0.1 0.41 14 -10000 0 14
BCAR1 0.029 0.012 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.061 0.033 -10000 0 -0.39 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.079 0.074 0.31 8 -0.3 4 12
VAV3 0.062 0.095 0.29 14 -0.29 11 25
MAP3K14 0.086 0.082 0.3 12 -0.3 4 16
ROCK2 0.032 0.026 -10000 0 -0.54 1 1
SPP1 0.094 0.086 -10000 0 -0.54 3 3
RAC1 0.034 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.071 0.087 0.28 8 -0.27 10 18
MMP2 -0.13 0.17 0.47 1 -0.41 72 73
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.046 0.041 -10000 0 -10000 0 0
GNB1/GNG2 -0.019 0.054 -10000 0 -0.18 46 46
AKT1 0.059 0.13 0.4 19 -0.28 9 28
EGF -0.15 0.27 -10000 0 -0.54 162 162
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.029 0.053 0.26 2 -10000 0 2
mol:Ca2+ 0.059 0.16 0.48 16 -0.3 36 52
LYN 0.026 0.051 0.26 3 -10000 0 3
RhoA/GTP 0.025 0.066 0.21 9 -0.14 3 12
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK 0.057 0.17 0.55 13 -0.34 42 55
GNG2 0.032 0.026 -10000 0 -0.54 1 1
ARRB2 0.031 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.014 0.12 -10000 0 -0.6 14 14
G beta5/gamma2 -0.013 0.075 -10000 0 -0.24 44 44
PRKCH 0.052 0.17 0.62 9 -0.36 44 53
DNM1 0.034 0.008 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.015 0.029 -10000 0 -0.53 1 1
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
PTGDR 0.03 0.06 -10000 0 -0.54 5 5
G12 family/GTP 0.005 0.11 -10000 0 -0.3 41 41
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
ADRBK2 0.03 0.037 -10000 0 -0.54 2 2
RhoA/GTP/ROCK1 0.044 0.012 -10000 0 -10000 0 0
mol:GDP -0.041 0.13 0.38 13 -0.46 9 22
mol:NADP 0.034 0.006 -10000 0 -10000 0 0
RAB11A 0.033 0.006 -10000 0 -10000 0 0
PRKG1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 0.058 0.18 0.64 9 -0.37 44 53
cell morphogenesis 0.044 0.012 -10000 0 -10000 0 0
PLCB2 0.05 0.22 0.7 8 -0.5 44 52
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.03 0.054 0.25 2 -10000 0 2
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.029 0.055 0.26 2 -10000 0 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
PTGIR 0.034 0.005 -10000 0 -10000 0 0
PRKCB1 0.055 0.18 0.63 9 -0.37 44 53
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.034 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.053 0.22 0.72 8 -0.51 45 53
LCK 0.038 0.06 0.26 4 -10000 0 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.044 0.041 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.098 -10000 0 -0.4 23 23
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.04 0.041 -10000 0 -10000 0 0
MAPK14 0.052 0.13 0.43 16 -0.25 8 24
TGM2/GTP 0.055 0.2 0.67 9 -0.41 35 44
MAPK11 0.05 0.13 0.41 19 -0.24 14 33
ARHGEF1 0.045 0.11 0.36 15 -0.2 6 21
GNAI2 0.033 0.01 -10000 0 -10000 0 0
JNK cascade 0.059 0.18 0.62 10 -0.38 45 55
RAB11/GDP 0.031 0.01 -10000 0 -10000 0 0
ICAM1 0.057 0.15 0.48 16 -0.28 39 55
cAMP biosynthetic process 0.054 0.17 0.6 9 -0.35 35 44
Gq family/GTP/EBP50 0.033 0.047 -10000 0 -0.22 6 6
actin cytoskeleton reorganization 0.044 0.012 -10000 0 -10000 0 0
SRC 0.027 0.052 0.26 2 -10000 0 2
GNB5 0.032 0.026 -10000 0 -0.54 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
EGF/EGFR -0.063 0.11 0.27 2 -0.29 41 43
VCAM1 0.053 0.16 0.48 16 -0.32 44 60
TP beta/Gq family/GDP/G beta5/gamma2 0.014 0.12 -10000 0 -0.6 14 14
platelet activation 0.063 0.16 0.54 13 -0.31 18 31
PGI2/IP 0.025 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.031 -10000 0 -0.27 5 5
Gq family/GDP/G beta5/gamma2 0.016 0.1 -10000 0 -0.52 14 14
TXA2/TP beta/beta Arrestin2 -0.003 0.061 -10000 0 -0.39 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.013 0.031 -10000 0 -0.25 5 5
mol:DAG 0.057 0.2 0.65 9 -0.42 44 53
EGFR -0.27 0.29 -10000 0 -0.54 264 264
TXA2/TP alpha 0.057 0.21 0.7 8 -0.46 40 48
Gq family/GTP 0.009 0.051 0.22 1 -0.22 17 18
YES1 0.029 0.057 0.26 2 -0.43 1 3
GNAI2/GTP 0.03 0.04 -10000 0 -0.24 4 4
PGD2/DP 0.023 0.044 -10000 0 -0.4 5 5
SLC9A3R1 0.058 0.056 -10000 0 -10000 0 0
FYN 0.026 0.055 0.27 1 -0.29 2 3
mol:NO 0.034 0.006 -10000 0 -10000 0 0
GNA15 0.036 0.019 -10000 0 -10000 0 0
PGK/cGMP 0.045 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.011 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.066 0.056 -10000 0 -0.34 1 1
NOS3 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.063 0.18 0.6 10 -0.35 39 49
PRKCB 0.053 0.17 0.61 9 -0.35 45 54
PRKCE 0.055 0.17 0.6 10 -0.36 43 53
PRKCD 0.053 0.18 0.63 9 -0.38 44 53
PRKCG 0.056 0.18 0.6 10 -0.38 44 54
muscle contraction 0.054 0.21 0.71 8 -0.47 45 53
PRKCZ 0.056 0.17 0.53 13 -0.34 44 57
ARR3 0.034 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.044 0.048 -10000 0 -0.25 5 5
PRKCQ 0.059 0.18 0.5 18 -0.35 44 62
MAPKKK cascade 0.054 0.2 0.68 8 -0.44 43 51
SELE 0.049 0.18 0.48 17 -0.38 48 65
TP beta/GNAI2/GDP/G beta/gamma 0.062 0.048 -10000 0 -0.34 1 1
ROCK1 0.033 0.006 -10000 0 -10000 0 0
GNA14 0.043 0.067 -10000 0 -0.54 4 4
chemotaxis 0.049 0.25 0.75 8 -0.59 48 56
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.033 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.026 0.005 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.04 0.016 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.033 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.02 0.081 -10000 0 -0.54 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.03 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.11 0.12 -10000 0 -0.23 236 236
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.031 0.027 -10000 0 -0.54 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
FYN 0.029 0.037 -10000 0 -0.54 2 2
MAP3K12 0.034 0.004 -10000 0 -10000 0 0
FGR 0.033 0.007 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.039 0.092 -10000 0 -0.31 37 37
PRKG1 0.034 0.005 -10000 0 -10000 0 0
DUSP8 0.033 0.007 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.013 0.12 -10000 0 -0.34 28 28
apoptosis -0.038 0.088 -10000 0 -0.3 37 37
RAL/GTP 0.044 0.01 -10000 0 -10000 0 0
LYN 0.03 0.015 -10000 0 -10000 0 0
DUSP1 -0.2 0.28 -10000 0 -0.54 209 209
PAK1 0.043 0.045 -10000 0 -10000 0 0
SRC 0.032 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.071 0.035 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.034 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.044 0.011 -10000 0 -10000 0 0
MAPK11 0.002 0.13 0.35 3 -0.36 31 34
BLK 0.039 0.043 -10000 0 -10000 0 0
HCK 0.036 0.022 -10000 0 -10000 0 0
MAP2K3 0.031 0.01 -10000 0 -10000 0 0
DUSP16 0.033 0.012 -10000 0 -10000 0 0
DUSP10 0.028 0.032 -10000 0 -0.54 1 1
TRAF6/MEKK3 0.038 0.015 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.13 0.33 3 -0.36 32 35
positive regulation of innate immune response 0.002 0.15 0.47 2 -0.42 34 36
LCK 0.048 0.043 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.015 0.15 0.58 1 -0.4 33 34
p38alpha-beta/MKP5 0.01 0.15 0.58 1 -0.41 30 31
PGK/cGMP 0.025 0.004 -10000 0 -10000 0 0
PAK2 0.033 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.086 0.2 -10000 0 -0.42 74 74
CDC42 0.033 0.007 -10000 0 -10000 0 0
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.034 0.005 -10000 0 -10000 0 0
PAK3 -0.31 0.28 -10000 0 -0.54 305 305
Regulation of Telomerase

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
Telomerase catalytic core complex -0.001 0.18 -10000 0 -0.81 9 9
RAD9A 0.031 0.01 -10000 0 -10000 0 0
AP1 -0.31 0.26 -10000 0 -0.46 353 353
IFNAR2 0.038 0.012 -10000 0 -10000 0 0
AKT1 -0.005 0.12 -10000 0 -0.38 13 13
ER alpha/Oestrogen -0.043 0.19 -10000 0 -0.39 110 110
NFX1/SIN3/HDAC complex 0.034 0.073 -10000 0 -0.33 13 13
EGF -0.15 0.27 -10000 0 -0.54 162 162
SMG5 0.029 0.016 -10000 0 -10000 0 0
SMG6 0.031 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.055 0.024 -10000 0 -10000 0 0
TERT/c-Abl 0.008 0.17 -10000 0 -0.78 8 8
SAP18 0.032 0.01 -10000 0 -10000 0 0
MRN complex 0.049 0.033 -10000 0 -10000 0 0
WT1 0.085 0.068 0.2 13 -10000 0 13
WRN 0.028 0.015 -10000 0 -10000 0 0
SP1 0.041 0.017 -10000 0 -10000 0 0
SP3 0.036 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.012 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.026 0.16 -10000 0 -0.7 8 8
Mad/Max 0.054 0.017 -10000 0 -10000 0 0
TERT -0.008 0.18 -10000 0 -0.89 8 8
CCND1 0.032 0.25 0.57 8 -1 14 22
MAX 0.035 0.01 -10000 0 -10000 0 0
RBBP7 0.038 0.021 -10000 0 -10000 0 0
RBBP4 0.034 0.006 -10000 0 -10000 0 0
TERF2 0.027 0.028 -10000 0 -0.49 1 1
PTGES3 0.033 0.026 -10000 0 -0.54 1 1
SIN3A 0.034 0.006 -10000 0 -10000 0 0
Telomerase/911 0.04 0.057 -10000 0 -0.45 2 2
CDKN1B 0.043 0.11 0.31 1 -0.61 10 11
RAD1 0.034 0.009 -10000 0 -10000 0 0
XRCC5 0.034 0.005 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
SAP30 0.034 0.009 -10000 0 -10000 0 0
TRF2/PARP2 0.042 0.028 -10000 0 -0.39 1 1
UBE3A 0.034 0.009 -10000 0 -10000 0 0
JUN -0.063 0.22 -10000 0 -0.54 86 86
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.028 0.012 -10000 0 -10000 0 0
FOS -0.36 0.27 -10000 0 -0.54 342 342
IFN-gamma/IRF1 0.081 0.083 0.29 3 -0.32 10 13
PARP2 0.033 0.006 -10000 0 -10000 0 0
BLM 0.073 0.065 -10000 0 -10000 0 0
Telomerase 0.005 0.092 -10000 0 -0.5 8 8
IRF1 0.045 0.047 -10000 0 -10000 0 0
ESR1 -0.059 0.26 0.18 36 -0.54 106 142
KU/TER 0.047 0.014 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.033 -10000 0 -0.29 1 1
ubiquitin-dependent protein catabolic process 0.043 0.067 -10000 0 -0.35 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.043 0.068 -10000 0 -0.36 6 6
HDAC1 0.034 0.006 -10000 0 -10000 0 0
HDAC2 0.038 0.021 -10000 0 -10000 0 0
ATM 0.017 0.021 0.21 1 -10000 0 1
SMAD3 0.009 0.016 -10000 0 -10000 0 0
ABL1 0.034 0.005 -10000 0 -10000 0 0
MXD1 0.037 0.009 -10000 0 -10000 0 0
MRE11A 0.03 0.011 -10000 0 -10000 0 0
HUS1 0.034 0.01 -10000 0 -10000 0 0
RPS6KB1 0.03 0.012 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.023 0.18 -10000 0 -0.74 11 11
NR2F2 0.008 0.094 -10000 0 -0.55 13 13
MAPK3 0.019 0.022 -10000 0 -0.4 1 1
MAPK1 0.019 0.022 -10000 0 -0.4 1 1
TGFB1/TGF beta receptor Type II 0.032 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
HNRNPC 0.033 0.006 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.017 0.021 0.21 1 -10000 0 1
NBN 0.028 0.015 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 264 264
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.31 0.26 -10000 0 -0.46 355 355
MYC -0.002 0.12 -10000 0 -0.54 25 25
IL2 0.039 0.031 -10000 0 -0.54 1 1
KU 0.047 0.014 -10000 0 -10000 0 0
RAD50 0.033 0.006 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
TGFB1 0.033 0.009 -10000 0 -10000 0 0
TRF2/BLM 0.065 0.055 -10000 0 -0.39 1 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.021 0.18 -10000 0 -0.78 8 8
SP1/HDAC2 0.06 0.032 -10000 0 -10000 0 0
PINX1 0.027 0.014 -10000 0 -10000 0 0
Telomerase/EST1A 0.021 0.16 -10000 0 -0.7 8 8
Smad3/Myc 0.005 0.082 -10000 0 -0.34 25 25
911 complex 0.061 0.025 0.25 1 -10000 0 1
IFNG 0.065 0.072 -10000 0 -0.22 9 9
Telomerase/PinX1 0.01 0.16 -10000 0 -0.7 8 8
Telomerase/AKT1/mTOR/p70S6K 0.021 0.12 -10000 0 -0.51 14 14
SIN3B 0.036 0.014 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.026 0.15 -10000 0 -0.72 7 7
response to DNA damage stimulus -0.001 0.03 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.061 0.051 -10000 0 -0.31 1 1
TRF2/WRN 0.036 0.03 -10000 0 -0.39 1 1
Telomerase/hnRNP C1/C2 0.026 0.16 -10000 0 -0.73 7 7
E2F1 0.053 0.047 0.2 7 -10000 0 7
ZNFX1 0.033 0.016 -10000 0 -10000 0 0
PIF1 0.038 0.028 -10000 0 -10000 0 0
NCL 0.033 0.006 -10000 0 -10000 0 0
DKC1 0.035 0.011 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.017 0.003 -10000 0 -10000 0 0
SMARCC1 0.017 0.054 -10000 0 -0.68 1 1
REL 0.036 0.022 -10000 0 -10000 0 0
HDAC7 -0.052 0.12 -10000 0 -0.35 33 33
JUN -0.064 0.22 -10000 0 -0.54 86 86
EP300 0.032 0.009 -10000 0 -10000 0 0
KAT2B 0 0 0.003 3 -10000 0 3
KAT5 0 0 -10000 0 -0.003 1 1
MAPK14 -0.003 0.063 -10000 0 -0.41 10 10
FOXO1 -0.023 0.17 -10000 0 -0.54 47 47
T-DHT/AR -0.026 0.14 -10000 0 -0.36 33 33
MAP2K6 0.008 0.084 -10000 0 -0.55 10 10
BRM/BAF57 0.046 0.018 -10000 0 -10000 0 0
MAP2K4 0.018 0.027 -10000 0 -10000 0 0
SMARCA2 0.033 0.009 -10000 0 -10000 0 0
PDE9A -0.059 0.26 -10000 0 -1 30 30
NCOA2 0.028 0.014 -10000 0 -10000 0 0
CEBPA 0.03 0.045 -10000 0 -0.54 3 3
EHMT2 0.034 0.004 -10000 0 -10000 0 0
cell proliferation 0.037 0.15 0.43 13 -0.46 3 16
NR0B1 -0.094 0.25 -10000 0 -0.54 118 118
EGR1 -0.43 0.23 -10000 0 -0.54 409 409
RXRs/9cRA 0.051 0.043 -10000 0 -0.31 4 4
AR/RACK1/Src 0.003 0.1 0.34 5 -0.34 7 12
AR/GR -0.04 0.14 -10000 0 -0.29 90 90
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
PKN1 0.034 0.01 -10000 0 -10000 0 0
RCHY1 0.028 0.051 -10000 0 -0.54 4 4
epidermal growth factor receptor activity 0 0.001 0.009 4 -10000 0 4
MAPK8 0.003 0.033 -10000 0 -0.44 1 1
T-DHT/AR/TIF2/CARM1 0.006 0.095 0.35 1 -0.37 6 7
SRC -0.011 0.072 -10000 0 -0.33 7 7
NR3C1 -0.011 0.15 -10000 0 -0.54 39 39
KLK3 -0.042 0.097 0.45 1 -10000 0 1
APPBP2 0.018 0.026 -10000 0 -10000 0 0
TRIM24 0.035 0.013 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.036 0.072 -10000 0 -0.36 11 11
TMPRSS2 -0.22 0.44 -10000 0 -1 120 120
RXRG 0.024 0.053 -10000 0 -0.54 4 4
mol:9cRA 0 0 0.003 4 -10000 0 4
RXRA 0.034 0.006 -10000 0 -10000 0 0
RXRB 0.034 0.005 -10000 0 -10000 0 0
CARM1 0.035 0.014 -10000 0 -10000 0 0
NR2C2 0.034 0.014 -10000 0 -10000 0 0
KLK2 0.013 0.078 0.34 3 -10000 0 3
AR -0.025 0.11 -10000 0 -0.27 62 62
SENP1 0.034 0.004 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
MDM2 0.032 0.013 -10000 0 -10000 0 0
SRY -0.001 0.002 -10000 0 -0.025 4 4
GATA2 0.041 0.032 -10000 0 -10000 0 0
MYST2 0 0.001 -10000 0 -0.006 4 4
HOXB13 0.078 0.068 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.001 0.1 0.35 6 -0.35 7 13
positive regulation of transcription 0.041 0.032 -10000 0 -10000 0 0
DNAJA1 0.019 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.032 -10000 0 -0.33 4 4
NCOA1 0.041 0.033 -10000 0 -0.57 1 1
SPDEF -0.02 0.17 -10000 0 -0.54 50 50
T-DHT/AR/TIF2 0.017 0.079 0.38 2 -0.32 4 6
T-DHT/AR/Hsp90 -0.011 0.099 0.36 2 -0.36 11 13
GSK3B 0.033 0.01 -10000 0 -10000 0 0
NR2C1 0.033 0.026 -10000 0 -0.54 1 1
mol:T-DHT -0.019 0.072 0.22 15 -0.36 10 25
SIRT1 0.034 0.005 -10000 0 -10000 0 0
ZMIZ2 0.032 0.008 -10000 0 -10000 0 0
POU2F1 0.003 0.065 -10000 0 -0.18 7 7
T-DHT/AR/DAX-1 -0.072 0.16 0.36 2 -0.34 109 111
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
SMARCE1 0.032 0.009 -10000 0 -10000 0 0
Syndecan-1-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
TGFB1 0.034 0.008 -10000 0 -10000 0 0
CCL5 0.028 0.06 -10000 0 -0.54 5 5
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
FGFR/FGF2/Syndecan-1 0.087 0.14 0.32 31 -0.36 7 38
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.069 0.14 0.29 14 -0.35 8 22
Syndecan-1/Syntenin 0.072 0.14 0.3 24 -0.36 7 31
MAPK3 0.072 0.13 0.29 21 -0.33 7 28
HGF/MET 0.005 0.14 -10000 0 -0.4 51 51
TGFB1/TGF beta receptor Type II 0.034 0.008 -10000 0 -10000 0 0
BSG 0.034 0.014 -10000 0 -10000 0 0
keratinocyte migration 0.069 0.14 0.29 14 -0.35 8 22
Syndecan-1/RANTES 0.076 0.15 0.31 22 -0.41 8 30
Syndecan-1/CD147 0.093 0.15 0.36 12 -0.35 7 19
Syndecan-1/Syntenin/PIP2 0.067 0.13 0.29 18 -0.34 7 25
LAMA5 0.032 0.012 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.065 0.13 0.28 19 -0.34 7 26
MMP7 -0.041 0.19 -10000 0 -0.54 63 63
HGF 0.034 0.01 -10000 0 -10000 0 0
Syndecan-1/CASK 0.058 0.13 0.25 23 -0.34 9 32
Syndecan-1/HGF/MET 0.063 0.18 0.34 10 -0.38 31 41
regulation of cell adhesion 0.062 0.12 0.32 7 -0.33 6 13
HPSE 0.045 0.039 -10000 0 -10000 0 0
positive regulation of cell migration 0.087 0.14 0.32 31 -0.36 7 38
SDC1 0.087 0.13 0.31 28 -0.35 3 31
Syndecan-1/Collagen 0.087 0.14 0.32 31 -0.36 7 38
PPIB 0.033 0.009 -10000 0 -10000 0 0
MET -0.023 0.17 -10000 0 -0.54 50 50
PRKACA 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.092 0.072 -10000 0 -10000 0 0
MAPK1 0.072 0.13 0.29 21 -0.34 6 27
homophilic cell adhesion 0.085 0.14 0.32 31 -0.35 7 38
MMP1 0.11 0.075 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.02 0.089 -10000 0 -0.48 1 1
UGCG 0.028 0.12 -10000 0 -0.65 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT 0 0.18 0.33 1 -0.4 42 43
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.029 0.11 -10000 0 -0.64 11 11
mol:DAG 0.005 0.11 -10000 0 -0.85 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.22 0.35 1 -0.41 84 85
FRAP1 -0.036 0.24 0.38 1 -0.47 85 86
FOXO3 0.005 0.18 0.37 3 -0.5 31 34
AKT1 0.002 0.2 0.38 1 -0.52 36 37
GAB2 0.027 0.014 -10000 0 -10000 0 0
SMPD1 0.008 0.12 -10000 0 -0.66 15 15
SGMS1 0.019 0.083 -10000 0 -0.62 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.027 0.096 -10000 0 -0.34 42 42
CALM1 0.033 0.006 -10000 0 -10000 0 0
cell proliferation 0.048 0.12 0.34 2 -0.44 11 13
EIF3A 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.005 0.12 -10000 0 -0.4 42 42
RPS6KB1 0 0.13 -10000 0 -0.83 8 8
mol:sphingomyelin 0.005 0.11 -10000 0 -0.85 7 7
natural killer cell activation -0.002 0.005 -10000 0 -0.02 3 3
JAK3 0.033 0.009 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
JAK1 0.033 0.01 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MYC 0.022 0.27 0.48 2 -0.92 31 33
MYB -0.049 0.34 -10000 0 -1.2 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.028 0.13 0.3 3 -0.36 17 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.13 -10000 0 -0.71 9 9
mol:PI-3-4-5-P3 0.03 0.13 0.3 3 -0.35 17 20
Rac1/GDP -0.01 0.094 -10000 0 -0.31 42 42
T cell proliferation 0.028 0.12 0.29 2 -0.33 16 18
SHC1 0.025 0.016 -10000 0 -10000 0 0
RAC1 0.033 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.028 0.092 25 -0.068 41 66
PRKCZ 0.027 0.12 0.29 2 -0.34 17 19
NF kappa B1 p50/RelA -0.009 0.23 0.37 1 -0.46 58 59
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.022 0.095 -10000 0 -0.39 8 8
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL2RA 0.039 0.035 -10000 0 -10000 0 0
IL2RB 0.035 0.023 -10000 0 -10000 0 0
TERT 0.032 0.028 -10000 0 -0.54 1 1
E2F1 0.012 0.14 0.33 1 -0.4 46 47
SOS1 0.032 0.009 -10000 0 -10000 0 0
RPS6 0.032 0.027 -10000 0 -0.54 1 1
mol:cAMP -0.002 0.014 0.032 41 -0.05 24 65
PTPN11 0.031 0.011 -10000 0 -10000 0 0
IL2RG 0.042 0.036 -10000 0 -10000 0 0
actin cytoskeleton organization 0.028 0.12 0.29 2 -0.33 16 18
GRB2 0.031 0.018 -10000 0 -10000 0 0
IL2 0.032 0.029 -10000 0 -0.54 1 1
PIK3CA 0.032 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.1 -10000 0 -0.29 42 42
LCK 0.047 0.045 -10000 0 -10000 0 0
BCL2 -0.12 0.38 0.52 1 -0.84 104 105
TCGA08_p53

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
CDKN2A 0.027 0.046 -10000 0 -10000 0 0
TP53 0 0.051 -10000 0 -0.19 30 30
Senescence -0.005 0.06 -10000 0 -0.19 39 39
Apoptosis -0.005 0.06 -10000 0 -0.19 39 39
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.009 0.067 0.3 18 -10000 0 18
MDM4 0.028 0.017 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.006 0.029 0.35 1 -0.34 1 2
SNTA1 0.032 0.027 -10000 0 -0.54 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.012 0.058 0.33 6 -0.34 1 7
MAPK12 0.008 0.086 0.21 39 -0.28 24 63
CCND1 0.008 0.083 0.21 1 -0.5 10 11
p38 gamma/SNTA1 0.027 0.086 0.39 1 -0.26 22 23
MAP2K3 0.031 0.01 -10000 0 -10000 0 0
PKN1 0.034 0.01 -10000 0 -10000 0 0
G2/M transition checkpoint 0.008 0.086 0.21 39 -0.27 24 63
MAP2K6 0.015 0.098 0.25 44 -0.3 25 69
MAPT 0.013 0.067 0.27 8 -0.26 10 18
MAPK13 0.018 0.027 -10000 0 -0.4 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.063 -10000 0 -0.33 17 17
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.037 0.15 -10000 0 -0.43 42 42
KLHL20 0.041 0.12 0.31 40 -0.26 14 54
CYFIP2 0.049 0.045 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.12 0.31 7 -0.35 5 12
ENAH -0.031 0.14 -10000 0 -0.44 33 33
AP1M1 0.034 0.005 -10000 0 -10000 0 0
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
CDC42/GTP 0.009 0.075 -10000 0 -0.29 2 2
ABI1/Sra1/Nap1 -0.016 0.04 -10000 0 -0.18 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.094 -10000 0 -0.31 25 25
RAPGEF1 -0.029 0.14 0.31 2 -0.4 36 38
CTNND1 0.033 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.16 -10000 0 -0.44 49 49
CRK -0.027 0.14 0.34 1 -0.43 37 38
E-cadherin/gamma catenin/alpha catenin 0.036 0.089 -10000 0 -0.34 21 21
alphaE/beta7 Integrin 0.046 0.015 -10000 0 -10000 0 0
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.055 0.042 -10000 0 -0.31 3 3
DLG1 -0.039 0.16 -10000 0 -0.43 47 47
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.06 -10000 0 -0.2 6 6
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GTP/NME1/Tiam1 0.058 0.025 -10000 0 -10000 0 0
PI3K -0.021 0.079 -10000 0 -0.27 5 5
ARF6 0.034 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.02 0.096 -10000 0 -0.33 31 31
TIAM1 0.035 0.012 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.046 0.088 -10000 0 -0.29 25 25
AKT1 -0.007 0.056 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
CDH1 0.006 0.12 -10000 0 -0.54 22 22
RhoA/GDP 0.001 0.12 0.3 7 -0.3 24 31
actin cytoskeleton organization 0.036 0.093 0.25 44 -0.19 12 56
CDC42/GDP 0.001 0.12 0.3 7 -0.35 5 12
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.004 0.067 -10000 0 -0.24 30 30
ITGB7 0.034 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.05 0.094 -10000 0 -0.31 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin 0.032 0.081 -10000 0 -0.29 25 25
mol:GDP -0.018 0.12 0.31 7 -0.35 24 31
CDC42/GTP/IQGAP1 0.043 0.013 -10000 0 -10000 0 0
JUP 0.033 0.01 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.007 0.12 0.32 5 -0.37 4 9
RAC1/GTP/IQGAP1 0.044 0.012 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.049 0.011 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.067 0.2 25 -0.23 11 36
NME1 0.031 0.011 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.036 0.16 -10000 0 -0.44 44 44
regulation of cell-cell adhesion 0 0.061 -10000 0 -0.26 2 2
WASF2 0.019 0.043 0.12 31 -0.12 2 33
Rap1/GTP 0.012 0.086 0.28 1 -0.33 2 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.059 0.092 -10000 0 -0.3 21 21
CCND1 0.016 0.079 0.23 22 -0.28 11 33
VAV2 -0.019 0.19 0.41 1 -0.68 15 16
RAP1/GDP 0.01 0.1 0.31 3 -0.36 3 6
adherens junction assembly -0.034 0.15 -10000 0 -0.43 44 44
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.033 0.006 -10000 0 -10000 0 0
PIP5K1C 0.034 0.009 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.044 0.088 -10000 0 -0.29 23 23
E-cadherin/beta catenin -0.007 0.089 -10000 0 -0.34 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.038 0.16 -10000 0 -0.44 45 45
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.011 0.14 0.28 57 -0.42 17 74
E-cadherin/beta catenin/alpha catenin 0.036 0.094 -10000 0 -0.34 25 25
ITGAE 0.031 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.032 0.17 -10000 0 -0.45 49 49
Noncanonical Wnt 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
NFATC2 0.03 0.027 -10000 0 -0.54 1 1
GNB1/GNG2 0.026 0.15 -10000 0 -0.45 25 25
mol:DAG 0.006 0.13 -10000 0 -0.42 23 23
PLCG1 0.005 0.13 -10000 0 -0.43 23 23
YES1 -0.002 0.13 0.25 1 -0.49 22 23
FZD3 0.014 0.092 -10000 0 -0.54 13 13
FZD6 0.006 0.11 -10000 0 -0.54 18 18
G protein 0.036 0.15 0.35 4 -0.43 23 27
MAP3K7 -0.005 0.11 0.25 1 -0.38 19 20
mol:Ca2+ 0.006 0.12 -10000 0 -0.41 23 23
mol:IP3 0.006 0.13 -10000 0 -0.42 23 23
NLK 0.004 0.13 -10000 0 -0.81 12 12
GNB1 0.034 0.011 -10000 0 -10000 0 0
CAMK2A 0 0.12 0.26 1 -0.41 19 20
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.015 0.13 -10000 0 -0.49 23 23
CSNK1A1 0.033 0.006 -10000 0 -10000 0 0
GNAS -0.005 0.13 0.25 1 -0.45 23 24
GO:0007205 0 0.12 -10000 0 -0.42 22 22
WNT6 0.033 0.04 -10000 0 -0.54 2 2
WNT4 0.04 0.033 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.017 0.14 -10000 0 -0.46 19 19
GNG2 0.032 0.026 -10000 0 -0.54 1 1
WNT5A 0.012 0.12 -10000 0 -0.54 23 23
WNT11 0.023 0.079 -10000 0 -0.54 9 9
CDC42 -0.003 0.12 -10000 0 -0.47 21 21
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.033 0.005 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
GNB1/GNG2 0.047 0.088 -10000 0 -0.34 23 23
forebrain development -0.044 0.2 -10000 0 -0.57 47 47
GNAO1 0.03 0.012 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.029 0.093 -10000 0 -0.4 22 22
SMO 0.012 0.12 -10000 0 -0.54 22 22
ARRB2 0.032 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.03 0.11 0.29 1 -0.48 9 10
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.077 0.031 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
XPO1 0.036 0.006 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.19 -10000 0 -0.66 26 26
SAP30 0.033 0.009 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 -10000 0 -0.54 22 22
MIM/GLI2A 0.033 0.029 0.31 1 -10000 0 1
IFT88 0.031 0.027 -10000 0 -0.54 1 1
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GLI2 0.016 0.084 -10000 0 -0.37 14 14
GLI3 0.016 0.11 0.3 1 -0.49 10 11
CSNK1D 0.032 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.008 -10000 0 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.031 0.027 -10000 0 -0.54 1 1
GNG2 0.032 0.026 -10000 0 -0.54 1 1
Gi family/GTP -0.083 0.16 -10000 0 -0.37 73 73
SIN3B 0.034 0.014 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.024 0.11 -10000 0 -0.46 14 14
GLI2/Su(fu) 0.019 0.11 -10000 0 -0.49 10 10
FOXA2 0.016 0.12 -10000 0 -0.7 11 11
neural tube patterning -0.044 0.2 -10000 0 -0.57 47 47
SPOP 0.03 0.011 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.027 0.064 -10000 0 -0.35 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
CSNK1G2 0.033 0.007 -10000 0 -10000 0 0
CSNK1G3 0.033 0.007 -10000 0 -10000 0 0
MTSS1 0.033 0.029 0.31 1 -10000 0 1
embryonic limb morphogenesis -0.044 0.2 -10000 0 -0.57 47 47
SUFU 0.019 0.05 -10000 0 -0.38 1 1
LGALS3 -0.029 0.18 -10000 0 -0.54 55 55
catabolic process 0.037 0.13 0.32 1 -0.6 12 13
GLI3A/CBP 0.001 0.12 -10000 0 -0.36 49 49
KIF3A 0.033 0.006 -10000 0 -10000 0 0
GLI1 -0.045 0.21 -10000 0 -0.58 47 47
RAB23 0.035 0.014 -10000 0 -10000 0 0
CSNK1A1 0.033 0.006 -10000 0 -10000 0 0
IFT172 0.033 0.026 -10000 0 -0.54 1 1
RBBP7 0.037 0.021 -10000 0 -10000 0 0
Su(fu)/Galectin3 -0.009 0.13 -10000 0 -0.33 58 58
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
RBBP4 0.033 0.006 -10000 0 -10000 0 0
CSNK1G1 0.033 0.007 -10000 0 -10000 0 0
PIAS1 0.033 0.007 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.028 0.088 -10000 0 -0.46 9 9
STK36 0.035 0.026 -10000 0 -0.54 1 1
Gi family/GNB1/GNG2/GDP -0.082 0.17 -10000 0 -0.39 70 70
PTCH1 -0.038 0.18 -10000 0 -0.69 18 18
MIM/GLI1 -0.024 0.18 -10000 0 -0.59 31 31
CREBBP 0.001 0.12 -10000 0 -0.36 49 49
Su(fu)/SIN3/HDAC complex 0.015 0.1 -10000 0 -0.46 16 16
Caspase cascade in apoptosis

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
TOP1 0.035 0.074 0.28 2 -0.34 8 10
ACTA1 0.007 0.083 0.24 3 -0.44 2 5
NUMA1 0.027 0.082 0.28 2 -0.38 8 10
SPTAN1 0.02 0.068 0.3 5 -0.48 1 6
LIMK1 0.033 0.074 0.28 12 -0.48 1 13
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BIRC2 0.03 0.011 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
CASP10 -0.003 0.04 0.24 8 -0.34 1 9
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 -10000 0 -0.001 36 36
PTK2 0.029 0.094 0.28 3 -0.47 9 12
DIABLO 0.034 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes 0.02 0.067 0.3 5 -0.48 1 6
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.034 0.005 -10000 0 -10000 0 0
GSN -0.054 0.13 0.35 1 -0.29 88 89
MADD 0.034 0.005 -10000 0 -10000 0 0
TFAP2A 0.04 0.099 -10000 0 -0.72 6 6
BID 0.013 0.025 0.16 9 -0.2 1 10
MAP3K1 0.01 0.096 -10000 0 -0.38 24 24
TRADD 0.029 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.049 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.025 0.07 0.3 5 -0.48 1 6
CASP9 0.033 0.008 -10000 0 -10000 0 0
DNA repair -0.034 0.059 0.32 3 -0.22 9 12
neuron apoptosis 0.01 0.14 -10000 0 -0.69 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.024 0.074 0.32 1 -0.63 1 2
APAF1 0.034 0.003 -10000 0 -10000 0 0
CASP6 0.022 0.14 -10000 0 -0.85 11 11
TRAF2 0.034 0.012 -10000 0 -10000 0 0
ICAD/CAD 0.017 0.062 0.31 1 -0.47 1 2
CASP7 0.015 0.081 0.27 19 -0.33 3 22
KRT18 0.035 0.095 -10000 0 -0.73 6 6
apoptosis 0.012 0.1 0.31 2 -0.44 9 11
DFFA 0.02 0.065 0.28 3 -0.48 1 4
DFFB 0.02 0.064 0.28 3 -0.48 1 4
PARP1 0.034 0.059 0.22 9 -0.32 3 12
actin filament polymerization 0.017 0.13 0.27 57 -0.29 10 67
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.023 0.045 0.2 9 -0.2 5 14
SATB1 -0.011 0.16 -10000 0 -0.78 13 13
SLK 0.02 0.068 0.29 4 -0.38 2 6
p15 BID/BAX 0.026 0.051 -10000 0 -0.31 3 3
CASP2 0.004 0.083 -10000 0 -0.32 13 13
JNK cascade -0.01 0.095 0.37 25 -10000 0 25
CASP3 0.024 0.07 0.31 3 -0.51 1 4
LMNB2 0.019 0.13 0.35 2 -0.52 20 22
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CASP4 0.024 0.058 -10000 0 -0.54 5 5
Mammalian IAPs/DIABLO 0.045 0.078 -10000 0 -0.31 17 17
negative regulation of DNA binding 0.04 0.097 -10000 0 -0.71 6 6
stress fiber formation 0.019 0.067 0.29 4 -0.37 2 6
GZMB 0.022 0.046 0.29 7 -0.4 2 9
CASP1 -0.016 0.12 -10000 0 -0.4 40 40
LMNB1 0.041 0.13 0.35 3 -0.57 13 16
APP 0.009 0.14 -10000 0 -0.7 18 18
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
response to stress 0 0 0.001 19 -0.001 26 45
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM 0.014 0.11 0.31 2 -0.46 9 11
LMNA 0.022 0.082 0.33 2 -0.38 8 10
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.087 -10000 0 -0.32 17 17
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.027 0.069 0.28 4 -0.41 1 5
APAF-1/Caspase 9 0.018 0.11 -10000 0 -0.6 15 15
nuclear fragmentation during apoptosis 0.027 0.081 0.28 2 -0.37 8 10
CFL2 -0.018 0.13 0.3 10 -0.28 60 70
GAS2 -0.15 0.15 0.3 5 -0.28 241 246
positive regulation of apoptosis 0.035 0.12 0.37 2 -0.48 17 19
PRF1 0.037 0.022 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.035 0.031 -10000 0 -0.54 1 1
ANTXR2 0.022 0.08 -10000 0 -0.54 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.01 -10000 0 -0.073 11 11
monocyte activation 0.013 0.085 -10000 0 -0.35 24 24
MAP2K2 0.005 0.094 -10000 0 -0.57 13 13
MAP2K1 -0.005 0.01 -10000 0 -10000 0 0
MAP2K7 -0.005 0.01 -10000 0 -10000 0 0
MAP2K6 -0.01 0.042 0.082 2 -0.3 10 12
CYAA -0.01 0.043 -10000 0 -0.29 11 11
MAP2K4 -0.005 0.012 -10000 0 -0.18 1 1
IL1B -0.012 0.048 0.18 2 -0.25 10 12
Channel 0.036 0.053 -10000 0 -0.31 11 11
NLRP1 -0.007 0.028 -10000 0 -0.27 5 5
CALM1 0.033 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.002 0.073 -10000 0 -0.41 15 15
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.01 0.073 11 -10000 0 11
MAPK3 -0.005 0.01 -10000 0 -10000 0 0
MAPK1 -0.005 0.01 -10000 0 -10000 0 0
PGR -0.063 0.14 0.086 112 -0.29 141 253
PA/Cellular Receptors 0.037 0.058 -10000 0 -0.34 11 11
apoptosis -0.002 0.01 -10000 0 -0.073 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.035 0.05 -10000 0 -0.29 11 11
macrophage activation -0.006 0.01 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
VCAM1 0.013 0.085 -10000 0 -0.36 24 24
platelet activation 0.002 0.073 -10000 0 -0.41 15 15
MAPKKK cascade -0.003 0.03 0.12 3 -0.14 6 9
IL18 -0.001 0.04 0.14 1 -0.18 9 10
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.073 11 11
LEF -0.002 0.011 -10000 0 -0.073 11 11
CASP1 -0.006 0.033 -10000 0 -0.11 35 35
mol:cAMP 0.002 0.074 -10000 0 -0.41 15 15
necrosis -0.002 0.01 -10000 0 -0.073 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.035 0.05 -10000 0 -0.29 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.058 0.055 -9999 0 -10000 0 0
mol:Halofuginone 0.003 0.004 -9999 0 -10000 0 0
ITGA1 0.031 0.037 -9999 0 -0.54 2 2
CDKN1A -0.08 0.099 -9999 0 -0.53 16 16
PRL-3/alpha Tubulin 0.042 0.027 -9999 0 -10000 0 0
mol:Ca2+ -0.005 0.042 -9999 0 -10000 0 0
AGT 0.041 0.047 -9999 0 -10000 0 0
CCNA2 -0.18 0.12 -9999 0 -10000 0 0
TUBA1B 0.035 0.012 -9999 0 -10000 0 0
EGR1 -0.31 0.16 -9999 0 -0.39 407 407
CDK2/Cyclin E1 -0.042 0.11 -9999 0 -0.46 16 16
MAPK3 0.015 0.018 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.051 0.017 -9999 0 -10000 0 0
MAPK1 0.015 0.019 -9999 0 -10000 0 0
PTP4A1 -0.22 0.13 -9999 0 -10000 0 0
PTP4A3 0.03 0.025 -9999 0 -10000 0 0
PTP4A2 0.036 0.02 -9999 0 -10000 0 0
ITGB1 0.015 0.019 -9999 0 -10000 0 0
SRC 0.032 0.008 -9999 0 -10000 0 0
RAC1 -0.058 0.079 -9999 0 -0.49 8 8
Rab GGTase beta/Rab GGTase alpha 0.048 0.011 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.21 0.12 -9999 0 -10000 0 0
RABGGTA 0.033 0.006 -9999 0 -10000 0 0
BCAR1 -0.019 0.018 -9999 0 -10000 0 0
RHOC -0.059 0.084 -9999 0 -0.52 9 9
RHOA -0.065 0.1 -9999 0 -0.54 15 15
cell motility -0.084 0.095 -9999 0 -0.48 13 13
PRL-1/alpha Tubulin -0.21 0.12 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin 0.04 0.034 -9999 0 -0.4 1 1
ROCK1 -0.082 0.095 -9999 0 -0.48 12 12
RABGGTB 0.033 0.006 -9999 0 -10000 0 0
CDK2 0.037 0.021 -9999 0 -10000 0 0
mitosis -0.22 0.13 -9999 0 -10000 0 0
ATF5 0.034 0.012 -9999 0 -10000 0 0
E-cadherin signaling 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
E-cadherin/beta catenin-gamma catenin 0.035 0.093 -9999 0 -0.34 24 24
E-cadherin/beta catenin 0.019 0.1 -9999 0 -0.4 25 25
CTNNB1 0.03 0.045 -9999 0 -0.54 3 3
JUP 0.033 0.01 -9999 0 -10000 0 0
CDH1 0.006 0.12 -9999 0 -0.54 22 22
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.028 0.015 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.048 0.14 -10000 0 -0.45 16 16
NEF 0.011 0.022 -10000 0 -10000 0 0
NFKBIA 0.029 0.036 -10000 0 -0.35 1 1
BIRC3 0.008 0.14 0.38 1 -0.5 25 26
CYCS 0.034 0.13 0.28 15 -0.44 14 29
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CD247 0.029 0.11 -10000 0 -0.55 15 15
MAP2K7 0.04 0.18 0.35 1 -0.7 17 18
protein ubiquitination 0.015 0.11 0.37 2 -0.39 15 17
CRADD 0.034 0.005 -10000 0 -10000 0 0
DAXX 0.034 0.008 -10000 0 -10000 0 0
FAS -0.002 0.14 -10000 0 -0.54 32 32
BID 0.032 0.13 0.25 8 -0.45 16 24
NF-kappa-B/RelA/I kappa B alpha 0.06 0.086 -10000 0 -0.3 16 16
TRADD 0.029 0.012 -10000 0 -10000 0 0
MAP3K5 0.004 0.12 -10000 0 -0.54 25 25
CFLAR 0.032 0.026 -10000 0 -0.54 1 1
FADD 0.028 0.015 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.06 0.086 -10000 0 -0.31 16 16
MAPK8 0.039 0.17 0.48 2 -0.67 15 17
APAF1 0.034 0.003 -10000 0 -10000 0 0
TRAF1 0.035 0.015 -10000 0 -10000 0 0
TRAF2 0.034 0.012 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.037 0.14 0.26 7 -0.46 17 24
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.13 -10000 0 -0.49 17 17
CHUK 0.013 0.12 0.37 2 -0.43 15 17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.039 0.12 -10000 0 -0.33 39 39
TCRz/NEF 0.023 0.084 -10000 0 -0.41 15 15
TNF 0.038 0.023 -10000 0 -10000 0 0
FASLG 0.036 0.11 0.31 43 -0.37 15 58
NFKB1 0.03 0.034 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.053 0.034 -10000 0 -10000 0 0
CASP6 0.053 0.15 -10000 0 -0.56 13 13
CASP7 0.021 0.19 0.39 16 -0.48 37 53
RELA 0.03 0.033 -10000 0 -0.17 1 1
CASP2 0.033 0.006 -10000 0 -10000 0 0
CASP3 0.017 0.19 0.4 15 -0.48 39 54
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.023 -10000 0 -10000 0 0
CASP8 0.034 0.005 -10000 0 -10000 0 0
CASP9 0.033 0.007 -10000 0 -10000 0 0
MAP3K14 0.016 0.13 0.36 1 -0.46 16 17
APAF-1/Caspase 9 0.019 0.13 0.25 2 -0.37 29 31
BCL2 -0.006 0.18 0.52 4 -0.56 20 24
FoxO family signaling

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
G6PC 0.004 0.097 -10000 0 -10000 0 0
PLK1 0.13 0.22 0.62 18 -0.86 4 22
CDKN1B 0.099 0.18 0.55 5 -0.45 14 19
FOXO3 0.11 0.23 0.54 24 -0.62 16 40
KAT2B 0.02 0.031 0.084 39 -0.054 16 55
FOXO1/SIRT1 0.006 0.1 -10000 0 -0.33 9 9
CAT 0.054 0.37 0.68 7 -1 42 49
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
AKT1 0.052 0.045 0.22 1 -10000 0 1
FOXO1 0.002 0.11 -10000 0 -0.28 33 33
MAPK10 0.024 0.059 0.22 6 -0.29 10 16
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
FOXO4 0.045 0.12 0.41 4 -0.38 9 13
response to oxidative stress 0.023 0.032 0.089 39 -0.055 13 52
FOXO3A/SIRT1 0.084 0.2 0.46 14 -0.58 16 30
XPO1 0.034 0.005 -10000 0 -10000 0 0
EP300 0.035 0.009 -10000 0 -10000 0 0
BCL2L11 0.057 0.082 -10000 0 -0.82 3 3
FOXO1/SKP2 0.016 0.1 -10000 0 -0.28 14 14
mol:GDP 0.023 0.032 0.089 39 -0.055 13 52
RAN 0.034 0.005 -10000 0 -10000 0 0
GADD45A 0.081 0.21 0.5 1 -0.8 15 16
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.036 0.15 -10000 0 -0.54 20 20
MST1 0.047 0.042 -10000 0 -10000 0 0
CSNK1D 0.032 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.026 0.14 -10000 0 -0.48 23 23
YWHAB 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.029 0.041 0.24 3 -0.27 1 4
MAPK9 0.029 0.04 0.24 3 -10000 0 3
YWHAG 0.034 0.008 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
SIRT1 0.022 0.023 -10000 0 -10000 0 0
SOD2 0.096 0.2 0.56 9 -0.56 11 20
RBL2 0.037 0.32 0.56 2 -0.77 46 48
RAL/GDP 0.057 0.035 -10000 0 -10000 0 0
CHUK 0.048 0.042 -10000 0 -10000 0 0
Ran/GTP 0.024 0.014 -10000 0 -10000 0 0
CSNK1G2 0.033 0.007 -10000 0 -10000 0 0
RAL/GTP 0.057 0.041 -10000 0 -10000 0 0
CSNK1G1 0.033 0.007 -10000 0 -10000 0 0
FASLG 0.075 0.12 -10000 0 -1.4 1 1
SKP2 0.035 0.018 -10000 0 -10000 0 0
USP7 0.032 0.01 -10000 0 -10000 0 0
IKBKB 0.041 0.041 -10000 0 -10000 0 0
CCNB1 0.15 0.24 0.6 20 -0.84 4 24
FOXO1-3a-4/beta catenin 0.097 0.22 0.53 12 -0.4 47 59
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.1 -10000 0 -0.28 14 14
CSNK1A1 0.033 0.006 -10000 0 -10000 0 0
SGK1 0.02 0.031 0.084 39 -0.054 16 55
CSNK1G3 0.033 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.02 -10000 0 -10000 0 0
ZFAND5 0.045 0.11 0.43 3 -0.38 1 4
SFN 0.033 0.04 -10000 0 -0.54 2 2
CDK2 0.039 0.021 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.055 0.13 -10000 0 -0.48 15 15
CREBBP 0.032 0.028 -10000 0 -0.54 1 1
FBXO32 0.12 0.35 0.65 26 -1.1 25 51
BCL6 0.021 0.4 -10000 0 -1.1 53 53
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.034 0.006 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.015 0.13 -9999 0 -0.49 23 23
FZD6 0.006 0.11 -9999 0 -0.54 18 18
WNT6 0.033 0.04 -9999 0 -0.54 2 2
WNT4 0.04 0.033 -9999 0 -10000 0 0
FZD3 0.014 0.092 -9999 0 -0.54 13 13
WNT5A 0.012 0.12 -9999 0 -0.54 23 23
WNT11 0.023 0.079 -9999 0 -0.54 9 9
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.016 0.15 0.36 6 -0.38 17 23
IKBKB 0.05 0.091 0.34 8 -0.31 3 11
AKT1 0.062 0.12 0.32 44 -0.25 2 46
IKBKG 0.056 0.077 0.33 8 -0.28 3 11
CALM1 0.031 0.086 0.28 8 -0.35 9 17
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
MAP3K1 0.067 0.14 0.42 5 -0.49 12 17
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.031 0.091 0.28 8 -0.34 11 19
DOK1 0.036 0.016 -10000 0 -10000 0 0
AP-1 -0.074 0.11 0.32 1 -0.24 65 66
LYN 0.03 0.015 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
BCR complex 0.041 0.07 0.25 3 -0.4 10 13
CD22 0.015 0.089 0.31 3 -0.45 11 14
CAMK2G 0.029 0.084 0.26 11 -0.37 6 17
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.023 0.044 -10000 0 -0.27 6 6
GO:0007205 0.032 0.092 0.28 8 -0.35 11 19
SYK 0.039 0.027 -10000 0 -10000 0 0
ELK1 0.033 0.09 0.28 8 -0.38 7 15
NFATC1 0.063 0.11 0.32 10 -0.41 8 18
B-cell antigen/BCR complex 0.041 0.07 0.25 3 -0.4 10 13
PAG1/CSK 0.043 0.028 0.25 1 -10000 0 1
NFKBIB 0.043 0.052 0.21 9 -0.13 13 22
HRAS 0.044 0.094 0.27 14 -0.35 8 22
NFKBIA 0.043 0.051 0.21 9 -0.12 10 19
NF-kappa-B/RelA/I kappa B beta 0.047 0.048 0.21 9 -10000 0 9
RasGAP/Csk 0.064 0.079 0.34 2 -0.39 6 8
mol:GDP 0.032 0.089 0.27 8 -0.32 12 20
PTEN 0.025 0.068 -10000 0 -0.54 7 7
CD79B 0.02 0.081 -10000 0 -0.54 10 10
NF-kappa-B/RelA/I kappa B alpha 0.047 0.047 0.21 9 -10000 0 9
GRB2 0.033 0.017 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.049 0.15 0.39 8 -0.46 16 24
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 0.03 0.09 0.29 7 -0.36 10 17
CSK 0.034 0.011 -10000 0 -10000 0 0
FOS -0.15 0.14 0.27 1 -0.36 59 60
CHUK 0.053 0.084 0.33 8 -0.3 8 16
IBTK 0.033 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.054 0.09 0.3 4 -0.36 6 10
PTPN6 0.03 0.1 0.28 9 -0.55 6 15
RELA 0.034 0.005 -10000 0 -10000 0 0
BCL2A1 0.042 0.043 0.2 9 -10000 0 9
VAV2 0.044 0.11 0.32 2 -0.57 6 8
ubiquitin-dependent protein catabolic process 0.046 0.052 0.21 9 -0.12 15 24
BTK 0.017 0.091 -10000 0 -0.97 4 4
CD19 0.022 0.093 0.31 3 -0.43 11 14
MAP4K1 0.036 0.02 -10000 0 -10000 0 0
CD72 0.062 0.058 -10000 0 -10000 0 0
PAG1 0.031 0.025 -10000 0 -10000 0 0
MAPK14 0.064 0.13 0.4 8 -0.42 12 20
SH3BP5 0.017 0.095 -10000 0 -0.54 14 14
PIK3AP1 0.029 0.096 0.33 6 -0.4 10 16
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.047 0.095 0.31 4 -0.44 7 11
RAF1 0.042 0.09 0.26 12 -0.4 4 16
RasGAP/p62DOK/SHIP 0.054 0.071 0.3 1 -0.37 6 7
CD79A 0.041 0.033 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.071 0.11 0.32 1 -0.24 58 59
RASA1 0.033 0.011 -10000 0 -10000 0 0
MAPK3 0.048 0.091 0.29 17 -0.34 4 21
MAPK1 0.038 0.083 0.3 6 -0.34 4 10
CD72/SHP1 0.092 0.12 0.37 18 -0.52 6 24
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.064 0.13 0.38 9 -0.42 12 21
actin cytoskeleton organization 0.069 0.11 0.32 17 -0.49 6 23
NF-kappa-B/RelA 0.092 0.087 0.37 8 -0.22 2 10
Calcineurin 0.042 0.091 0.28 1 -0.34 8 9
PI3K -0.001 0.073 -10000 0 -0.4 7 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.032 0.095 0.29 9 -0.42 10 19
SOS1 0.034 0.004 -10000 0 -10000 0 0
Bam32/HPK1 0.064 0.16 -10000 0 -0.63 16 16
DAPP1 0.031 0.16 -10000 0 -0.7 17 17
cytokine secretion 0.062 0.11 0.3 15 -0.38 8 23
mol:DAG 0.03 0.09 0.29 7 -0.36 10 17
PLCG2 0.021 0.074 -10000 0 -0.54 8 8
MAP2K1 0.039 0.087 0.28 6 -0.37 4 10
B-cell antigen/BCR complex/FcgammaRIIB 0.046 0.074 0.34 1 -0.43 7 8
mol:PI-3-4-5-P3 0.031 0.1 0.32 18 -0.3 6 24
ETS1 0.026 0.081 0.26 12 -0.34 7 19
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.075 0.079 0.43 1 -0.3 9 10
B-cell antigen/BCR complex/LYN 0.016 0.084 -10000 0 -0.47 11 11
MALT1 0.033 0.009 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.062 0.11 0.33 14 -0.52 6 20
B-cell antigen/BCR complex/LYN/SYK 0.043 0.098 0.35 2 -0.53 6 8
CARD11 0.033 0.094 0.28 12 -0.35 9 21
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
PPP3CA 0.029 0.052 -10000 0 -0.54 4 4
BCL10 0.033 0.007 -10000 0 -10000 0 0
IKK complex 0.044 0.058 0.18 31 -0.14 1 32
PTPRC 0.035 0.034 -10000 0 -10000 0 0
PDPK1 0.038 0.095 0.28 29 -0.22 4 33
PPP3CB 0.034 0.004 -10000 0 -10000 0 0
PPP3CC 0.024 0.046 -10000 0 -0.54 3 3
POU2F2 0.036 0.038 0.24 5 -10000 0 5
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.098 0.13 0.37 20 -10000 0 20
regulation of axonogenesis -0.021 0.05 0.24 1 -10000 0 1
myoblast fusion -0.065 0.073 -10000 0 -0.24 10 10
mol:GTP 0.048 0.044 -10000 0 -0.16 2 2
regulation of calcium-dependent cell-cell adhesion -0.09 0.065 -10000 0 -0.25 7 7
ARF1/GTP 0.052 0.043 -10000 0 -10000 0 0
mol:GM1 0.033 0.04 -10000 0 -10000 0 0
mol:Choline 0.018 0.075 -10000 0 -0.31 19 19
lamellipodium assembly 0.056 0.079 0.25 7 -0.33 1 8
MAPK3 0.071 0.077 0.21 114 -10000 0 114
ARF6/GTP/NME1/Tiam1 0.092 0.067 0.25 7 -10000 0 7
ARF1 0.027 0.014 -10000 0 -10000 0 0
ARF6/GDP 0.065 0.073 0.24 10 -10000 0 10
ARF1/GDP 0.056 0.069 -10000 0 -10000 0 0
ARF6 0.054 0.025 -10000 0 -10000 0 0
RAB11A 0.033 0.006 -10000 0 -10000 0 0
TIAM1 0.039 0.014 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.073 0.079 0.21 121 -10000 0 121
actin filament bundle formation -0.075 0.063 -10000 0 -0.23 7 7
KALRN 0.04 0.056 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.045 0.017 -10000 0 -10000 0 0
RhoA/GDP 0.076 0.064 0.23 7 -10000 0 7
NME1 0.035 0.015 -10000 0 -10000 0 0
Rac1/GDP 0.078 0.063 0.23 7 -10000 0 7
substrate adhesion-dependent cell spreading 0.048 0.044 -10000 0 -0.16 2 2
cortical actin cytoskeleton organization 0.056 0.079 0.25 7 -0.33 1 8
RAC1 0.034 0.005 -10000 0 -10000 0 0
liver development 0.048 0.044 -10000 0 -0.16 2 2
ARF6/GTP 0.048 0.044 -10000 0 -0.16 2 2
RhoA/GTP 0.062 0.04 -10000 0 -10000 0 0
mol:GDP 0.052 0.076 0.2 100 -0.2 1 101
ARF6/GTP/RAB11FIP3/RAB11A 0.075 0.044 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
PLD1 0.029 0.085 -10000 0 -0.35 19 19
RAB11FIP3 0.031 0.01 -10000 0 -10000 0 0
tube morphogenesis 0.056 0.079 0.25 7 -0.33 1 8
ruffle organization 0.021 0.05 -10000 0 -0.24 1 1
regulation of epithelial cell migration 0.048 0.044 -10000 0 -0.16 2 2
PLD2 0.042 0.045 -10000 0 -0.36 1 1
PIP5K1A 0.021 0.05 -10000 0 -0.24 1 1
mol:Phosphatidic acid 0.018 0.075 -10000 0 -0.31 19 19
Rac1/GTP 0.056 0.079 0.25 7 -0.33 1 8
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.087 0.074 0.31 1 -0.28 5 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.032 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.098 0.11 0.4 35 -10000 0 35
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.063 0.055 -10000 0 -0.34 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.003 0.096 0.16 4 -0.28 35 39
CaM/Ca2+ 0.085 0.071 -10000 0 -0.27 5 5
RAP1A 0.034 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.074 0.088 0.31 24 -0.27 5 29
AKT1 0.019 0.11 0.33 8 -0.33 14 22
MAP2K1 0.026 0.073 0.31 4 -0.26 3 7
MAP3K11 0.043 0.069 0.32 4 -0.27 5 9
IFNGR1 0.03 0.058 -10000 0 -0.54 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.047 0.089 -10000 0 -0.44 7 7
Rap1/GTP 0.018 0.035 -10000 0 -10000 0 0
CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.095 0.075 -10000 0 -0.3 5 5
CEBPB 0.057 0.14 0.4 8 -0.55 6 14
STAT3 0.033 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.092 0.1 -10000 0 -0.75 4 4
STAT1 0.058 0.092 0.3 27 -0.27 5 32
CALM1 0.033 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.061 0.063 -10000 0 -0.55 1 1
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.074 0.089 0.3 27 -0.27 2 29
CEBPB/PTGES2/Cbp/p300 0.039 0.085 0.29 3 -0.37 5 8
mol:Ca2+ 0.082 0.071 0.29 1 -0.28 5 6
MAPK3 0.042 0.12 -10000 0 -0.63 9 9
STAT1 (dimer) 0.021 0.15 0.32 3 -0.43 23 26
MAPK1 0.01 0.2 -10000 0 -0.7 33 33
JAK2 0.035 0.016 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
JAK1 0.036 0.013 -10000 0 -10000 0 0
CAMK2D 0.029 0.052 -10000 0 -0.54 4 4
DAPK1 0.058 0.11 0.4 13 -0.35 4 17
SMAD7 0.022 0.07 0.23 8 -0.19 5 13
CBL/CRKL/C3G 0.069 0.069 0.33 3 -10000 0 3
PI3K 0.05 0.12 -10000 0 -0.31 31 31
IFNG 0.061 0.063 -10000 0 -0.55 1 1
apoptosis 0.048 0.12 0.38 11 -0.46 9 20
CAMK2G 0.034 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.033 0.007 -10000 0 -10000 0 0
CAMK2A 0.033 0.006 -10000 0 -10000 0 0
CAMK2B 0.039 0.064 -10000 0 -0.54 4 4
FRAP1 0.003 0.1 0.3 10 -0.36 7 17
PRKCD 0.019 0.11 0.34 9 -0.39 5 14
RAP1B 0.033 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.003 0.096 0.16 4 -0.28 35 39
PTPN2 0.033 0.007 -10000 0 -10000 0 0
EP300 0.033 0.009 -10000 0 -10000 0 0
IRF1 0.066 0.11 0.4 35 -10000 0 35
STAT1 (dimer)/PIASy 0.072 0.09 0.3 26 -0.27 2 28
SOCS1 0.018 0.1 -10000 0 -1 5 5
mol:GDP 0.064 0.065 0.31 3 -10000 0 3
CASP1 0.006 0.11 0.25 11 -0.27 55 66
PTGES2 0.034 0.005 -10000 0 -10000 0 0
IRF9 0.052 0.068 0.27 17 -10000 0 17
mol:PI-3-4-5-P3 0.032 0.1 -10000 0 -0.3 31 31
RAP1/GDP 0.051 0.051 -10000 0 -10000 0 0
CBL 0.04 0.068 0.31 4 -0.27 5 9
MAP3K1 0.045 0.071 0.33 3 -0.27 6 9
PIAS1 0.033 0.007 -10000 0 -10000 0 0
PIAS4 0.034 0.015 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.003 0.096 0.16 4 -0.28 35 39
PTPN11 0.044 0.072 0.3 6 -0.28 5 11
CREBBP 0.031 0.028 -10000 0 -0.54 1 1
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.042 0.027 -10000 0 -10000 0 0
CDKN1B 0.019 0.07 0.31 3 -0.36 6 9
CDKN1A 0.021 0.065 0.28 2 -0.35 8 10
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.031 0.019 -10000 0 -10000 0 0
FOXO3 0.024 0.061 0.28 1 -0.38 5 6
AKT1 0.022 0.063 -10000 0 -0.33 12 12
BAD 0.033 0.007 -10000 0 -10000 0 0
AKT3 0.015 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.02 0.061 -10000 0 -0.35 8 8
AKT1/ASK1 0.034 0.093 -10000 0 -0.35 8 8
BAD/YWHAZ 0.051 0.032 -10000 0 -10000 0 0
RICTOR 0.033 0.006 -10000 0 -10000 0 0
RAF1 0.033 0.006 -10000 0 -10000 0 0
JNK cascade -0.033 0.091 0.34 8 -10000 0 8
TSC1 0.021 0.055 -10000 0 -0.37 5 5
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
AKT1/RAF1 0.056 0.076 0.3 2 -0.35 8 10
EP300 0.032 0.008 -10000 0 -10000 0 0
mol:GDP 0.022 0.062 -10000 0 -0.32 12 12
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.027 0.079 0.28 21 -0.35 8 29
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.003 0.046 0.25 2 -0.32 9 11
MAP3K5 0.004 0.12 -10000 0 -0.54 25 25
MAPKAP1 0.034 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.042 0.078 0.28 9 -0.28 2 11
YWHAH 0.033 0.014 -10000 0 -10000 0 0
AKT1S1 0.023 0.066 -10000 0 -0.35 8 8
CASP9 0.022 0.047 -10000 0 -0.3 4 4
YWHAB 0.032 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.05 0.083 0.32 4 -0.34 7 11
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
SRC 0.032 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.023 0.061 -10000 0 -0.32 8 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.054 -10000 0 -0.33 9 9
CHUK 0.021 0.059 -10000 0 -0.35 7 7
BAD/BCL-XL 0.057 0.072 0.3 2 -0.35 6 8
mTORC2 0.042 0.01 -10000 0 -10000 0 0
AKT2 0.017 0.006 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.044 0.11 0.37 4 -0.39 11 15
PDPK1 0.031 0.01 -10000 0 -10000 0 0
MDM2 0.025 0.069 0.28 4 -0.35 8 12
MAPKKK cascade -0.055 0.074 0.34 8 -0.3 2 10
MDM2/Cbp/p300 0.061 0.08 0.36 2 -0.37 4 6
TSC1/TSC2 0.025 0.079 0.28 22 -0.34 8 30
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.077 0.35 2 -0.35 4 6
glucose import -0.15 0.15 0.21 1 -0.31 235 236
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.021 0.054 0.18 3 -0.3 4 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 0.21 1 -0.31 235 236
GSK3A 0.021 0.063 -10000 0 -0.35 8 8
FOXO1 -0.004 0.093 -10000 0 -0.41 8 8
GSK3B 0.021 0.061 0.28 1 -0.35 7 8
SFN 0.033 0.04 -10000 0 -0.54 2 2
G1/S transition of mitotic cell cycle 0.032 0.075 0.33 2 -0.34 8 10
p27Kip1/14-3-3 family 0.031 0.044 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
KPNA1 0.034 0.005 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
RHEB 0.034 0.008 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.004 0.13 0.28 1 -0.46 21 22
BAG4 0.028 0.015 -10000 0 -10000 0 0
BAD 0.007 0.047 0.2 2 -0.19 5 7
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BAX 0.007 0.051 0.3 2 -0.18 8 10
EnzymeConsortium:3.1.4.12 0.003 0.032 0.089 4 -0.099 18 22
IKBKB 0.012 0.12 0.35 1 -0.45 14 15
MAP2K2 0.012 0.059 0.23 10 -0.24 1 11
MAP2K1 0.012 0.06 0.23 11 -0.24 1 12
SMPD1 0.004 0.04 0.16 2 -0.16 11 13
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.032 0.14 0.36 4 -0.43 20 24
MAP2K4 0.007 0.052 0.2 2 -0.24 5 7
protein ubiquitination 0.002 0.13 0.36 3 -0.43 20 23
EnzymeConsortium:2.7.1.37 0.011 0.062 0.25 8 -0.24 2 10
response to UV 0 0.001 0.003 11 -0.002 1 12
RAF1 0.011 0.06 0.23 11 -0.23 2 13
CRADD 0.034 0.005 -10000 0 -10000 0 0
mol:ceramide 0.008 0.049 0.16 3 -0.15 19 22
I-kappa-B-alpha/RELA/p50/ubiquitin 0.043 0.014 -10000 0 -0.14 1 1
MADD 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.008 0.054 0.2 2 -0.24 7 9
TRADD 0.03 0.012 -10000 0 -10000 0 0
RELA/p50 0.034 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.06 0.23 11 -0.24 1 12
MAPK1 0.01 0.068 0.23 11 -0.24 4 15
p50/RELA/I-kappa-B-alpha 0.048 0.016 -10000 0 -0.17 1 1
FADD 0.027 0.14 0.3 8 -0.45 18 26
KSR1 0.012 0.057 0.2 14 -0.19 5 19
MAPK8 0.004 0.056 0.28 3 -0.24 5 8
TRAF2 0.034 0.012 -10000 0 -10000 0 0
response to radiation 0 0 0.003 2 -10000 0 2
CHUK -0.006 0.12 -10000 0 -0.46 18 18
TNF R/SODD 0.038 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.025 0.07 0.19 19 -0.18 6 25
IKBKG -0.006 0.12 0.45 1 -0.45 18 19
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.002 0.14 -10000 0 -0.48 21 21
RELA 0.034 0.005 -10000 0 -10000 0 0
RIPK1 0.033 0.006 -10000 0 -10000 0 0
AIFM1 0.024 0.069 0.19 18 -0.18 7 25
TNF/TNF R/SODD 0.053 0.034 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
response to heat 0 0 0.003 2 -10000 0 2
CASP8 0.019 0.12 -10000 0 -0.66 15 15
NSMAF 0.016 0.13 0.28 4 -0.44 19 23
response to hydrogen peroxide 0 0.001 0.003 11 -0.002 1 12
BCL2 -0.074 0.22 -10000 0 -0.54 94 94
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
AKT1 0.026 0.14 0.36 3 -0.46 14 17
PTK2B 0.015 0.085 0.36 2 -0.43 1 3
VEGFR2 homodimer/Frs2 0.021 0.087 -10000 0 -0.33 27 27
CAV1 -0.38 0.26 -10000 0 -0.54 360 360
CALM1 0.033 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.048 0.092 -10000 0 -0.3 22 22
endothelial cell proliferation 0.051 0.13 0.39 11 -0.44 8 19
mol:Ca2+ 0.02 0.091 0.37 1 -0.5 4 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.068 0.093 -10000 0 -0.29 22 22
RP11-342D11.1 0.002 0.087 0.27 1 -0.54 4 5
CDH5 0.03 0.012 -10000 0 -10000 0 0
VEGFA homodimer 0.069 0.059 -10000 0 -0.28 3 3
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 0.006 0.12 -10000 0 -0.54 24 24
HRAS/GDP 0.03 0.08 -10000 0 -0.41 4 4
SH2D2A 0.043 0.047 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.056 0.12 -10000 0 -0.48 10 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.048 0.095 -10000 0 -0.31 19 19
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.056 0.1 -10000 0 -0.44 4 4
GRB10 0.017 0.11 -10000 0 -0.61 7 7
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
PAK1 0.043 0.045 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.067 0.099 -10000 0 -0.43 1 1
HRAS 0.034 0.013 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.027 0.081 -10000 0 -0.37 8 8
HIF1A 0.031 0.054 -10000 0 -0.54 4 4
FRS2 0.032 0.029 -10000 0 -0.54 1 1
oxygen and reactive oxygen species metabolic process 0.065 0.091 -10000 0 -0.29 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.033 0.006 -10000 0 -10000 0 0
Nck/Pak 0.052 0.037 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.044 0.095 -10000 0 -0.31 26 26
mol:GDP 0.042 0.09 -10000 0 -0.43 4 4
mol:NADP 0.032 0.11 0.58 1 -0.42 13 14
eNOS/Hsp90 0.046 0.11 0.57 1 -0.4 12 13
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 0.02 0.092 0.37 1 -0.5 4 5
HIF1A/ARNT 0.037 0.042 -10000 0 -0.4 3 3
SHB 0.035 0.018 -10000 0 -10000 0 0
VEGFA 0.05 0.047 -10000 0 -10000 0 0
VEGFC 0.02 0.084 -10000 0 -0.54 11 11
FAK1/Vinculin 0.04 0.11 0.37 1 -0.41 4 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.067 0.096 -10000 0 -0.29 24 24
PTPN6 0.033 0.015 -10000 0 -10000 0 0
EPAS1 0.009 0.14 -10000 0 -0.54 29 29
mol:L-citrulline 0.032 0.11 0.58 1 -0.42 13 14
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.062 0.093 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.049 0.11 -10000 0 -0.35 25 25
VEGFR2/3 heterodimer 0.022 0.088 -10000 0 -0.34 28 28
VEGFB 0.033 0.006 -10000 0 -10000 0 0
MAPK11 0.002 0.1 -10000 0 -0.46 8 8
VEGFR2 homodimer 0.003 0.096 -10000 0 -0.39 28 28
FLT1 0.032 0.013 -10000 0 -10000 0 0
NEDD4 0.028 0.058 -10000 0 -0.54 5 5
MAPK3 0.016 0.094 0.37 1 -0.45 4 5
MAPK1 0.012 0.094 0.34 2 -0.45 4 6
VEGFA145/NRP2 0.06 0.037 0.25 1 -10000 0 1
VEGFR1/2 heterodimer 0.021 0.088 -10000 0 -0.34 28 28
KDR 0.003 0.096 -10000 0 -0.39 28 28
VEGFA165/NRP1/VEGFR2 homodimer 0.052 0.1 -10000 0 -0.54 4 4
SRC 0.032 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.018 0.098 0.37 2 -0.46 4 6
PI3K 0.018 0.12 -10000 0 -0.5 8 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.05 0.092 -10000 0 -0.31 24 24
FES 0.017 0.096 -10000 0 -0.55 4 4
GAB1 0.041 0.1 -10000 0 -0.41 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.049 0.089 -10000 0 -0.31 21 21
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
SOS1 0.034 0.004 -10000 0 -10000 0 0
ARNT 0.027 0.014 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.13 0.15 -10000 0 -0.44 40 40
VEGFR2 homodimer/VEGFA homodimer/Yes 0.048 0.093 -10000 0 -0.31 24 24
PI3K/GAB1 0.029 0.14 0.39 1 -0.45 14 15
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.075 0.096 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.031 0.1 -10000 0 -0.32 38 38
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
CDC42 0.019 0.098 0.37 1 -0.55 4 5
actin cytoskeleton reorganization 0.048 0.094 -10000 0 -0.31 19 19
PTK2 0.023 0.091 -10000 0 -0.4 6 6
EDG1 0.002 0.087 0.27 1 -0.54 4 5
mol:DAG 0.02 0.092 0.37 1 -0.5 4 5
CaM/Ca2+ 0.033 0.088 -10000 0 -0.47 4 4
MAP2K3 0.003 0.087 -10000 0 -0.53 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.045 0.12 -10000 0 -0.63 7 7
PLCG1 0.02 0.093 0.37 1 -0.51 4 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.066 0.093 -10000 0 -0.44 1 1
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
YES1 0.031 0.027 -10000 0 -0.54 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.051 0.093 -10000 0 -0.31 24 24
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.048 0.092 -10000 0 -0.31 23 23
cell migration 0.044 0.11 0.39 2 -0.47 2 4
mol:PI-3-4-5-P3 0.018 0.11 -10000 0 -0.47 8 8
FYN 0.029 0.037 -10000 0 -0.54 2 2
VEGFB/NRP1 0.022 0.09 -10000 0 -0.52 4 4
mol:NO 0.032 0.11 0.58 1 -0.42 13 14
PXN 0.034 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.013 0.071 -10000 0 -0.41 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.037 0.11 -10000 0 -0.62 7 7
VHL 0.035 0.018 -10000 0 -10000 0 0
ITGB3 0.035 0.018 -10000 0 -10000 0 0
NOS3 0.031 0.12 0.6 1 -0.47 13 14
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.12 -10000 0 -0.32 38 38
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.006 0.08 0.37 1 -0.44 4 5
PRKCB 0.005 0.085 0.36 1 -0.48 4 5
VCL 0.034 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.026 0.094 -10000 0 -0.54 4 4
VEGFR1/2 heterodimer/VEGFA homodimer 0.046 0.093 -10000 0 -0.31 24 24
VEGFA165/NRP2 0.06 0.037 0.25 1 -10000 0 1
MAPKKK cascade 0.062 0.12 0.39 5 -0.56 5 10
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFC homodimer 0.02 0.084 -10000 0 -0.54 11 11
NCK1 0.034 0.005 -10000 0 -10000 0 0
ROCK1 0.033 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.11 0.44 2 -0.41 4 6
MAP3K13 0.017 0.095 -10000 0 -0.55 4 4
PDPK1 0.005 0.098 0.29 1 -0.42 8 9
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.034 0.005 -10000 0 -10000 0 0
SPHK1 0.033 0.059 -10000 0 -0.54 4 4
GNAI2 0.033 0.01 -10000 0 -10000 0 0
mol:S1P 0.02 0.034 0.2 2 -0.26 4 6
GNAO1 0.03 0.012 -10000 0 -10000 0 0
mol:Sphinganine-1-P 0.018 0.045 -10000 0 -0.4 4 4
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.053 0.04 -10000 0 -0.21 2 2
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.045 0.017 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.011 0.031 -10000 0 -0.24 4 4
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
S1P/S1P5/G12 0.042 0.039 -10000 0 -0.22 4 4
S1P/S1P3/Gq 0.036 0.053 -10000 0 -0.29 6 6
S1P/S1P4/Gi -0.067 0.15 0.27 1 -0.34 59 60
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
GNA14 0.043 0.067 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.033 0.006 -10000 0 -10000 0 0
ABCC1 0.035 0.023 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.017 0.1 -9999 0 -0.54 16 16
PLK4 0.055 0.051 -9999 0 -10000 0 0
regulation of centriole replication 0.024 0.085 -9999 0 -0.39 15 15
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.033 0.006 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 64 64
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
NUDC 0.033 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.069 0.091 -10000 0 -0.32 20 20
CaM/Ca2+ 0.025 0.004 -10000 0 -10000 0 0
KATNA1 0.032 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.029 0.079 0.28 3 -0.31 14 17
IQGAP1/CaM 0.047 0.014 -10000 0 -10000 0 0
DAB1 0.033 0.006 -10000 0 -10000 0 0
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
PLA2G7 0.043 0.097 -10000 0 -0.54 10 10
CALM1 0.033 0.006 -10000 0 -10000 0 0
DYNLT1 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.072 0.047 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.034 0.007 -10000 0 -10000 0 0
CDK5R1 0.033 0.014 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.011 0.004 -10000 0 -10000 0 0
CDK5R2 0.034 0.005 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.007 0.16 -10000 0 -0.36 79 79
YWHAE 0.031 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.041 0.079 0.38 2 -0.32 2 4
MAP1B -0.022 0.09 -10000 0 -0.29 49 49
RAC1 0.016 0.007 -10000 0 -10000 0 0
p35/CDK5 0.034 0.074 0.27 3 -0.28 13 16
RELN 0.012 0.11 -10000 0 -0.54 20 20
PAFAH/LIS1 0.039 0.067 -10000 0 -0.34 10 10
LIS1/CLIP170 0.034 0.014 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.032 0.069 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.008 0.13 -10000 0 -0.3 54 54
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.025 0.074 0.32 4 -0.33 2 6
LIS1/IQGAP1 0.032 0.014 -10000 0 -10000 0 0
RHOA 0.016 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.015 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.08 0.067 -10000 0 -10000 0 0
PAFAH1B2 0.03 0.011 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.005 0.076 -10000 0 -0.36 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.048 0.087 0.36 3 -0.31 2 5
LRP8 0.071 0.063 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.035 0.082 0.38 2 -0.32 2 4
P39/CDK5 0.035 0.073 0.27 2 -0.28 13 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.013 -10000 0 -10000 0 0
CDK5 0.006 0.076 0.28 2 -0.3 13 15
PPP2R5D 0.033 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.029 0.012 -10000 0 -10000 0 0
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.002 0.14 -10000 0 -0.32 79 79
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 79 79
CDC42 0.016 0.007 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.079 0.054 0.39 6 -10000 0 6
MAP4K1 0.036 0.02 -10000 0 -10000 0 0
MAP3K8 -0.039 0.19 -10000 0 -0.54 64 64
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.035 0.012 -10000 0 -10000 0 0
CRKL 0.032 0.008 -10000 0 -10000 0 0
MAP3K1 0.031 0.058 0.3 3 -0.3 4 7
JUN -0.039 0.13 -10000 0 -0.36 37 37
MAP3K7 0.029 0.052 0.27 3 -0.27 3 6
GRAP2 0.034 0.019 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
MAP2K4 0.002 0.1 0.28 3 -0.35 20 23
LAT 0.035 0.024 -10000 0 -10000 0 0
LCP2 0.036 0.023 -10000 0 -10000 0 0
MAPK8 0.011 0.081 -10000 0 -0.58 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.037 0.06 0.26 6 -0.29 4 10
LAT/GRAP2/SLP76/HPK1/HIP-55 0.089 0.059 0.39 6 -10000 0 6
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.021 0.15 -10000 0 -10000 0 0
CRKL 0.015 0.067 0.3 3 -10000 0 3
mol:DAG 0.024 0.074 -10000 0 -10000 0 0
HRAS 0.05 0.088 0.33 12 -10000 0 12
MAPK8 0.047 0.075 0.27 12 -0.32 1 13
RAP1A 0.015 0.067 0.3 3 -10000 0 3
GAB1 0.016 0.066 0.3 2 -10000 0 2
MAPK14 0.048 0.073 0.26 14 -10000 0 14
EPO 0.045 0.051 -10000 0 -10000 0 0
PLCG1 0.024 0.075 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.028 0.024 -10000 0 -10000 0 0
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.053 0.077 -10000 0 -0.35 10 10
GAB1/SHC/GRB2/SOS1 0.043 0.064 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.052 0.047 -10000 0 -10000 0 0
IRS2 -0.054 0.14 -10000 0 -0.32 91 91
STAT1 0.041 0.12 -10000 0 -0.36 2 2
STAT5B 0.028 0.1 -10000 0 -10000 0 0
cell proliferation 0.025 0.08 0.26 15 -0.3 1 16
GAB1/SHIP/PIK3R1/SHP2/SHC 0.003 0.085 -10000 0 -0.34 1 1
TEC 0.016 0.067 0.3 3 -10000 0 3
SOCS3 0.019 0.084 -10000 0 -0.54 11 11
STAT1 (dimer) 0.041 0.12 -10000 0 -0.35 2 2
JAK2 0.031 0.018 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
EPO/EPOR (dimer)/JAK2 0.067 0.091 -10000 0 -10000 0 0
EPO/EPOR 0.052 0.047 -10000 0 -10000 0 0
LYN 0.021 0.026 -10000 0 -10000 0 0
TEC/VAV2 0.032 0.072 0.29 4 -10000 0 4
elevation of cytosolic calcium ion concentration 0.028 0.024 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.054 0.058 -10000 0 -10000 0 0
mol:IP3 0.024 0.074 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.07 0.15 -10000 0 -0.31 118 118
SH2B3 0.033 0.016 -10000 0 -10000 0 0
NFKB1 0.047 0.073 0.27 13 -10000 0 13
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.048 -10000 0 -0.23 9 9
PTPN6 0.01 0.06 -10000 0 -10000 0 0
TEC/VAV2/GRB2 0.045 0.075 -10000 0 -10000 0 0
EPOR 0.028 0.024 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.04 0.065 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG2 0.021 0.074 -10000 0 -0.54 8 8
CRKL/CBL/C3G 0.038 0.077 -10000 0 -10000 0 0
VAV2 0.018 0.068 0.3 4 -10000 0 4
CBL 0.014 0.066 0.3 3 -10000 0 3
SHC/Grb2/SOS1 0.029 0.059 -10000 0 -10000 0 0
STAT5A 0.027 0.1 -10000 0 -0.32 1 1
GRB2 0.033 0.017 -10000 0 -10000 0 0
STAT5 (dimer) 0.023 0.15 -10000 0 -0.37 16 16
LYN/PLCgamma2 0.029 0.061 0.24 1 -0.35 10 11
PTPN11 0.034 0.004 -10000 0 -10000 0 0
BTK 0.02 0.07 0.3 3 -10000 0 3
BCL2 -0.093 0.36 -10000 0 -0.82 98 98
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.073 0.038 -10000 0 -0.32 1 1
HDAC3 0.033 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.002 -10000 0 -10000 0 0
GATA1/HDAC4 0.049 0.01 -10000 0 -10000 0 0
GATA1/HDAC5 0.048 0.011 -10000 0 -10000 0 0
GATA2/HDAC5 0.053 0.025 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.024 0.12 -10000 0 -0.34 48 48
HDAC9 0.035 0.016 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.033 0.11 -10000 0 -0.34 39 39
HDAC4/ANKRA2 0.045 0.032 -10000 0 -0.4 2 2
HDAC5/YWHAB 0.046 0.016 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.02 -10000 0 -0.17 3 3
GATA2 0.041 0.032 -10000 0 -10000 0 0
HDAC4/RFXANK 0.048 0.012 -10000 0 -10000 0 0
BCOR 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.031 0.028 -10000 0 -0.54 1 1
HDAC5 0.033 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.047 0.024 -10000 0 -0.4 1 1
Histones 0.024 0.05 -10000 0 -0.28 4 4
ADRBK1 0.031 0.01 -10000 0 -10000 0 0
HDAC4 0.033 0.006 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.045 0.033 -10000 0 -0.4 2 2
HDAC4/Ubc9 0.045 0.017 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.045 0.018 -10000 0 -0.17 1 1
TUBA1B 0.035 0.012 -10000 0 -10000 0 0
HDAC6 0.034 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.048 0.013 -10000 0 -10000 0 0
CAMK4 0.035 0.017 -10000 0 -10000 0 0
Tubulin/HDAC6 0.059 0.057 -10000 0 -0.34 9 9
SUMO1 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.032 0.008 -10000 0 -10000 0 0
GATA1 0.034 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
NR3C1 -0.011 0.15 -10000 0 -0.54 39 39
SUMO1/HDAC4 0.051 0.051 -10000 0 -0.25 3 3
SRF 0.033 0.006 -10000 0 -10000 0 0
HDAC4/YWHAB 0.046 0.015 -10000 0 -10000 0 0
Tubulin 0.041 0.061 -10000 0 -0.4 9 9
HDAC4/14-3-3 E 0.045 0.019 -10000 0 -0.17 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
RANGAP1 0.038 0.029 -10000 0 -10000 0 0
BCL6/BCoR 0.005 0.13 -10000 0 -0.39 50 50
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.017 -10000 0 -10000 0 0
HDAC4/SRF 0.065 0.021 -10000 0 -10000 0 0
HDAC4/ER alpha -0.029 0.2 -10000 0 -0.39 110 110
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.024 0.05 -10000 0 -0.28 4 4
cell motility 0.059 0.056 -10000 0 -0.34 9 9
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
HDAC7/HDAC3 0.025 0.004 -10000 0 -10000 0 0
BCL6 -0.023 0.17 -10000 0 -0.54 49 49
HDAC4/CaMK II delta B 0.033 0.006 -10000 0 -10000 0 0
Hsp90/HDAC6 0.049 0.01 -10000 0 -10000 0 0
ESR1 -0.06 0.26 0.18 103 -0.54 106 209
HDAC6/HDAC11 0.052 0.019 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.051 0.049 -10000 0 -0.26 3 3
NPC 0.02 0.002 -10000 0 -10000 0 0
MEF2C 0.005 0.12 -10000 0 -0.54 25 25
RAN 0.034 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.066 0.092 -10000 0 -0.3 24 24
GNG2 0.032 0.026 -10000 0 -0.54 1 1
NCOR2 0.034 0.004 -10000 0 -10000 0 0
TUBB2A 0.023 0.077 -10000 0 -0.54 9 9
HDAC11 0.038 0.025 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
ANKRA2 0.03 0.037 -10000 0 -0.54 2 2
RFXANK 0.034 0.005 -10000 0 -10000 0 0
nuclear import -0.038 0.02 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.011 0.11 -10000 0 -0.54 19 19
positive regulation of NF-kappaB transcription factor activity 0.022 0.085 -10000 0 -0.38 20 20
MAP2K4 0.015 0.085 -10000 0 -0.4 12 12
IKBKB 0.029 0.013 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.028 0.018 -10000 0 -10000 0 0
SMPD1 0.004 0.057 -10000 0 -0.27 18 18
IKBKG 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.014 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.022 0.086 -10000 0 -0.37 21 21
TRAIL/TRAILR3 0.023 0.086 -10000 0 -0.38 20 20
TRAIL/TRAILR1 0.023 0.086 -10000 0 -0.37 21 21
TRAIL/TRAILR4 0.023 0.086 -10000 0 -0.38 20 20
TRAIL/TRAILR1/DAP3/GTP 0.031 0.066 -10000 0 -0.31 13 13
IKK complex 0.024 0.074 -10000 0 -0.42 5 5
RIPK1 0.033 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.01 -10000 0 -10000 0 0
MAPK3 0 0.079 -10000 0 -0.4 19 19
MAP3K1 0.016 0.099 -10000 0 -0.42 16 16
TRAILR4 (trimer) 0.027 0.014 -10000 0 -10000 0 0
TRADD 0.029 0.012 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.028 0.018 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.081 -10000 0 -0.37 15 15
CFLAR 0.032 0.026 -10000 0 -0.54 1 1
MAPK1 0.001 0.077 -10000 0 -0.4 18 18
TRAIL/TRAILR1/FADD/TRADD/RIP 0.047 0.079 -10000 0 -0.29 14 14
mol:ceramide 0.004 0.057 -10000 0 -0.26 18 18
FADD 0.028 0.015 -10000 0 -10000 0 0
MAPK8 -0.001 0.1 -10000 0 -0.4 17 17
TRAF2 0.034 0.012 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.027 0.017 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.033 0.073 -10000 0 -0.33 14 14
DAP3 0.028 0.013 -10000 0 -10000 0 0
CASP10 0.024 0.077 0.34 3 -0.34 5 8
JNK cascade 0.022 0.085 -10000 0 -0.38 20 20
TRAIL (trimer) 0.011 0.11 -10000 0 -0.54 19 19
TNFRSF10C 0.028 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.035 0.064 -10000 0 -0.29 9 9
TRAIL/TRAILR2/FADD 0.032 0.074 -10000 0 -0.34 14 14
cell death 0.004 0.057 -10000 0 -0.26 18 18
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.002 0.081 -10000 0 -0.36 16 16
TRAILR2 (trimer) 0.027 0.016 -10000 0 -10000 0 0
CASP8 0.02 0.057 -10000 0 -0.58 3 3
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.046 0.08 -10000 0 -0.3 14 14
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.012 0.018 0.14 11 -10000 0 11
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.053 0.028 -10000 0 -10000 0 0
STXBP1 0.034 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.023 0.03 -10000 0 -0.16 1 1
RAB3GAP2/RIMS1/UNC13B 0.057 0.037 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.041 0.034 -10000 0 -10000 0 0
mol:ACh 0 0.031 0.092 12 -0.12 10 22
RAB3GAP2 0.028 0.014 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.041 0.054 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.023 0.03 -10000 0 -0.16 1 1
UNC13B 0.034 0.014 -10000 0 -10000 0 0
CHRNA1 0.034 0.01 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.052 0.077 0.17 13 -0.33 9 22
SNAP25 0.007 0.035 -10000 0 -0.3 5 5
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 0.069 0.1 0.18 159 -0.54 8 167
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.033 0.014 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.041 0.054 -10000 0 -10000 0 0
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.037 0.039 -10000 0 -0.34 4 4
VEGFR1 homodimer/NRP1 0.015 0.034 -10000 0 -0.33 4 4
mol:DAG 0.019 0.041 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.042 0.044 -10000 0 -0.3 3 3
CaM/Ca2+ 0.037 0.04 -10000 0 -10000 0 0
HIF1A 0.039 0.055 -10000 0 -0.54 4 4
GAB1 0.033 0.027 -10000 0 -0.54 1 1
AKT1 -0.007 0.097 -10000 0 -0.4 1 1
PLCG1 0.019 0.041 -10000 0 -10000 0 0
NOS3 0.02 0.081 -10000 0 -0.45 5 5
CBL 0.03 0.011 -10000 0 -10000 0 0
mol:NO 0.021 0.088 -10000 0 -0.45 6 6
FLT1 0.021 0.043 -10000 0 -0.39 4 4
PGF 0.034 0.011 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.061 0.05 -10000 0 -0.31 3 3
CALM1 0.033 0.006 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
eNOS/Hsp90 0.037 0.09 -10000 0 -0.44 6 6
endothelial cell proliferation 0.027 0.069 0.46 1 -10000 0 1
mol:Ca2+ 0.019 0.041 -10000 0 -10000 0 0
MAPK3 -0.005 0.035 0.25 1 -10000 0 1
MAPK1 -0.006 0.038 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
PLGF homodimer 0.034 0.011 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.38 0.26 -10000 0 -0.54 360 360
VEGFA homodimer 0.05 0.046 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.046 0.049 -10000 0 -0.34 3 3
platelet activating factor biosynthetic process 0.019 0.073 0.34 2 -10000 0 2
PI3K 0.038 0.11 -10000 0 -0.56 1 1
PRKCA -0.004 0.04 0.26 1 -10000 0 1
PRKCB -0.003 0.039 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.038 0.039 -10000 0 -0.34 4 4
VEGFA 0.05 0.046 -10000 0 -10000 0 0
VEGFB 0.033 0.006 -10000 0 -10000 0 0
mol:IP3 0.019 0.041 -10000 0 -10000 0 0
RASA1 0.02 0.042 -10000 0 -10000 0 0
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer 0.021 0.043 -10000 0 -0.39 4 4
VEGFB homodimer 0.033 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.16 0.15 -10000 0 -0.49 20 20
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.036 0.11 -10000 0 -0.55 1 1
mol:L-citrulline 0.021 0.088 -10000 0 -0.45 6 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.075 0.058 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.061 0.049 -10000 0 -10000 0 0
CD2AP 0.033 0.009 -10000 0 -10000 0 0
PI3K/GAB1 0.048 0.12 -10000 0 -0.54 1 1
PDPK1 -0.001 0.093 -10000 0 -0.36 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.062 0.049 -10000 0 -10000 0 0
mol:NADP 0.021 0.088 -10000 0 -0.45 6 6
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.071 0.055 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.038 0.04 -10000 0 -0.34 4 4
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.1 0.085 -10000 0 -10000 0 0
CLOCK 0.038 0.009 -10000 0 -10000 0 0
TIMELESS/CRY2 0.068 0.069 -10000 0 -10000 0 0
DEC1/BMAL1 0.051 0.025 -10000 0 -0.4 1 1
ATR 0.033 0.006 -10000 0 -10000 0 0
NR1D1 0.04 0.052 -10000 0 -10000 0 0
ARNTL 0.037 0.028 -10000 0 -0.54 1 1
TIMELESS 0.058 0.09 -10000 0 -10000 0 0
NPAS2 0.041 0.019 -10000 0 -10000 0 0
CRY2 0.034 0.005 -10000 0 -10000 0 0
mol:CO -0.02 0.03 -10000 0 -0.11 53 53
CHEK1 0.086 0.073 -10000 0 -10000 0 0
mol:HEME 0.02 0.03 0.11 53 -10000 0 53
PER1 0.024 0.063 -10000 0 -0.54 6 6
BMAL/CLOCK/NPAS2 0.087 0.044 -10000 0 -0.34 1 1
BMAL1/CLOCK 0.057 0.073 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.1 0.085 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.1 0.086 -10000 0 -10000 0 0
mol:NADPH 0.02 0.03 0.11 53 -10000 0 53
PER1/TIMELESS 0.059 0.074 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.034 0.01 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.027 0.026 -10000 0 -10000 0 0
CRKL 0.032 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DOCK1 0.03 0.045 -10000 0 -0.54 3 3
ITGA4 0.039 0.028 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.084 0.032 -10000 0 -10000 0 0
EPO 0.053 0.049 0.18 69 -10000 0 69
alpha4/beta7 Integrin 0.053 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.052 0.022 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.062 0.036 -10000 0 -10000 0 0
lamellipodium assembly -0.003 0.11 -10000 0 -0.37 17 17
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
PI3K 0.006 0.12 -10000 0 -0.38 46 46
ARF6 0.034 0.005 -10000 0 -10000 0 0
JAK2 0.042 0.034 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
MADCAM1 0.034 0.013 -10000 0 -10000 0 0
cell adhesion 0.081 0.031 -10000 0 -10000 0 0
CRKL/CBL 0.044 0.018 -10000 0 -10000 0 0
ITGB1 0.033 0.006 -10000 0 -10000 0 0
SRC 0.02 0.064 0.38 2 -0.31 11 13
ITGB7 0.034 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.061 0.067 -10000 0 -0.34 11 11
p130Cas/Crk/Dock1 0.04 0.071 0.37 1 -0.28 14 15
VCAM1 0.023 0.086 -10000 0 -0.54 11 11
RHOA 0.033 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.081 0.035 -10000 0 -10000 0 0
BCAR1 -0.007 0.061 0.39 2 -0.29 11 13
EPOR 0.034 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.11 -10000 0 -0.39 16 16
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.032 0.008 -10000 0 -10000 0 0
HDAC4 0.033 0.006 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.008 -10000 0 -10000 0 0
CDKN1A -0.01 0.044 -10000 0 -0.66 2 2
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
FOXO3 -0.006 0.004 -10000 0 -10000 0 0
FOXO1 -0.023 0.17 -10000 0 -0.54 47 47
FOXO4 0.017 0.015 -10000 0 -0.28 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
TAT 0.031 0.035 -10000 0 -0.54 1 1
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0.03 -10000 0 -0.4 2 2
PPARGC1A -0.024 0.18 -10000 0 -0.54 51 51
FHL2 -0.024 0.18 -10000 0 -0.54 52 52
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.044 0.016 -10000 0 -10000 0 0
HIST2H4A -0.005 0.008 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.022 0.03 -10000 0 -0.2 1 1
SIRT1 0.03 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.053 0.029 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.051 0.053 -10000 0 -0.23 3 3
apoptosis -0.061 0.022 -10000 0 -10000 0 0
SIRT1/PGC1A 0.003 0.12 -10000 0 -0.34 50 50
p53/SIRT1 0.036 0.024 0.42 1 -10000 0 1
SIRT1/FOXO4 0.032 0.045 -10000 0 -0.23 3 3
FOXO1/FHL2/SIRT1 -0.018 0.16 -10000 0 -0.34 88 88
HIST1H1E 0.039 0.043 -10000 0 -0.28 1 1
SIRT1/p300 0.044 0.015 -10000 0 -10000 0 0
muscle cell differentiation -0.018 0.026 0.34 2 -10000 0 2
TP53 0.028 0.017 0.22 1 -10000 0 1
KU70/SIRT1/BAX 0.062 0.022 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
MEF2D 0.028 0.013 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.041 0.033 -10000 0 -0.4 1 1
ACSS2 0.014 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.018 0.026 -10000 0 -0.34 2 2
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.047 0.037 -10000 0 -0.29 3 3
RGS9BP 0.053 0.064 -10000 0 -0.54 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.043 0.042 0.22 1 -0.34 2 3
mol:ADP 0.008 0.019 0.14 1 -0.4 1 2
GNAT2 0.03 0.045 -10000 0 -0.54 3 3
RGS9-1/Gbeta5/R9AP 0.048 0.1 -10000 0 -0.32 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.04 0.039 -10000 0 -0.34 4 4
GRK7 0.033 0.027 -10000 0 -0.54 1 1
CNGB3 0.032 0.03 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.025 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.056 0.075 0.25 16 -0.31 2 18
Cone PDE6 0.068 0.1 -10000 0 -0.28 26 26
Cone Metarhodopsin II 0.021 0.015 -10000 0 -0.31 1 1
Na + (4 Units) 0.056 0.045 0.23 1 -0.31 2 3
GNAT2/GDP 0.056 0.096 -10000 0 -0.28 30 30
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.021 0.046 -10000 0 -0.31 5 5
Cone Transducin 0.051 0.04 -10000 0 -0.31 3 3
SLC24A2 0.033 0.01 -10000 0 -10000 0 0
GNB3/GNGT2 0.043 0.02 -10000 0 -10000 0 0
GNB3 0.032 0.011 -10000 0 -10000 0 0
GNAT2/GTP 0.022 0.034 -10000 0 -0.34 4 4
CNGA3 0.042 0.052 0.18 37 -0.54 2 39
ARR3 0.034 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.044 0.042 0.23 1 -0.34 2 3
mol:Pi 0.048 0.099 -10000 0 -0.32 28 28
Cone CNG Channel 0.063 0.062 -10000 0 -0.28 7 7
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.033 0.01 -10000 0 -10000 0 0
RGS9 0.001 0.13 -10000 0 -0.54 27 27
PDE6C 0.033 0.028 -10000 0 -0.54 1 1
GNGT2 0.031 0.011 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.032 0.03 -10000 0 -0.54 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.033 0.007 -10000 0 -10000 0 0
NFATC1 0.042 0.085 0.34 3 -0.42 4 7
NFATC2 0.003 0.074 0.29 1 -0.26 15 16
NFATC3 0.013 0.007 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.03 0.062 0.26 2 -0.27 6 8
Exportin 1/Ran/NUP214 0.065 0.017 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.053 0.065 -10000 0 -10000 0 0
BCL2/BAX -0.036 0.17 -10000 0 -0.4 94 94
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.012 -10000 0 -10000 0 0
CaM/Ca2+ 0.023 0.012 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
BAD 0.033 0.007 -10000 0 -10000 0 0
CABIN1/MEF2D 0.037 0.06 -10000 0 -0.26 6 6
Calcineurin A alpha-beta B1/BCL2 -0.074 0.22 -10000 0 -0.54 94 94
FKBP8 0.034 0.008 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.036 0.059 0.26 6 -10000 0 6
KPNB1 0.032 0.008 -10000 0 -10000 0 0
KPNA2 0.057 0.058 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
SFN 0.033 0.04 -10000 0 -0.54 2 2
MAP3K8 -0.04 0.19 -10000 0 -0.54 64 64
NFAT4/CK1 alpha 0.029 0.038 -10000 0 -0.32 1 1
MEF2D/NFAT1/Cbp/p300 0.033 0.099 -10000 0 -0.3 18 18
CABIN1 0.03 0.061 0.26 2 -0.28 6 8
CALM1 0.033 0.008 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
CAMK4 0.035 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.009 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.053 0.039 -10000 0 -0.4 2 2
YWHAB 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.032 0.027 -10000 0 -0.54 1 1
MAPK9 0.034 0.009 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
FKBP1A 0.033 0.012 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.044 0.097 0.3 2 -0.38 8 10
PRKCH 0.029 0.051 -10000 0 -0.54 4 4
CABIN1/Cbp/p300 0.04 0.031 -10000 0 -0.4 1 1
CASP3 0.033 0.008 -10000 0 -10000 0 0
PIM1 0.035 0.015 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.009 -10000 0 -10000 0 0
apoptosis -0.003 0.058 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.04 0.047 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.01 0.063 -10000 0 -10000 0 0
BAD/BCL-XL 0.047 0.013 -10000 0 -10000 0 0
PRKCD 0.034 0.016 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0.002 -10000 0 -10000 0 0
PRKCA 0.031 0.013 -10000 0 -10000 0 0
PRKCG 0.033 0.006 -10000 0 -10000 0 0
PRKCQ 0.039 0.03 -10000 0 -10000 0 0
FKBP38/BCL2 -0.035 0.17 -10000 0 -0.4 91 91
EP300 0.03 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
NFATc/JNK1 0.057 0.085 0.34 1 -0.4 4 5
CaM/Ca2+/FKBP38 0.043 0.015 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSNK1A1 0.016 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.044 0.018 -10000 0 -10000 0 0
NFATc/ERK1 0.055 0.085 0.34 1 -0.4 4 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.065 0.063 -10000 0 -0.26 2 2
NR4A1 0.025 0.14 -10000 0 -0.47 24 24
GSK3B 0.033 0.009 -10000 0 -10000 0 0
positive T cell selection 0.013 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.006 0.061 -10000 0 -0.31 5 5
RCH1/ KPNB1 0.062 0.045 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
AKAP5 0.039 0.051 -10000 0 -0.54 2 2
MEF2D 0.027 0.016 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
NFATc/p38 alpha 0.057 0.084 0.34 1 -0.4 4 5
CREBBP 0.028 0.029 -10000 0 -0.54 1 1
BCL2 -0.074 0.22 -10000 0 -0.54 94 94
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.032 0.008 -9999 0 -10000 0 0
Rac1/GDP 0.03 0.013 -9999 0 -10000 0 0
DOCK1 0.03 0.045 -9999 0 -0.54 3 3
ITGA4 0.039 0.028 -9999 0 -10000 0 0
RAC1 0.034 0.005 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.053 0.022 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.031 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.069 0.024 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.059 0.022 -9999 0 -10000 0 0
lamellipodium assembly -0.03 0.16 -9999 0 -0.43 55 55
PIK3CA 0.032 0.008 -9999 0 -10000 0 0
PI3K 0.006 0.12 -9999 0 -0.38 46 46
ARF6 0.034 0.005 -9999 0 -10000 0 0
TLN1 0.033 0.006 -9999 0 -10000 0 0
PXN 0.017 0.003 -9999 0 -10000 0 0
PIK3R1 -0.019 0.16 -9999 0 -0.54 45 45
ARF6/GTP 0.067 0.032 -9999 0 -10000 0 0
cell adhesion 0.072 0.028 -9999 0 -10000 0 0
CRKL/CBL 0.044 0.018 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.058 0.023 -9999 0 -10000 0 0
ITGB1 0.033 0.006 -9999 0 -10000 0 0
ITGB7 0.034 0.004 -9999 0 -10000 0 0
ARF6/GDP 0.03 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.069 0.064 -9999 0 -0.3 11 11
p130Cas/Crk/Dock1 0.052 0.043 -9999 0 -0.34 3 3
VCAM1 0.023 0.086 -9999 0 -0.54 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.075 0.029 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.072 0.033 -9999 0 -10000 0 0
BCAR1 0.029 0.012 -9999 0 -10000 0 0
mol:GDP -0.07 0.032 -9999 0 -10000 0 0
CBL 0.03 0.011 -9999 0 -10000 0 0
PRKACA 0.034 0.005 -9999 0 -10000 0 0
GIT1 0.032 0.011 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.075 0.029 -9999 0 -10000 0 0
Rac1/GTP -0.036 0.18 -9999 0 -0.49 55 55
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.26 0.28 -10000 0 -0.54 252 252
CLTC 0.033 0.055 -10000 0 -0.42 3 3
calcium ion-dependent exocytosis 0.012 0.041 -10000 0 -0.37 2 2
Dynamin 2/GTP 0.03 0.013 -10000 0 -10000 0 0
EXOC4 0.034 0.005 -10000 0 -10000 0 0
CD59 0.02 0.045 -10000 0 -0.32 3 3
CPE -0.042 0.13 -10000 0 -0.34 84 84
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
membrane fusion 0.012 0.035 -10000 0 -0.35 1 1
CTNND1 0.031 0.055 0.37 1 -10000 0 1
DNM2 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.043 0.25 1 -0.41 1 2
TSHR 0.015 0.028 -10000 0 -0.34 3 3
INS 0.008 0.1 -10000 0 -0.5 18 18
BIN1 0.034 0.005 -10000 0 -10000 0 0
mol:Choline 0.012 0.035 -10000 0 -0.35 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.006 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.034 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.012 -10000 0 -10000 0 0
JUP 0.021 0.036 -10000 0 -0.29 2 2
ASAP2/amphiphysin II 0.042 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.004 -10000 0 -10000 0 0
CDH1 0.007 0.066 -10000 0 -0.38 4 4
clathrin-independent pinocytosis 0.025 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.03 0.038 -10000 0 -0.54 2 2
positive regulation of endocytosis 0.025 0.004 -10000 0 -10000 0 0
EXOC2 0.04 0.031 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.036 0.053 -10000 0 -0.35 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.031 0.011 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.045 0.081 0.35 4 -10000 0 4
positive regulation of phagocytosis 0.017 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.04 0.029 -10000 0 -0.34 2 2
ACAP1 0.011 0.034 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.039 -10000 0 -0.29 2 2
clathrin heavy chain/ACAP1 0.029 0.068 0.29 4 -0.42 2 6
JIP4/KLC1 0.056 0.024 -10000 0 -10000 0 0
EXOC1 0.034 0.005 -10000 0 -10000 0 0
exocyst 0.036 0.053 -10000 0 -0.36 3 3
RALA/GTP 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.015 -10000 0 -10000 0 0
receptor recycling 0.025 0.004 -10000 0 -10000 0 0
CTNNA1 0.032 0.055 0.37 1 -10000 0 1
NME1 0.016 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0.037 0.065 0.32 1 -0.42 3 4
IL2RA 0.027 0.047 -10000 0 -0.36 3 3
VAMP3 0.017 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.1 0.13 -10000 0 -0.34 17 17
EXOC6 0.033 0.027 -10000 0 -0.54 1 1
PLD1 0.006 0.061 -10000 0 -0.29 20 20
PLD2 0.016 0.016 -10000 0 -0.27 1 1
EXOC5 0.033 0.006 -10000 0 -10000 0 0
PIP5K1C 0.019 0.037 -10000 0 -0.42 1 1
SDC1 0.035 0.051 -10000 0 -0.36 3 3
ARF6/GDP 0.028 0.011 -10000 0 -10000 0 0
EXOC7 0.032 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.047 0.084 -10000 0 -0.36 4 4
mol:Phosphatidic acid 0.012 0.035 -10000 0 -0.35 1 1
endocytosis -0.041 0.009 -10000 0 -10000 0 0
SCAMP2 0.033 0.007 -10000 0 -10000 0 0
ADRB2 -0.11 0.15 -10000 0 -0.41 13 13
EXOC3 0.032 0.008 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.034 0.014 -10000 0 -10000 0 0
KLC1 0.033 0.006 -10000 0 -10000 0 0
AVPR2 0.032 0.068 0.3 1 -0.38 4 5
RALA 0.034 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.041 0.083 0.34 2 -0.4 2 4
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.008 0.069 -10000 0 -0.28 25 25
TRAF2/ASK1 0.023 0.086 -10000 0 -0.34 25 25
ATM 0.03 0.012 -10000 0 -10000 0 0
MAP2K3 -0.015 0.13 0.28 1 -0.4 29 30
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.013 0.13 0.32 1 -0.37 33 34
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.036 0.017 -10000 0 -10000 0 0
TXN 0.01 0.006 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
GADD45A 0.024 0.072 -10000 0 -0.54 8 8
GADD45B 0.031 0.037 -10000 0 -0.54 2 2
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
MAP3K6 0.033 0.007 -10000 0 -10000 0 0
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
MAP3K4 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.022 0.1 -10000 0 -0.4 25 25
TAK1/TAB family -0.002 0.021 -10000 0 -0.21 1 1
RAC1/OSM/MEKK3 0.057 0.023 -10000 0 -10000 0 0
TRAF2 0.034 0.012 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.009 0.11 -10000 0 -0.34 21 21
TRAF6 0.009 0.002 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.039 0.064 -10000 0 -0.54 4 4
CCM2 0.034 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.047 0.043 -10000 0 -0.34 4 4
MAPK11 0.032 0.009 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.042 0.091 -10000 0 -0.3 29 29
OSM/MEKK3 0.044 0.017 -10000 0 -10000 0 0
TAOK1 0.016 0.013 -10000 0 -10000 0 0
TAOK2 0.015 0.007 -10000 0 -10000 0 0
TAOK3 0.016 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.004 0.12 -10000 0 -0.54 25 25
MAP3K10 0.032 0.039 -10000 0 -0.54 2 2
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TRX/ASK1 0.01 0.081 -10000 0 -0.32 27 27
GADD45/MTK1/MTK1 0.066 0.059 -10000 0 -0.29 10 10
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.075 0.14 0.38 1 -0.3 26 27
CaM/Ca2+ 0.025 0.004 -10000 0 -10000 0 0
AKT1 0.035 0.016 -10000 0 -10000 0 0
AKT2 0.033 0.006 -10000 0 -10000 0 0
STXBP4 0.031 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.09 0.13 0.41 1 -0.28 51 52
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.006 0.068 -10000 0 -0.4 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
YWHAB 0.032 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.053 0.031 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.034 0.017 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.025 0.004 -10000 0 -10000 0 0
RHOQ 0.033 0.026 -10000 0 -0.54 1 1
GYS1 0.016 0.018 0.25 2 -10000 0 2
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.032 0.026 -10000 0 -0.54 1 1
TC10/GTP/CIP4/Exocyst 0.043 0.026 -10000 0 -0.34 2 2
AS160/14-3-3 0.026 0.074 -10000 0 -0.35 7 7
VAMP2 0.031 0.011 -10000 0 -10000 0 0
SLC2A4 -0.099 0.14 0.42 1 -0.31 52 53
STX4 0.031 0.01 -10000 0 -10000 0 0
GSK3B 0.027 0.014 -10000 0 -10000 0 0
SFN 0.033 0.04 -10000 0 -0.54 2 2
LNPEP 0.034 0.016 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.033 0.006 -10000 0 -10000 0 0
VDR 0.032 0.037 -10000 0 -0.54 2 2
Cbp/p300/PCAF 0.039 0.023 -10000 0 -0.34 1 1
EP300 0.032 0.008 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.001 0.088 -10000 0 -0.34 12 12
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.007 0.11 0.27 4 -0.26 51 55
RAR alpha/9cRA/Cyclin H 0.076 0.065 0.28 1 -0.28 2 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.001 0.1 -10000 0 -0.34 16 16
CDC2 0 0.003 -10000 0 -10000 0 0
response to UV 0.001 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.045 0.046 -10000 0 -0.45 1 1
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RXRs/RARs/NRIP1/9cRA 0.023 0.12 0.38 1 -0.53 9 10
NCOA2 0.028 0.014 -10000 0 -10000 0 0
NCOA3 0.032 0.01 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
VDR/VDR/DNA 0.032 0.037 -10000 0 -0.54 2 2
RARG 0.034 0.008 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.046 0.009 -10000 0 -10000 0 0
MAPK3 0.031 0.013 -10000 0 -10000 0 0
MAPK1 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.033 0.028 -10000 0 -0.54 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.068 0.066 -10000 0 -0.36 1 1
RARA 0.021 0.023 0.2 1 -0.24 1 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.001 0.091 -10000 0 -0.34 13 13
PRKCA 0.032 0.019 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.027 0.13 0.46 2 -0.54 9 11
RXRG 0.021 0.033 -10000 0 -0.32 3 3
RXRA 0.039 0.054 0.22 1 -0.26 4 5
RXRB 0.027 0.019 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RBP1 0.006 0.13 -10000 0 -0.54 26 26
CRBP1/9-cic-RA 0.005 0.094 -10000 0 -0.4 26 26
RARB -0.053 0.21 -10000 0 -0.54 77 77
PRKCG 0.035 0.015 -10000 0 -10000 0 0
MNAT1 0.033 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.01 0.11 -10000 0 -0.49 3 3
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.027 0.1 -10000 0 -0.43 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.095 0.25 6 -0.34 8 14
RXRs/RARs/NRIP1/9cRA/HDAC3 0.027 0.13 0.46 2 -0.56 9 11
positive regulation of DNA binding 0.059 0.055 -10000 0 -0.27 2 2
NRIP1 0.02 0.19 0.56 2 -1.1 9 11
RXRs/RARs 0.029 0.12 0.33 4 -0.51 6 10
RXRs/RXRs/DNA/9cRA 0.026 0.056 -10000 0 -0.34 2 2
PRKACA 0.034 0.005 -10000 0 -10000 0 0
CDK7 0.033 0.007 -10000 0 -10000 0 0
TFIIH 0.065 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.08 0.049 -10000 0 -10000 0 0
CCNH 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
RAR gamma2/9cRA 0.063 0.023 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.039 0.085 0.34 1 -0.34 6 7
PDGFB-D/PDGFRB/SLAP 0.04 0.027 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.041 0.017 -10000 0 -10000 0 0
AKT1 0.025 0.12 0.39 16 -10000 0 16
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.045 0.094 0.35 3 -0.38 6 9
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
FGR 0.01 0.1 -10000 0 -0.53 10 10
mol:Ca2+ 0.037 0.092 0.34 3 -0.39 9 12
MYC 0.047 0.23 0.41 15 -0.78 29 44
SHC1 0.027 0.014 -10000 0 -10000 0 0
HRAS/GDP 0.048 0.045 0.26 1 -10000 0 1
LRP1/PDGFRB/PDGFB 0.065 0.023 -10000 0 -10000 0 0
GRB10 0.029 0.051 -10000 0 -0.54 4 4
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0.036 0.093 0.34 3 -0.4 9 12
PTEN 0.025 0.068 -10000 0 -0.54 7 7
GRB2 0.033 0.017 -10000 0 -10000 0 0
GRB7 0.029 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.05 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.046 0.041 -10000 0 -0.4 4 4
cell cycle arrest 0.04 0.027 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
HIF1A 0.019 0.11 0.37 16 -0.34 1 17
GAB1 0.039 0.1 0.33 4 -0.41 7 11
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.038 0.096 0.36 5 -0.35 5 10
PDGFB-D/PDGFRB 0.06 0.036 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.048 0.018 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.029 0.079 -10000 0 -0.39 3 3
positive regulation of MAPKKK cascade 0.05 0.01 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 0.037 0.093 0.34 3 -0.4 9 12
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.033 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.042 0.02 -10000 0 -10000 0 0
SHB 0.035 0.018 -10000 0 -10000 0 0
BLK -0.034 0.17 -10000 0 -0.41 58 58
PTPN2 0.034 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.049 0.011 -10000 0 -10000 0 0
BCAR1 0.029 0.012 -10000 0 -10000 0 0
VAV2 0.038 0.11 0.36 4 -0.42 10 14
CBL 0.03 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.05 0.015 -10000 0 -10000 0 0
LCK 0.024 0.096 -10000 0 -0.54 8 8
PDGFRB 0.034 0.009 -10000 0 -10000 0 0
ACP1 0.033 0.006 -10000 0 -10000 0 0
HCK 0.024 0.07 -10000 0 -0.61 3 3
ABL1 0.032 0.096 0.35 3 -0.39 8 11
PDGFB-D/PDGFRB/CBL 0.033 0.11 0.34 1 -0.44 11 12
PTPN1 0.036 0.028 -10000 0 -10000 0 0
SNX15 0.034 0.005 -10000 0 -10000 0 0
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT1 0.058 0.054 -10000 0 -10000 0 0
cell proliferation 0.051 0.21 0.38 20 -0.68 29 49
SLA 0.029 0.024 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.05 0.059 0.42 3 -10000 0 3
SRC 0.02 0.06 -10000 0 -0.53 3 3
PI3K -0.01 0.065 -10000 0 -0.28 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.046 0.034 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.046 0.096 0.35 3 -0.39 6 9
LYN 0.02 0.055 -10000 0 -0.41 3 3
LRP1 0.034 0.004 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
STAT5B 0.033 0.01 -10000 0 -10000 0 0
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
NCK1-2/p130 Cas 0.075 0.053 -10000 0 -10000 0 0
SPHK1 0.034 0.06 -10000 0 -0.55 4 4
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.037 0.093 0.34 3 -0.4 9 12
PLCG1 0.037 0.095 0.34 3 -0.41 9 12
NHERF/PDGFRB 0.073 0.049 -10000 0 -10000 0 0
YES1 0.008 0.11 -10000 0 -0.52 16 16
cell migration 0.072 0.049 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.066 0.055 -10000 0 -10000 0 0
SLC9A3R2 0.032 0.015 -10000 0 -10000 0 0
SLC9A3R1 0.058 0.056 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.08 0.069 -10000 0 -0.31 4 4
FYN 0.005 0.1 -10000 0 -0.43 18 18
DOK1 0.035 0.049 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.009 -10000 0 -10000 0 0
PDGFB 0.033 0.015 -10000 0 -10000 0 0
RAC1 0.024 0.16 0.38 2 -0.5 28 30
PRKCD 0.035 0.051 0.26 1 -10000 0 1
FER 0.034 0.049 -10000 0 -10000 0 0
MAPKKK cascade 0.05 0.1 0.34 24 -10000 0 24
RASA1 0.034 0.049 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0.007 -10000 0 -10000 0 0
p62DOK/Csk 0.053 0.044 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.05 0.019 -10000 0 -10000 0 0
chemotaxis 0.033 0.094 0.33 4 -0.38 8 12
STAT1-3-5/STAT1-3-5 0.079 0.048 -10000 0 -0.29 1 1
Bovine Papilomavirus E5/PDGFRB 0.025 0.007 -10000 0 -10000 0 0
PTPRJ 0.035 0.016 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.047 0.031 -10000 0 -10000 0 0
KIRREL 0.032 0.017 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.047 0.031 -10000 0 -10000 0 0
PLCG1 0.032 0.008 -10000 0 -10000 0 0
ARRB2 0.031 0.01 -10000 0 -10000 0 0
WASL 0.033 0.026 -10000 0 -0.54 1 1
Nephrin/NEPH1/podocin/CD2AP 0.071 0.046 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.031 0.027 -10000 0 -10000 0 0
FYN 0.065 0.096 0.29 69 -0.24 2 71
mol:Ca2+ 0.066 0.046 -10000 0 -10000 0 0
mol:DAG 0.067 0.047 -10000 0 -10000 0 0
NPHS2 0.032 0.017 -10000 0 -10000 0 0
mol:IP3 0.067 0.047 -10000 0 -10000 0 0
regulation of endocytosis 0.053 0.043 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/Cholesterol 0.055 0.038 -10000 0 -10000 0 0
establishment of cell polarity 0.047 0.031 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.083 0.052 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.056 0.045 -10000 0 -10000 0 0
NPHS1 0.048 0.031 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.056 0.043 -10000 0 -0.24 2 2
TJP1 0.032 0.027 -10000 0 -0.54 1 1
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0.007 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.068 0.048 -10000 0 -10000 0 0
CD2AP 0.033 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.068 0.049 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.056 0.12 0.3 65 -0.31 13 78
cytoskeleton organization 0.032 0.053 0.28 4 -10000 0 4
Nephrin/NEPH1 0.04 0.026 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.057 0.042 -10000 0 -0.37 1 1
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.035 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.064 0.12 0.34 6 -0.33 9 15
ERC1 0.033 0.014 -10000 0 -10000 0 0
RIP2/NOD2 0.053 0.05 0.25 3 -10000 0 3
NFKBIA 0.014 0.022 -10000 0 -0.33 1 1
BIRC2 0.03 0.011 -10000 0 -10000 0 0
IKBKB 0.029 0.013 -10000 0 -10000 0 0
RIPK2 0.029 0.021 -10000 0 -10000 0 0
IKBKG 0.02 0.13 -10000 0 -0.39 41 41
IKK complex/A20 0.042 0.14 -10000 0 -0.42 20 20
NEMO/A20/RIP2 0.029 0.021 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.031 0.15 -10000 0 -0.41 30 30
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.045 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.13 -10000 0 -0.41 20 20
BCL10/MALT1/TRAF6 0.064 0.021 -10000 0 -10000 0 0
NOD2 0.058 0.06 -10000 0 -10000 0 0
NFKB1 0.036 0.007 -10000 0 -10000 0 0
RELA 0.036 0.007 -10000 0 -10000 0 0
MALT1 0.033 0.009 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.045 0.017 -10000 0 -10000 0 0
ATM 0.03 0.012 -10000 0 -10000 0 0
TNF/TNFR1A 0.05 0.021 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
PRKCA 0.031 0.013 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
UBE2D3 0.034 0.005 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.074 0.023 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.022 -10000 0 -0.32 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.008 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
IKK complex 0.034 0.14 -10000 0 -0.42 24 24
CYLD 0.03 0.012 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.037 0.14 -10000 0 -0.42 18 18
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.076 0.054 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.064 -10000 0 -0.29 2 2
SUMO1 0.034 0.005 -10000 0 -10000 0 0
ZFPM1 0.029 0.014 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.02 -10000 0 -0.17 3 3
FKBP3 0.034 0.005 -10000 0 -10000 0 0
Histones 0.076 0.049 -10000 0 -10000 0 0
YY1/LSF 0.031 0.057 -10000 0 -0.26 9 9
SMG5 0.029 0.016 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.031 0.025 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.042 0.044 -10000 0 -0.25 1 1
SAP18 0.032 0.009 -10000 0 -10000 0 0
RELA 0.028 0.043 -10000 0 -0.23 8 8
HDAC1/Smad7 0.064 0.019 -10000 0 -10000 0 0
RANGAP1 0.038 0.029 -10000 0 -10000 0 0
HDAC3/TR2 0.044 0.041 -10000 0 -0.29 1 1
NuRD/MBD3 Complex 0.039 0.06 -10000 0 -0.32 5 5
NF kappa B1 p50/RelA 0.043 0.068 0.4 1 -0.33 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.041 0.032 -10000 0 -10000 0 0
GATA1 0.034 0.003 -10000 0 -10000 0 0
Mad/Max 0.048 0.013 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.029 0.093 -10000 0 -0.36 14 14
RBBP7 0.037 0.021 -10000 0 -10000 0 0
NPC 0.02 0.002 -10000 0 -10000 0 0
RBBP4 0.033 0.006 -10000 0 -10000 0 0
MAX 0.033 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
NFKBIA 0.028 0.019 -10000 0 -0.27 1 1
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.027 0.054 -10000 0 -0.29 6 6
SIN3 complex 0.078 0.032 -10000 0 -10000 0 0
SMURF1 0.034 0.005 -10000 0 -10000 0 0
CHD3 0.031 0.015 -10000 0 -10000 0 0
SAP30 0.033 0.009 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.031 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.031 0.05 -10000 0 -0.36 2 2
YY1/HDAC2 0.034 0.047 -10000 0 -0.23 6 6
YY1/HDAC1 0.034 0.05 -10000 0 -0.24 7 7
NuRD/MBD2 Complex (MeCP1) 0.039 0.057 -10000 0 -0.25 5 5
PPARG -0.21 0.16 -10000 0 -0.31 336 336
HDAC8/hEST1B 0.057 0.028 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.045 0.039 -10000 0 -10000 0 0
MBD3L2 0.032 0.026 -10000 0 -0.54 1 1
ubiquitin-dependent protein catabolic process 0.063 0.019 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
NuRD/MBD3/MBD3L2 Complex 0.04 0.08 -10000 0 -0.35 9 9
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.03 0.013 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
YY1 0.016 0.015 -10000 0 -0.28 1 1
HDAC8 0.034 0.002 -10000 0 -10000 0 0
SMAD7 0.033 0.007 -10000 0 -10000 0 0
NCOR2 0.034 0.004 -10000 0 -10000 0 0
MXD1 0.034 0.007 -10000 0 -10000 0 0
STAT3 0.023 0.019 -10000 0 -0.33 1 1
NFKB1 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.049 0.058 -10000 0 -0.28 4 4
YY1/SAP30/HDAC1 0.05 0.053 -10000 0 -0.26 2 2
EP300 0.032 0.008 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.023 0.019 -10000 0 -0.32 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.019 -10000 0 -0.27 1 1
histone deacetylation 0.039 0.06 -10000 0 -0.27 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.033 0.042 -10000 0 -0.26 1 1
nuclear export -0.056 0.028 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GATAD2B 0.028 0.013 -10000 0 -10000 0 0
GATAD2A 0.037 0.02 -10000 0 -10000 0 0
GATA2/HDAC3 0.049 0.044 -10000 0 -10000 0 0
GATA1/HDAC1 0.049 0.009 -10000 0 -10000 0 0
GATA1/HDAC3 0.045 0.038 -10000 0 -10000 0 0
CHD4 0.032 0.008 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.05 0.021 -10000 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.028 0.063 -10000 0 -0.31 10 10
NuRD Complex 0.041 0.076 -10000 0 -0.33 5 5
positive regulation of chromatin silencing 0.072 0.047 -10000 0 -10000 0 0
SIN3B 0.035 0.014 -10000 0 -10000 0 0
MTA2 0.033 0.006 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.052 0.05 -10000 0 -0.25 3 3
HDAC complex 0.081 0.031 -10000 0 -10000 0 0
GATA1/Fog1 0.042 0.02 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.063 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
negative regulation of cell growth 0.025 0.072 -10000 0 -0.33 14 14
NuRD/MBD2/PRMT5 Complex 0.039 0.057 -10000 0 -0.25 5 5
Ran/GTP/Exportin 1 0.051 0.049 -10000 0 -0.26 3 3
NF kappa B/RelA/I kappa B alpha 0.031 0.047 -10000 0 -0.32 1 1
SIN3/HDAC complex/NCoR1 0.021 0.064 -10000 0 -0.31 11 11
TFCP2 0.032 0.036 -10000 0 -0.54 2 2
NR2C1 0.033 0.026 -10000 0 -0.54 1 1
MBD3 0.033 0.007 -10000 0 -10000 0 0
MBD2 0.034 0.011 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.05 0.013 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.032 0.021 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.052 -10000 0 -10000 0 0
NFKBIA 0.033 0.037 -10000 0 -0.28 1 1
MAPK14 0.034 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.03 0.016 -10000 0 -10000 0 0
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.037 0.022 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.032 0.018 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0.015 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.022 0.015 0.26 1 -10000 0 1
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
NFKB1 0.014 0.007 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.04 0.05 -10000 0 -0.24 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.042 0.057 -10000 0 -0.29 2 2
SRC 0.032 0.008 -10000 0 -10000 0 0
PI3K 0.006 0.12 -10000 0 -0.38 46 46
NF kappa B1 p50/RelA 0.04 0.05 -10000 0 -0.25 1 1
IKBKB 0.029 0.013 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -10000 0 0
SYK 0.039 0.027 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.018 0.099 -10000 0 -0.28 35 35
cell death 0.04 0.055 -10000 0 -0.28 2 2
NF kappa B1 p105/c-Rel 0.032 0.021 -10000 0 -10000 0 0
LCK 0.048 0.043 -10000 0 -10000 0 0
BCL3 0.035 0.014 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.03 0.012 -10000 0 -10000 0 0
ELF1 0.045 0.029 -10000 0 -10000 0 0
CCNA2 0.08 0.067 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
JAK3 0.034 0.005 -10000 0 -10000 0 0
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
JAK1 0.034 0.007 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.067 0.11 0.32 5 -0.37 7 12
SHC1 0.028 0.014 -10000 0 -10000 0 0
SP1 0.036 0.05 -10000 0 -0.36 8 8
IL2RA 0.036 0.057 -10000 0 -10000 0 0
IL2RB 0.036 0.022 -10000 0 -10000 0 0
SOS1 0.035 0.004 -10000 0 -10000 0 0
IL2RG 0.044 0.034 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.047 0.15 0.38 2 -0.73 12 14
PTPN11 0.035 0.004 -10000 0 -10000 0 0
CCND2 0.009 0.11 -10000 0 -0.77 9 9
LCK 0.049 0.043 -10000 0 -10000 0 0
GRB2 0.034 0.017 -10000 0 -10000 0 0
IL2 0.033 0.027 -10000 0 -0.54 1 1
CDK6 0.028 0.064 -10000 0 -0.54 6 6
CCND3 0.067 0.11 0.47 3 -0.45 1 4
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.005 0.053 0.29 3 -10000 0 3
DAPP1 0.034 0.1 0.28 7 -0.32 19 26
Src family/SYK family/BLNK-LAT/BTK-ITK 0.045 0.14 0.42 9 -0.46 16 25
mol:DAG 0.041 0.093 0.28 29 -10000 0 29
HRAS 0.035 0.013 -10000 0 -10000 0 0
RAP1A 0.035 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.047 0.076 -10000 0 -0.33 6 6
PLCG2 0.021 0.074 -10000 0 -0.54 8 8
PLCG1 0.032 0.008 -10000 0 -10000 0 0
ARF5 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.006 0.054 0.32 6 -10000 0 6
ARF1/GTP 0.003 0.048 0.36 4 -10000 0 4
RHOA 0.033 0.007 -10000 0 -10000 0 0
YES1 0.031 0.027 -10000 0 -0.54 1 1
RAP1A/GTP -0.004 0.054 0.24 10 -10000 0 10
ADAP1 -0.006 0.051 0.3 6 -10000 0 6
ARAP3 -0.006 0.054 0.32 6 -10000 0 6
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PREX1 0.054 0.078 -10000 0 -0.54 4 4
ARHGEF6 0.014 0.11 -10000 0 -0.54 18 18
ARHGEF7 0.031 0.012 -10000 0 -10000 0 0
ARF1 0.027 0.014 -10000 0 -10000 0 0
NRAS 0.036 0.016 -10000 0 -10000 0 0
FYN 0.029 0.037 -10000 0 -0.54 2 2
ARF6 0.034 0.005 -10000 0 -10000 0 0
FGR 0.033 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.024 0.058 0.21 17 -0.16 1 18
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.035 0.012 -10000 0 -10000 0 0
ZAP70 0.038 0.024 -10000 0 -10000 0 0
mol:IP3 0.026 0.071 0.25 18 -0.23 1 19
LYN 0.03 0.015 -10000 0 -10000 0 0
ARF1/GDP 0.038 0.074 0.43 1 -0.32 7 8
RhoA/GDP 0.05 0.057 0.29 4 -10000 0 4
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.035 0.082 0.38 5 -0.35 2 7
SRC 0.032 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.005 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PTEN 0.024 0.066 -10000 0 -0.52 7 7
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.059 0.37 4 -10000 0 4
RhoA/GTP -0.005 0.056 0.33 5 -10000 0 5
Src family/SYK family/BLNK-LAT 0.043 0.091 0.32 8 -0.36 6 14
BLK 0.039 0.043 -10000 0 -10000 0 0
PDPK1 0.031 0.01 -10000 0 -10000 0 0
CYTH1 -0.006 0.051 0.3 6 -10000 0 6
HCK 0.036 0.022 -10000 0 -10000 0 0
CYTH3 -0.006 0.051 0.3 6 -10000 0 6
CYTH2 -0.006 0.051 0.3 6 -10000 0 6
KRAS 0.035 0.017 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.015 0.034 0.3 2 -10000 0 2
SGK1 0.019 0.042 0.41 2 -10000 0 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.031 0.076 0.45 1 -0.33 7 8
SOS1 0.034 0.004 -10000 0 -10000 0 0
SYK 0.039 0.027 -10000 0 -10000 0 0
ARF6/GDP 0.033 0.063 0.35 6 -10000 0 6
mol:PI-3-4-5-P3 -0.006 0.057 0.34 7 -10000 0 7
ARAP3/RAP1A/GTP -0.004 0.054 0.24 10 -10000 0 10
VAV1 0.038 0.025 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.008 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.053 0.04 0.29 2 -10000 0 2
PLEKHA1 -0.008 0.021 -10000 0 -0.34 2 2
Rac1/GDP 0.048 0.075 -10000 0 -0.32 7 7
LAT 0.035 0.024 -10000 0 -10000 0 0
Rac1/GTP 0.027 0.08 -10000 0 -0.3 18 18
ITK -0.003 0.059 0.35 4 -0.29 2 6
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.042 0.11 0.34 21 -0.28 1 22
LCK 0.048 0.043 -10000 0 -10000 0 0
BTK -0.002 0.058 0.36 4 -10000 0 4
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.01 0.033 -10000 0 -0.34 5 5
ADCY5 -0.006 0.022 -10000 0 -0.34 1 1
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.003 0.019 -10000 0 -10000 0 0
ADCY1 -0.006 0.009 -10000 0 -10000 0 0
ADCY2 -0.009 0.043 -10000 0 -0.34 7 7
ADCY3 -0.007 0.007 -10000 0 -10000 0 0
ADCY8 -0.004 0.014 -10000 0 -10000 0 0
PRKCE 0.009 0.001 -10000 0 -10000 0 0
ADCY9 -0.004 0.016 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.035 0.069 0.23 16 -10000 0 16
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.046 0.055 -10000 0 -0.29 8 8
BIRC5 0.11 0.073 -10000 0 -10000 0 0
NFKBIA 0.023 0.041 0.27 5 -10000 0 5
CPEB1 0.019 0.092 -10000 0 -0.54 13 13
AKT1 0.024 0.041 0.3 3 -10000 0 3
NDEL1 0.031 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.04 0.034 -10000 0 -10000 0 0
NDEL1/TACC3 0.094 0.065 0.25 1 -10000 0 1
GADD45A 0.024 0.072 -10000 0 -0.54 8 8
GSK3B 0.005 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.056 0.049 -10000 0 -10000 0 0
MDM2 0.033 0.012 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.11 0.059 -10000 0 -10000 0 0
TP53 0.023 0.058 -10000 0 -10000 0 0
DLG7 0.023 0.032 -10000 0 -10000 0 0
AURKAIP1 0.034 0.013 -10000 0 -10000 0 0
ARHGEF7 0.031 0.012 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.1 0.069 0.27 2 -10000 0 2
G2/M transition of mitotic cell cycle 0.04 0.034 -10000 0 -10000 0 0
AURKA 0.033 0.041 -10000 0 -10000 0 0
AURKB 0.044 0.053 -10000 0 -10000 0 0
CDC25B 0.036 0.046 -10000 0 -10000 0 0
G2/M transition checkpoint 0.01 0.024 -10000 0 -10000 0 0
mRNA polyadenylation 0.03 0.059 -10000 0 -0.28 13 13
Aurora A/CPEB 0.031 0.06 -10000 0 -0.28 13 13
Aurora A/TACC1/TRAP/chTOG 0.053 0.089 -10000 0 -0.29 18 18
BRCA1 0.036 0.021 -10000 0 -10000 0 0
centrosome duplication 0.056 0.049 -10000 0 -10000 0 0
regulation of centrosome cycle 0.091 0.063 0.25 1 -10000 0 1
spindle assembly 0.051 0.087 -10000 0 -0.29 18 18
TDRD7 0.034 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.071 0.28 1 -10000 0 1
CENPA 0.061 0.056 -10000 0 -0.23 1 1
Aurora A/PP2A 0.052 0.037 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.029 0.036 0.27 1 -10000 0 1
negative regulation of DNA binding 0.023 0.058 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.043 0.02 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
Ajuba/Aurora A 0.016 0.028 -10000 0 -10000 0 0
mitotic prometaphase 0.006 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.041 -10000 0 -10000 0 0
TACC1 0.001 0.12 -10000 0 -0.54 24 24
TACC3 0.094 0.072 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.069 0.037 -10000 0 -10000 0 0
Aurora A/RasGAP 0.05 0.036 -10000 0 -10000 0 0
OAZ1 0.033 0.007 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.005 0.026 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.059 0.043 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.11 0.059 -10000 0 -10000 0 0
PPP2R5D 0.033 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.062 0.25 3 -10000 0 3
PAK1 0.043 0.045 -10000 0 -10000 0 0
CKAP5 0.035 0.015 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.032 0.027 -10000 0 -0.54 1 1
SMAD2 -0.007 0.051 -10000 0 -0.28 4 4
SMAD3 0.027 0.045 0.29 2 -10000 0 2
SMAD3/SMAD4 0.058 0.065 -10000 0 -0.4 5 5
SMAD4/Ubc9/PIASy 0.058 0.034 -10000 0 -0.34 1 1
SMAD2/SMAD2/SMAD4 0.064 0.074 -10000 0 -0.3 2 2
PPM1A 0.033 0.006 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.009 0.057 -10000 0 -0.3 4 4
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
TRAP-1/SMAD4 0.047 0.025 -10000 0 -0.29 2 2
MAPK3 0.032 0.009 -10000 0 -10000 0 0
MAPK1 0.032 0.008 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
CTDSP1 0.034 0.005 -10000 0 -10000 0 0
CTDSP2 0.033 0.006 -10000 0 -10000 0 0
CTDSPL 0.031 0.037 -10000 0 -0.54 2 2
KPNB1 0.032 0.008 -10000 0 -10000 0 0
TGFBRAP1 0.034 0.004 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
NUP153 0.033 0.006 -10000 0 -10000 0 0
KPNA2 0.057 0.058 -10000 0 -10000 0 0
PIAS4 0.035 0.015 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.043 0.022 -9999 0 -0.34 1 1
EFNA5 0.032 0.029 -9999 0 -0.54 1 1
FYN 0.017 0.031 -9999 0 -0.31 3 3
neuron projection morphogenesis 0.043 0.022 -9999 0 -0.34 1 1
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.043 0.022 -9999 0 -0.34 1 1
EPHA5 0.034 0.005 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.034 0.004 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.031 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.013 -10000 0 -10000 0 0
HIF1A/p53 0.046 0.06 -10000 0 -0.27 7 7
HIF1A 0.03 0.05 -10000 0 -0.27 6 6
COPS5 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.07 0.05 -10000 0 -10000 0 0
FIH (dimer) 0.034 0.005 -10000 0 -10000 0 0
CDKN2A 0.052 0.053 -10000 0 -10000 0 0
ARNT/IPAS 0.04 0.021 -10000 0 -10000 0 0
HIF1AN 0.034 0.005 -10000 0 -10000 0 0
GNB2L1 0.033 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.033 0.056 -10000 0 -0.28 7 7
CUL2 0.034 0.009 -10000 0 -10000 0 0
OS9 0.033 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.03 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.049 0.059 -10000 0 -0.28 7 7
PHD1-3/OS9 0.076 0.057 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.057 0.064 -10000 0 -0.32 1 1
VHL 0.035 0.018 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
HIF1A/JAB1 0.04 0.059 -10000 0 -0.28 6 6
EGLN3 0.06 0.057 -10000 0 -10000 0 0
EGLN2 0.035 0.016 -10000 0 -10000 0 0
EGLN1 0.027 0.014 -10000 0 -10000 0 0
TP53 0.031 0.014 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.044 0.066 -10000 0 -0.46 7 7
ARNT 0.027 0.014 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.032 0.008 -10000 0 -10000 0 0
HIF1A/p19ARF 0.059 0.068 0.27 2 -0.26 6 8
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.053 0.036 -10000 0 -0.29 4 4
MAPK9 0.009 0.005 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.01 0.017 0.14 9 -10000 0 9
GNB1/GNG2 0.043 0.021 -10000 0 -0.34 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.019 0.026 -10000 0 -0.31 3 3
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.001 0.006 0.08 3 -10000 0 3
GNAL 0.03 0.045 -10000 0 -0.54 3 3
GNG2 0.032 0.026 -10000 0 -0.54 1 1
CRH 0.031 0.023 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.016 -10000 0 -0.34 1 1
MAPK11 0.009 0.002 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.015 0.035 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.035 0.052 0.17 1 -0.19 2 3
AP2 0.049 0.017 0.25 1 -10000 0 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.043 0.015 -10000 0 -10000 0 0
CLTB 0.033 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.019 -10000 0 -10000 0 0
CD4 0.032 0.009 -10000 0 -10000 0 0
CLTA 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.008 0.14 2 -10000 0 2
mol:PI-4-5-P2 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP 0.015 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.012 0.021 0.18 5 -10000 0 5
mol:Choline 0.008 0.02 -10000 0 -0.2 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.015 -10000 0 -10000 0 0
DDEF1 0.008 0.02 -10000 0 -0.2 1 1
ARF1/GDP 0.002 0.022 -10000 0 -10000 0 0
AP2M1 0.034 0.009 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.008 -10000 0 -10000 0 0
Rac/GTP 0.028 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.033 0.024 -10000 0 -10000 0 0
ARFIP2 0.021 0.026 -10000 0 -10000 0 0
COPA 0.028 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.016 0.032 -10000 0 -0.2 3 3
ARF1/GTP/ARHGAP10 0.018 0.01 -10000 0 -10000 0 0
GGA3 0.032 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.016 0.041 -10000 0 -0.24 8 8
AP2A1 0.034 0.012 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.032 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.018 0.05 -10000 0 -0.25 13 13
Arfaptin 2/Rac/GDP 0.041 0.016 -10000 0 -10000 0 0
CYTH2 -0.001 0.002 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.021 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.025 0.032 -10000 0 -10000 0 0
PLD2 0.008 0.02 -10000 0 -0.2 1 1
ARF-GAP1/v-SNARE 0.009 0.008 0.14 2 -10000 0 2
PIP5K1A 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP/Membrin/GBF1/p115 0.016 0.024 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.02 -10000 0 -0.2 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.008 0.14 2 -10000 0 2
GOSR2 0.013 0.018 -10000 0 -0.26 1 1
USO1 0.012 0.024 -10000 0 -0.31 2 2
GBF1 0.013 0.02 -10000 0 -0.31 1 1
ARF1/GTP/Arfaptin 2 0.035 0.022 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.062 0.025 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.048 0.022 -10000 0 -10000 0 0
ATM 0.03 0.012 -10000 0 -10000 0 0
UBE2D3 0.034 0.005 -10000 0 -10000 0 0
PRKDC 0.031 0.019 -10000 0 -10000 0 0
ATR 0.033 0.006 -10000 0 -10000 0 0
UBE2L3 0.032 0.008 -10000 0 -10000 0 0
FANCD2 0.024 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.089 0.058 0.32 1 -10000 0 1
XRCC5 0.034 0.005 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.049 0.033 -10000 0 -10000 0 0
MRE11A 0.03 0.011 -10000 0 -10000 0 0
DNA-PK 0.056 0.03 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.026 0.11 -10000 0 -0.55 7 7
FANCF 0.033 0.006 -10000 0 -10000 0 0
BRCA1 0.036 0.021 -10000 0 -10000 0 0
CCNE1 0.058 0.055 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.067 0.046 0.25 8 -10000 0 8
FANCG 0.034 0.011 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.052 0.024 -10000 0 -10000 0 0
FANCE 0.033 0.027 -10000 0 -0.54 1 1
FANCC 0.035 0.016 -10000 0 -10000 0 0
NBN 0.028 0.015 -10000 0 -10000 0 0
FANCA 0.061 0.063 -10000 0 -10000 0 0
DNA repair 0.075 0.1 0.35 6 -0.46 1 7
BRCA1/BARD1/ubiquitin 0.052 0.024 -10000 0 -10000 0 0
BARD1/DNA-PK 0.072 0.039 -10000 0 -10000 0 0
FANCL 0.034 0.004 -10000 0 -10000 0 0
mRNA polyadenylation -0.047 0.022 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.073 -10000 0 -0.31 3 3
BRCA1/BACH1/BARD1/TopBP1 0.068 0.028 0.25 1 -10000 0 1
BRCA1/BARD1/P53 0.078 0.037 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.063 0.031 -10000 0 -10000 0 0
BRCA1/BACH1 0.036 0.021 -10000 0 -10000 0 0
BARD1 0.037 0.022 -10000 0 -10000 0 0
PCNA 0.037 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.069 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.067 0.028 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.12 0.069 0.35 2 -10000 0 2
BARD1/DNA-PK/P53 0.077 0.05 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.052 0.024 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.048 0.039 -10000 0 -0.32 2 2
FA complex 0.043 0.054 -10000 0 -0.3 2 2
BARD1/EWS 0.049 0.02 -10000 0 -10000 0 0
RBBP8 0.013 0.028 -10000 0 -0.4 2 2
TP53 0.031 0.014 -10000 0 -10000 0 0
TOPBP1 0.034 0.012 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.075 0.036 -10000 0 -10000 0 0
BRCA1/BARD1 0.097 0.063 0.34 1 -10000 0 1
CSTF1 0.031 0.01 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.027 0.016 -10000 0 -10000 0 0
CDK2 0.037 0.021 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.072 -10000 0 -10000 0 0
RAD50 0.033 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.052 0.024 -10000 0 -10000 0 0
EWSR1 0.032 0.008 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.033 0.006 -9999 0 -9999 0 0
ITGB7 0.034 0.004 -9999 0 -9999 0 0
ITGA4 0.039 0.028 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.053 0.022 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.052 0.022 -9999 0 -9999 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.045 0.04 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.078 0.054 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.017 0.029 -9999 0 -0.31 3 3
AURKB 0.056 0.057 -9999 0 -10000 0 0
AURKC 0.035 0.019 -9999 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.043 0.036 -9999 0 -9999 0 0
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine 0.032 0.025 -9999 0 -9999 0 0
neuron projection morphogenesis 0.032 0.025 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.013 -10000 0 -10000 0 0
MDM2/SUMO1 0.049 0.052 -10000 0 -0.25 3 3
HDAC4 0.033 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.013 -10000 0 -10000 0 0
SUMO1 0.034 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.016 0.026 -10000 0 -0.29 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.034 -10000 0 -0.27 3 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.051 0.051 -10000 0 -0.25 3 3
SUMO1/HDAC1 0.052 0.05 -10000 0 -0.25 3 3
RANGAP1 0.038 0.029 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.077 0.03 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0.02 -10000 0 -0.17 3 3
Ran/GTP 0.036 0.046 -10000 0 -0.26 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.012 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.05 0.26 2 -0.26 3 5
NPC 0.02 0.002 -10000 0 -10000 0 0
PIAS2 0.033 0.007 -10000 0 -10000 0 0
PIAS1 0.033 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.048 0.015 -10000 0 -0.16 1 1
FBXW11 0.033 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
NF kappa B2 p100/RelB 0.094 0.035 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAP3K14 0.033 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelB 0.051 0.016 -10000 0 -10000 0 0
RELB 0.036 0.019 -10000 0 -10000 0 0
NFKB2 0.035 0.012 -10000 0 -10000 0 0
NF kappa B2 p52/RelB 0.047 0.017 0.23 1 -10000 0 1
regulation of B cell activation 0.046 0.017 0.22 1 -10000 0 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 507 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.E2.A1BD TCGA.E2.A1BC TCGA.E2.A1B6 TCGA.E2.A1B5
109_MAP3K5 0.039 0.039 0.093 0.093
47_PPARGC1A 0.034 0.034 0.034 0.18
105_BMP4 0.034 0.034 0.034 0.034
105_BMP6 0.034 0.034 0.034 0.034
105_BMP7 0.034 0.034 0.034 0.034
105_BMP2 0.034 0.034 0.034 0.034
131_RELN/VLDLR 0.088 0.088 -0.32 0.17
30_TGFB1/TGF beta receptor Type II 0.034 0.034 0.034 0.034
84_STAT5B -0.21 -0.0041 -0.03 -0.21
84_STAT5A -0.21 -0.0041 -0.03 -0.21
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/2585245/2.GDAC_MergeDataFiles.Finished/BRCA-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BRCA-TP/2660865/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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