Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNA expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 53 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 243
Signaling events mediated by Stem cell factor receptor (c-Kit) 220
Endothelins 152
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 149
EGFR-dependent Endothelin signaling events 142
Class IB PI3K non-lipid kinase events 124
IGF1 pathway 120
Arf6 signaling events 107
FOXM1 transcription factor network 104
Nongenotropic Androgen signaling 93
Results
Summary Table

The following list describes the columns found in Table 2.

  • 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 243 10706 44 -0.6 0.034 1000 -1000 -0.005 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 220 17201 78 -1 0.32 1000 -1000 -0.024 -1000
Endothelins 152 14608 96 -0.81 0.16 1000 -1000 -0.026 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 149 10193 68 -0.88 0.45 1000 -1000 -0.061 -1000
EGFR-dependent Endothelin signaling events 142 2991 21 -0.31 0.047 1000 -1000 -0.031 -1000
Class IB PI3K non-lipid kinase events 124 372 3 -0.11 -1000 1000 -1000 -0.02 -1000
IGF1 pathway 120 6875 57 -0.27 0.11 1000 -1000 -0.032 -1000
Arf6 signaling events 107 6694 62 -0.31 0.08 1000 -1000 -0.002 -1000
FOXM1 transcription factor network 104 5318 51 -0.13 0.69 1000 -1000 0.013 -1000
Nongenotropic Androgen signaling 93 4859 52 -0.57 0.3 1000 -1000 -0.025 -1000
Glucocorticoid receptor regulatory network 82 9459 114 -0.95 0.29 1000 -1000 -0.046 -1000
Signaling events mediated by PTP1B 76 5836 76 -0.36 0.19 1000 -1000 -0.034 -1000
S1P1 pathway 75 2712 36 -0.62 0.045 1000 -1000 -0.022 -1000
Calcium signaling in the CD4+ TCR pathway 71 2208 31 -0.36 0.039 1000 -1000 -0.029 -1000
PDGFR-alpha signaling pathway 70 3084 44 -0.7 0.063 1000 -1000 -0.025 -1000
HIF-1-alpha transcription factor network 69 5301 76 -0.39 0.072 1000 -1000 -0.005 -1000
BMP receptor signaling 68 5533 81 -0.4 0.11 1000 -1000 -0.032 -1000
Ephrin B reverse signaling 67 3245 48 -0.18 0.06 1000 -1000 -0.032 -1000
Ras signaling in the CD4+ TCR pathway 65 1106 17 -0.2 0.033 1000 -1000 -0.009 -1000
IL23-mediated signaling events 61 3676 60 -0.79 0.064 1000 -1000 -0.004 -1000
IL6-mediated signaling events 57 4285 75 -0.37 0.072 1000 -1000 -0.024 -1000
Plasma membrane estrogen receptor signaling 57 4958 86 -0.25 0.17 1000 -1000 -0.05 -1000
FAS signaling pathway (CD95) 56 2647 47 -0.88 0.059 1000 -1000 -0.024 -1000
IL4-mediated signaling events 54 4999 91 -0.52 0.14 1000 -1000 -0.1 -1000
Integrins in angiogenesis 53 4457 84 -0.39 0.13 1000 -1000 -0.018 -1000
Visual signal transduction: Rods 49 2566 52 -0.43 0.073 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 48 4669 97 -0.36 0.04 1000 -1000 -0.052 -1000
EPHB forward signaling 47 4021 85 -0.18 0.14 1000 -1000 -0.054 -1000
PLK1 signaling events 43 3677 85 -0.035 0.17 1000 -1000 -0.027 -1000
Signaling events mediated by the Hedgehog family 42 2195 52 -0.14 0.067 1000 -1000 -0.011 -1000
E-cadherin signaling in keratinocytes 41 1801 43 -0.26 0.035 1000 -1000 -0.016 -1000
Aurora B signaling 41 2772 67 -0.38 0.23 1000 -1000 -0.021 -1000
Glypican 1 network 40 1933 48 -0.39 0.069 1000 -1000 -0.022 -1000
S1P5 pathway 39 671 17 -0.17 0.067 1000 -1000 -0.004 -1000
Insulin Pathway 38 2885 74 -0.28 0.09 1000 -1000 -0.025 -1000
Nectin adhesion pathway 37 2355 63 -0.073 0.054 1000 -1000 -0.032 -1000
p75(NTR)-mediated signaling 36 4613 125 -0.12 0.092 1000 -1000 -0.042 -1000
TCGA08_retinoblastoma 36 292 8 -0.024 0.057 1000 -1000 -0.008 -1000
Presenilin action in Notch and Wnt signaling 35 2168 61 -0.38 0.1 1000 -1000 -0.031 -1000
Stabilization and expansion of the E-cadherin adherens junction 35 2647 74 -0.26 0.072 1000 -1000 -0.06 -1000
LPA receptor mediated events 34 3510 102 -0.36 0.092 1000 -1000 -0.043 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 33 2852 85 -0.54 0.046 1000 -1000 -0.03 -1000
S1P4 pathway 33 830 25 -0.17 0.045 1000 -1000 -0.013 -1000
ErbB2/ErbB3 signaling events 31 2062 65 -0.35 0.046 1000 -1000 -0.056 -1000
Neurotrophic factor-mediated Trk receptor signaling 31 3737 120 -0.24 0.12 1000 -1000 -0.037 -1000
Signaling events regulated by Ret tyrosine kinase 30 2519 82 -0.1 0.11 1000 -1000 -0.048 -1000
TCGA08_p53 30 212 7 -0.009 0.028 1000 -1000 -0.003 -1000
IL27-mediated signaling events 30 1573 51 -0.37 0.068 1000 -1000 -0.033 -1000
ErbB4 signaling events 29 2021 69 -0.36 0.13 1000 -1000 -0.016 -1000
Syndecan-3-mediated signaling events 28 1010 35 -0.36 0.074 1000 -1000 -0.016 -1000
TCGA08_rtk_signaling 28 750 26 -0.26 0.042 1000 -1000 -0.02 -1000
Syndecan-2-mediated signaling events 27 1867 69 -0.32 0.13 1000 -1000 -0.013 -1000
TCR signaling in naïve CD8+ T cells 27 2577 93 -0.04 0.082 1000 -1000 -0.04 -1000
Regulation of nuclear SMAD2/3 signaling 26 3539 136 -0.37 0.075 1000 -1000 -0.042 -1000
mTOR signaling pathway 25 1344 53 -0.051 0.043 1000 -1000 -0.031 -1000
amb2 Integrin signaling 25 2115 82 -0.52 0.13 1000 -1000 -0.026 -1000
FOXA2 and FOXA3 transcription factor networks 24 1127 46 -0.75 0.05 1000 -1000 -0.022 -1000
IL12-mediated signaling events 23 2024 87 -0.83 0.087 1000 -1000 -0.034 -1000
Syndecan-1-mediated signaling events 23 798 34 -0.041 0.11 1000 -1000 -0.016 -1000
Reelin signaling pathway 23 1327 56 -0.054 0.082 1000 -1000 -0.018 -1000
IL1-mediated signaling events 23 1455 62 -0.049 0.066 1000 -1000 -0.023 -1000
S1P3 pathway 23 984 42 -0.17 0.062 1000 -1000 -0.029 -1000
Angiopoietin receptor Tie2-mediated signaling 23 2092 88 -0.39 0.13 1000 -1000 -0.064 -1000
Osteopontin-mediated events 22 839 38 -0.36 0.13 1000 -1000 0 -1000
Ceramide signaling pathway 22 1736 76 -0.25 0.083 1000 -1000 -0.017 -1000
RXR and RAR heterodimerization with other nuclear receptor 22 1159 52 -0.38 0.1 1000 -1000 -0.018 -1000
HIF-2-alpha transcription factor network 22 987 43 -0.22 0.26 1000 -1000 -0.1 -1000
Canonical Wnt signaling pathway 22 1122 51 -0.38 0.16 1000 -1000 -0.032 -1000
Coregulation of Androgen receptor activity 20 1580 76 -0.22 0.053 1000 -1000 -0.03 -1000
Regulation of Telomerase 20 2054 102 -0.36 0.085 1000 -1000 -0.012 -1000
Syndecan-4-mediated signaling events 20 1386 67 -0.39 0.15 1000 -1000 -0.026 -1000
Regulation of Androgen receptor activity 20 1437 70 -0.43 0.077 1000 -1000 -0.031 -1000
Thromboxane A2 receptor signaling 19 2094 105 -0.26 0.066 1000 -1000 -0.034 -1000
Regulation of p38-alpha and p38-beta 19 1066 54 -0.31 0.071 1000 -1000 -0.043 -1000
Signaling mediated by p38-gamma and p38-delta 18 271 15 -0.006 0.034 1000 -1000 -0.023 -1000
IL2 signaling events mediated by PI3K 17 992 58 -0.12 0.048 1000 -1000 -0.021 -1000
Noncanonical Wnt signaling pathway 16 429 26 -0.015 0.04 1000 -1000 -0.026 -1000
Hedgehog signaling events mediated by Gli proteins 16 1049 65 -0.17 0.076 1000 -1000 -0.023 -1000
Signaling events mediated by PRL 16 573 34 -0.31 0.051 1000 -1000 -0.022 -1000
E-cadherin signaling events 16 84 5 0.006 0.035 1000 -1000 0.021 -1000
Wnt signaling 15 108 7 -0.015 0.04 1000 -1000 -0.011 -1000
E-cadherin signaling in the nascent adherens junction 15 1197 76 -0.039 0.059 1000 -1000 -0.049 -1000
Cellular roles of Anthrax toxin 14 571 39 -0.063 0.037 1000 -1000 -0.015 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 14 644 45 -0.007 0.061 1000 -1000 -0.033 -1000
Caspase cascade in apoptosis 13 973 74 -0.16 0.048 1000 -1000 -0.026 -1000
BCR signaling pathway 12 1259 99 -0.15 0.092 1000 -1000 -0.046 -1000
Class I PI3K signaling events mediated by Akt 11 802 68 -0.15 0.061 1000 -1000 -0.018 -1000
ceramide signaling pathway 11 577 49 -0.074 0.053 1000 -1000 -0.023 -1000
FoxO family signaling 11 715 64 0.001 0.15 1000 -1000 -0.016 -1000
Sphingosine 1-phosphate (S1P) pathway 10 304 28 -0.17 0.053 1000 -1000 -0.007 -1000
PLK2 and PLK4 events 10 31 3 0.017 0.054 1000 -1000 0.001 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 10 551 54 -0.041 0.08 1000 -1000 -0.023 -1000
IFN-gamma pathway 10 694 68 -0.019 0.097 1000 -1000 -0.046 -1000
Signaling events mediated by VEGFR1 and VEGFR2 10 1287 125 -0.38 0.074 1000 -1000 -0.028 -1000
VEGFR1 specific signals 10 590 56 -0.38 0.075 1000 -1000 -0.03 -1000
JNK signaling in the CD4+ TCR pathway 9 163 17 -0.04 0.089 1000 -1000 -0.014 -1000
EPO signaling pathway 9 546 55 -0.094 0.067 1000 -1000 -0.019 -1000
TRAIL signaling pathway 8 415 48 -0.001 0.046 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class II 7 550 75 -0.06 0.066 1000 -1000 -0.032 -1000
Visual signal transduction: Cones 7 270 38 0 0.068 1000 -1000 0 -1000
Circadian rhythm pathway 7 165 22 -0.02 0.1 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class III 7 302 40 -0.061 0.061 1000 -1000 -0.035 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 7 585 83 -0.074 0.065 1000 -1000 -0.006 -1000
Paxillin-dependent events mediated by a4b1 6 227 36 -0.069 0.075 1000 -1000 -0.031 -1000
Arf6 trafficking events 6 478 71 -0.26 0.056 1000 -1000 -0.025 -1000
p38 MAPK signaling pathway 6 287 44 -0.013 0.065 1000 -1000 -0.009 -1000
Insulin-mediated glucose transport 5 169 32 -0.099 0.053 1000 -1000 -0.012 -1000
Paxillin-independent events mediated by a4b1 and a4b7 5 189 37 -0.019 0.084 1000 -1000 -0.02 -1000
Retinoic acid receptors-mediated signaling 5 334 58 -0.053 0.079 1000 -1000 -0.017 -1000
IL2 signaling events mediated by STAT5 5 111 22 -0.018 0.08 1000 -1000 -0.006 -1000
Class I PI3K signaling events 5 427 73 -0.008 0.058 1000 -1000 -0.018 -1000
PDGFR-beta signaling pathway 5 579 97 -0.034 0.079 1000 -1000 -0.04 -1000
Nephrin/Neph1 signaling in the kidney podocyte 4 168 34 -0.047 0.082 1000 -1000 -0.022 -1000
Canonical NF-kappaB pathway 4 168 39 0 0.073 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class I 4 484 104 -0.21 0.08 1000 -1000 -0.035 -1000
Atypical NF-kappaB pathway 4 140 31 -0.019 0.048 1000 -1000 -0.003 -1000
Aurora A signaling 3 213 60 0 0.12 1000 -1000 -0.008 -1000
Arf6 downstream pathway 3 162 43 -0.09 0.091 1000 -1000 -0.034 -1000
Aurora C signaling 3 21 7 0 0.077 1000 -1000 -0.005 -1000
Effects of Botulinum toxin 3 78 26 0 0.069 1000 -1000 0 -1000
LPA4-mediated signaling events 2 29 12 -0.01 0.035 1000 -1000 -0.019 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 27 23 -0.007 0.063 1000 -1000 -0.007 -1000
Ephrin A reverse signaling 1 7 7 0 0.043 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 1 27 27 0 0.077 1000 -1000 -0.026 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 1 57 33 0 0.076 1000 -1000 -0.018 -1000
Arf1 pathway 1 59 54 -0.001 0.062 1000 -1000 -0.01 -1000
BARD1 signaling events 0 44 57 -0.075 0.12 1000 -1000 -0.039 -1000
a4b1 and a4b7 Integrin signaling 0 0 5 0.033 0.053 1000 -1000 0.019 -1000
Glypican 2 network 0 0 4 0 0.031 1000 -1000 0 -1000
Rapid glucocorticoid signaling 0 16 20 0 0.043 1000 -1000 0 -1000
Alternative NF-kappaB pathway 0 3 13 0 0.094 1000 -1000 0 -1000
Total 4318 261574 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 -0.35 301 301
ATF2/c-Jun -0.26 0.32 -10000 0 -0.69 139 139
MAPK11 -0.18 0.2 -10000 0 -0.36 281 281
MITF -0.24 0.23 -10000 0 -0.42 302 302
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 0.011 -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 -0.41 299 299
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.24 0.24 -10000 0 -0.42 300 300
p38alpha-beta/MNK1 -0.24 0.28 -10000 0 -0.45 300 300
JUN -0.26 0.31 -10000 0 -0.68 139 139
PPARGC1A -0.28 0.29 0.28 1 -0.48 307 308
USF1 -0.21 0.21 -10000 0 -0.39 287 287
RAB5/GDP/GDI1 -0.17 0.18 -10000 0 -0.31 295 295
NOS2 -0.24 0.22 -10000 0 -0.41 302 302
DDIT3 -0.23 0.22 -10000 0 -0.41 300 300
RAB5A 0.034 0.005 -10000 0 -10000 0 0
HSPB1 -0.18 0.18 -10000 0 -0.34 268 268
p38alpha-beta/HBP1 -0.24 0.28 -10000 0 -0.45 300 300
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 -0.41 299 299
PLA2G4A -0.35 0.27 -10000 0 -0.52 349 349
GDI1 -0.23 0.22 -10000 0 -0.41 302 302
TP53 -0.3 0.3 -10000 0 -0.54 292 292
RPS6KA5 -0.24 0.23 -10000 0 -0.42 308 308
ESR1 -0.29 0.27 0.31 1 -0.46 311 312
HBP1 0.033 0.005 -10000 0 -10000 0 0
MEF2C -0.26 0.26 -10000 0 -0.44 307 307
MEF2A -0.23 0.23 0.3 1 -0.41 298 299
EIF4EBP1 -0.25 0.25 -10000 0 -0.44 294 294
KRT19 -0.21 0.23 -10000 0 -0.4 292 292
ELK4 -0.21 0.21 -10000 0 -0.39 283 283
ATF6 -0.22 0.21 -10000 0 -0.39 290 290
ATF1 -0.25 0.24 -10000 0 -0.43 303 303
p38alpha-beta/MAPKAPK2 -0.22 0.24 -10000 0 -0.42 280 280
p38alpha-beta/MAPKAPK3 -0.24 0.28 -10000 0 -0.45 301 301
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 -0.38 367 367
CRKL -0.32 0.17 -10000 0 -0.4 384 384
HRAS -0.23 0.15 -10000 0 -0.34 223 223
mol:PIP3 -0.28 0.18 -10000 0 -0.39 291 291
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 -0.38 270 270
AKT1 -0.29 0.18 -10000 0 -0.39 324 324
BAD -0.28 0.16 -10000 0 -0.38 259 259
megakaryocyte differentiation -0.32 0.18 -10000 0 -0.41 392 392
GSK3B -0.28 0.16 -10000 0 -0.38 270 270
RAF1 -0.19 0.13 -10000 0 -0.29 206 206
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 -1 413 413
HRAS/SPRED1 -0.19 0.14 -10000 0 -0.32 57 57
cell proliferation -0.33 0.17 -10000 0 -0.41 394 394
PIK3CA 0.031 0.008 -10000 0 -10000 0 0
TEC 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.32 0.18 -10000 0 -0.4 394 394
HRAS/SPRED2 -0.19 0.14 -10000 0 -0.32 55 55
LYN/TEC/p62DOK -0.29 0.18 -10000 0 -0.4 322 322
MAPK3 -0.13 0.098 -10000 0 -0.26 21 21
STAP1 -0.32 0.18 -10000 0 -0.42 389 389
GRAP2 0.034 0.019 -10000 0 -10000 0 0
JAK2 -0.68 0.37 -10000 0 -0.85 401 401
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 -0.33 0.17 -10000 0 -0.41 396 396
LYN 0.03 0.015 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.47 0.26 -10000 0 -0.58 402 402
PIK3R1 -0.019 0.16 -10000 0 -0.55 45 45
CBL/CRKL/GRB2 -0.28 0.17 -10000 0 -0.38 340 340
PI3K -0.32 0.2 -10000 0 -0.42 368 368
PTEN 0.025 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) -0.33 0.17 -10000 0 -0.41 388 388
positive regulation of transcription -0.11 0.083 -10000 0 -0.23 12 12
mol:GDP -0.24 0.16 -10000 0 -0.36 229 229
PIK3C2B -0.3 0.18 -10000 0 -0.42 321 321
CBL/CRKL -0.3 0.16 -10000 0 -0.39 372 372
FER -0.33 0.18 -10000 0 -0.42 394 394
SH2B3 -0.33 0.18 -10000 0 -0.42 395 395
PDPK1 -0.25 0.17 -10000 0 -0.37 257 257
SNAI2 -0.34 0.2 -10000 0 -0.45 357 357
positive regulation of cell proliferation -0.58 0.31 -10000 0 -0.73 403 403
KITLG -0.011 0.069 -10000 0 -0.56 2 2
cell motility -0.58 0.31 -10000 0 -0.73 403 403
PTPN6 0.05 0.02 -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 0.031 0.012 -10000 0 -10000 0 0
cell migration 0.32 0.17 0.41 389 -10000 0 389
SOS1 0.034 0.004 -10000 0 -10000 0 0
EPO 0.009 0.063 -10000 0 -10000 0 0
VAV1 0.038 0.024 -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 -0.28 21 21
CBL 0.03 0.011 -10000 0 -10000 0 0
KIT -1 0.53 -10000 0 -1.3 397 397
MAP2K2 -0.15 0.11 -10000 0 -0.28 22 22
SHC/Grb2/SOS1 -0.27 0.18 -10000 0 -0.4 288 288
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 -0.44 357 358
SHC/GRAP2 0.039 0.026 -10000 0 -10000 0 0
PTPRO -0.33 0.18 -10000 0 -0.42 392 392
SH2B2 -0.33 0.18 -10000 0 -0.42 397 397
DOK1 0.035 0.016 -10000 0 -10000 0 0
MATK -0.33 0.18 -10000 0 -0.42 390 390
CREBBP -0.082 0.075 -10000 0 -0.55 1 1
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 -0.54 148 148
EDN3 -0.39 0.25 -10000 0 -0.54 369 369
EDN2 0.096 0.076 -10000 0 -0.54 1 1
HRAS/GDP -0.25 0.23 -10000 0 -0.44 241 241
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.18 -10000 0 -0.34 155 155
ADCY4 -0.08 0.15 0.34 2 -0.3 137 139
ADCY5 -0.077 0.15 0.35 1 -0.3 134 135
ADCY6 -0.078 0.15 0.34 2 -0.3 137 139
ADCY7 -0.073 0.15 0.34 2 -0.29 131 133
ADCY1 -0.078 0.15 -10000 0 -0.3 133 133
ADCY2 -0.079 0.16 0.34 2 -0.3 136 138
ADCY3 -0.078 0.15 0.35 1 -0.3 138 139
ADCY8 -0.065 0.13 0.35 1 -0.3 99 100
ADCY9 -0.071 0.14 -10000 0 -0.3 119 119
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 -0.36 289 289
GNAO1 0.029 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 -0.32 138 138
ETA receptor/Endothelin-1/Gs/GTP -0.085 0.15 -10000 0 -0.31 140 140
mol:GTP -0.007 0.008 -10000 0 -10000 0 0
COL3A1 -0.096 0.17 -10000 0 -0.35 127 127
EDNRB -0.21 0.28 -10000 0 -0.54 220 220
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.095 0.16 -10000 0 -0.34 137 137
CYSLTR1 -0.097 0.17 0.38 2 -0.35 130 132
SLC9A1 -0.065 0.11 -10000 0 -0.23 135 135
mol:GDP -0.27 0.24 -10000 0 -0.47 247 247
SLC9A3 -0.39 0.39 -10000 0 -0.7 264 264
RAF1 -0.35 0.26 -10000 0 -0.51 330 330
JUN -0.25 0.43 -10000 0 -1 109 109
JAK2 -0.097 0.16 -10000 0 -0.35 137 137
mol:IP3 -0.21 0.21 -10000 0 -0.41 206 206
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 0.015 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.29 0.19 -10000 0 -0.4 370 370
FOS -0.68 0.43 -10000 0 -0.95 362 362
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 -0.53 198 198
BCAR1 0.029 0.012 -10000 0 -10000 0 0
PRKCB1 -0.21 0.21 -10000 0 -0.4 213 213
GNAQ -0.009 0.009 -10000 0 -10000 0 0
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
GNAL 0.029 0.045 -10000 0 -0.54 3 3
Gs family/GDP -0.24 0.22 -10000 0 -0.44 229 229
ETA receptor/Endothelin-1/Gq/GTP -0.095 0.15 -10000 0 -0.3 129 129
MAPK14 -0.22 0.22 -10000 0 -0.4 246 246
TRPC6 -0.18 0.31 -10000 0 -0.78 77 77
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
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.23 -10000 0 -0.4 282 282
ETB receptor/Endothelin-2 -0.11 0.22 -10000 0 -0.34 219 219
ETB receptor/Endothelin-3 -0.42 0.27 -10000 0 -0.52 412 412
ETB receptor/Endothelin-1 -0.26 0.28 -10000 0 -0.48 290 290
MAPK3 -0.61 0.39 -10000 0 -0.83 366 366
MAPK1 -0.62 0.41 -10000 0 -0.86 365 365
Rac1/GDP -0.25 0.23 -10000 0 -0.45 233 233
cAMP biosynthetic process -0.028 0.15 0.4 5 -0.35 26 31
MAPK8 -0.18 0.3 -10000 0 -0.64 117 117
SRC 0.032 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.27 0.29 -10000 0 -0.55 225 225
p130Cas/CRK/Src/PYK2 -0.27 0.28 -10000 0 -0.57 196 196
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.25 0.23 -10000 0 -0.45 234 234
COL1A2 -0.22 0.27 0.42 1 -0.48 216 217
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.07 0.076 0.26 2 -0.4 3 5
mol:DAG -0.21 0.21 -10000 0 -0.41 207 207
MAP2K2 -0.47 0.31 -10000 0 -0.64 368 368
MAP2K1 -0.47 0.32 0.36 1 -0.64 368 369
EDNRA 0.006 0.057 -10000 0 -0.43 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 -0.43 186 186
HRAS/GTP -0.26 0.23 -10000 0 -0.44 261 261
PRKCH -0.21 0.21 -10000 0 -0.42 199 199
RAC1 0.033 0.005 -10000 0 -10000 0 0
PRKCA -0.19 0.21 -10000 0 -0.43 175 175
PRKCB -0.21 0.21 -10000 0 -0.4 216 216
PRKCE -0.21 0.21 -10000 0 -0.42 192 192
PRKCD -0.21 0.21 -10000 0 -0.43 185 185
PRKCG -0.21 0.21 0.3 1 -0.43 188 189
regulation of vascular smooth muscle contraction -0.81 0.5 -10000 0 -1.1 362 362
PRKCQ -0.2 0.21 -10000 0 -0.42 187 187
PLA2G4A -0.59 0.4 -10000 0 -0.78 373 373
GNA14 0.025 0.071 -10000 0 -0.55 4 4
GNA15 0.021 0.03 -10000 0 -10000 0 0
GNA12 0.033 0.005 -10000 0 -10000 0 0
GNA11 0.018 0.024 -10000 0 -10000 0 0
Rac1/GTP -0.089 0.16 -10000 0 -0.32 137 137
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 0.48 2 -0.55 56 58
NFATC3 -0.15 0.17 0.31 1 -0.32 215 216
CD40LG -0.68 0.53 0.78 4 -1 331 335
ITCH -0.065 0.14 -10000 0 -0.52 1 1
CBLB -0.068 0.14 -10000 0 -0.86 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.31 0.74 7 -0.7 68 75
JUNB 0.03 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.078 0.17 -10000 0 -0.3 189 189
T cell anergy -0.13 0.21 -10000 0 -0.4 179 179
TLE4 -0.067 0.2 -10000 0 -0.56 43 43
Jun/NFAT1-c-4/p21SNFT -0.58 0.55 0.69 3 -0.96 316 319
AP-1/NFAT1-c-4 -0.8 0.68 0.91 5 -1.2 333 338
IKZF1 -0.045 0.17 0.46 10 -0.46 26 36
T-helper 2 cell differentiation -0.12 0.29 0.52 1 -0.78 46 47
AP-1/NFAT1 -0.3 0.3 0.55 5 -0.51 290 295
CALM1 -0.037 0.11 -10000 0 -0.31 1 1
EGR2 -0.8 0.76 0.72 3 -1.5 259 262
EGR3 -0.88 0.76 0.7 3 -1.4 320 323
NFAT1/FOXP3 -0.032 0.18 0.46 8 -0.41 45 53
EGR1 -0.43 0.23 -10000 0 -0.54 409 409
JUN -0.065 0.22 0.26 1 -0.54 86 87
EGR4 0.001 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.089 -10000 0 -0.17 185 185
GBP3 -0.08 0.24 0.43 2 -0.71 48 50
FOSL1 0.034 0.01 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.54 0.53 0.66 3 -0.91 312 315
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 0.55 -10000 0 -1.1 345 345
CTLA4 -0.025 0.16 0.42 14 -0.41 21 35
NFAT1-c-4 (dimer)/EGR1 -0.78 0.57 -10000 0 -1.1 349 349
NFAT1-c-4 (dimer)/EGR4 -0.56 0.52 0.67 1 -0.92 320 321
FOS -0.35 0.27 0.25 1 -0.54 342 343
IFNG -0.099 0.3 0.58 6 -0.78 47 53
T cell activation -0.39 0.34 0.68 3 -0.68 233 236
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 0.72 329 -0.62 4 333
TNF -0.67 0.48 -10000 0 -0.97 345 345
FASLG -0.88 0.78 0.85 3 -1.4 328 331
TBX21 0.027 0.15 0.28 12 -0.54 30 42
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.043 0.035 0.23 6 -10000 0 6
PTPN1 -0.049 0.16 0.42 1 -0.46 27 28
NFAT1-c-4/ICER1 -0.56 0.53 0.6 1 -0.92 316 317
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 47 53
IL2RA -0.26 0.31 0.73 6 -0.68 78 84
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.052 0.16 -10000 0 -0.41 45 45
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 -0.42 41 41
IRF4 0.038 0.027 -10000 0 -10000 0 0
PTGS2 -0.77 0.57 0.73 4 -1.1 351 355
CSF2 -0.68 0.53 0.78 4 -1 331 335
JunB/Fra1/NFAT1-c-4 -0.53 0.52 0.6 2 -0.9 313 315
IL4 -0.13 0.3 -10000 0 -0.82 46 46
IL5 -0.68 0.52 0.73 4 -1 333 337
IL2 -0.39 0.35 0.68 3 -0.7 231 234
IL3 -0.09 0.15 -10000 0 -0.91 13 13
RNF128 -0.21 0.33 -10000 0 -0.63 190 190
NFATC1 -0.45 0.41 0.62 4 -0.72 329 333
CDK4 0.28 0.28 0.62 66 -0.68 1 67
PTPRK -0.089 0.24 -10000 0 -0.72 49 49
IL8 -0.67 0.53 0.73 5 -1 326 331
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 -10000 0 -10000 0 0
EGFR -0.26 0.29 -10000 0 -0.54 261 261
EGF/EGFR -0.29 0.26 -10000 0 -0.43 357 357
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.18 0.21 -10000 0 -0.36 262 262
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.032 0.038 0.17 2 -0.54 2 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.15 0.27 -10000 0 -0.54 161 161
EGF/EGFR dimer/SHC -0.23 0.23 -10000 0 -0.42 277 277
mol:GDP -0.18 0.21 -10000 0 -0.36 262 262
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.13 0.26 -10000 0 -0.54 147 147
GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
HRAS/GTP -0.18 0.19 -10000 0 -0.34 252 252
SHC1 0.027 0.014 -10000 0 -10000 0 0
HRAS/GDP -0.18 0.2 -10000 0 -0.35 251 251
FRAP1 -0.2 0.17 -10000 0 -0.35 255 255
EGF/EGFR dimer -0.31 0.26 -10000 0 -0.46 348 348
SOS1 0.034 0.004 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.085 0.2 -10000 0 -0.39 154 154
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 0.54 124 -10000 0 124
PI3K Class IB/PDE3B -0.11 0.25 -10000 0 -0.54 124 124
PDE3B -0.11 0.25 -10000 0 -0.54 124 124
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 -0.35 242 242
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 -0.36 219 219
AKT1 -0.16 0.19 0.23 1 -0.35 207 208
BAD -0.16 0.18 0.22 1 -0.45 90 91
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.17 0.2 -10000 0 -0.35 245 245
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.21 -10000 0 -0.34 256 256
RAF1 -0.12 0.18 -10000 0 -0.45 75 75
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 -0.37 257 257
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.18 0.23 1 -0.35 191 192
GNB2L1 0.033 0.005 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.1 0.15 0.3 2 -0.39 64 66
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 -0.32 167 167
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 -0.05 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 -0.42 265 265
PI3K -0.15 0.24 -10000 0 -0.37 240 240
apoptosis 0.11 0.15 0.4 58 -0.28 2 60
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
PRKCD -0.18 0.23 -10000 0 -0.4 231 231
RAF1/14-3-3 E -0.097 0.17 0.34 1 -0.39 73 74
BAD/14-3-3 -0.12 0.16 0.29 2 -0.43 58 60
PRKCZ -0.16 0.19 0.22 1 -0.34 223 224
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.17 -10000 0 -0.4 77 77
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 -0.41 243 243
BCAR1 0.029 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.095 0.19 -10000 0 -0.33 179 179
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 -0.35 244 244
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 -0.45 246 246
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 -0.48 232 232
SHC1 0.027 0.014 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.018 0.018 -10000 0 -0.34 1 1
ARNO/beta Arrestin1-2 -0.11 0.14 -10000 0 -0.26 242 242
EGFR -0.26 0.29 -10000 0 -0.54 261 261
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 -0.46 348 348
ARRB2 0.015 0.029 -10000 0 -0.33 3 3
mol:GTP 0.012 0.029 0.12 26 -10000 0 26
ARRB1 0.03 0.027 -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 -0.54 161 161
somatostatin receptor activity 0 0 -10000 0 -0.001 234 234
ARAP2 0 0 -10000 0 0 254 254
mol:GDP -0.14 0.14 -10000 0 -0.27 215 215
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 237 237
ITGA2B 0.033 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 0 154 154
KIF13B 0.027 0.029 -10000 0 -0.54 1 1
HGF/MET 0.005 0.14 -10000 0 -0.4 50 50
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.14 0.12 -10000 0 -0.26 218 218
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.26 0.24 -10000 0 -0.41 340 340
ADRB2 -0.26 0.29 -10000 0 -0.54 260 260
receptor agonist activity 0 0 -10000 0 0 211 211
actin filament binding 0 0 -10000 0 0 255 255
SRC 0.032 0.008 -10000 0 -10000 0 0
ITGB3 0.034 0.018 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -0.001 154 154
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 154 154
ARF6/GDP -0.03 0.083 -10000 0 -0.27 28 28
ARF6/GDP/GULP/ACAP1 -0.16 0.18 -10000 0 -0.34 200 200
alphaIIb/beta3 Integrin/paxillin/GIT1 0.08 0.031 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 0 1 1
ACAP2 0 0 -10000 0 0 251 251
LHCGR/beta Arrestin2 0.022 0.048 -10000 0 -0.47 3 3
EFNA1 0.027 0.015 -10000 0 -10000 0 0
HGF 0.034 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 211 211
CYTH2 -0.002 0.002 -10000 0 -0.004 253 253
NCK1 0.033 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 146 146
endosomal lumen acidification 0 0 0.001 4 0 154 158
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.07 0.22 -10000 0 -0.54 91 91
GNAQ/ARNO -0.003 0.003 -10000 0 -0.007 143 143
mol:Phosphatidic acid 0 0 -10000 0 0 251 251
PIP3-E 0 0 -10000 0 0 346 346
MET -0.023 0.17 -10000 0 -0.54 50 50
GNA14 0.042 0.066 -10000 0 -0.54 4 4
GNA15 0.035 0.017 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -0.001 203 203
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 0.021 0.048 -10000 0 -0.46 3 3
IPCEF1/ARNO -0.21 0.18 -10000 0 -0.32 348 348
alphaIIb/beta3 Integrin 0.05 0.019 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.55 0.46 1.1 108 -1 2 110
PLK1 0.22 0.19 0.66 33 -10000 0 33
BIRC5 0.36 0.25 0.7 104 -0.66 3 107
HSPA1B 0.55 0.46 1.1 136 -0.95 3 139
MAP2K1 0.17 0.13 0.35 107 -10000 0 107
BRCA2 0.59 0.49 1.2 125 -1.1 2 127
FOXM1 0.6 0.61 1.3 141 -1.2 3 144
XRCC1 0.56 0.46 1.1 108 -1.1 2 110
FOXM1B/p19 0.074 0.29 0.94 6 -1.1 3 9
Cyclin D1/CDK4 0.47 0.46 1 108 -0.9 8 116
CDC2 0.61 0.52 1.2 142 -1 3 145
TGFA 0.44 0.52 1 124 -0.94 20 144
SKP2 0.56 0.47 1.1 120 -0.95 3 123
CCNE1 0.085 0.062 0.22 39 -10000 0 39
CKS1B 0.61 0.5 1.2 135 -1.1 2 137
RB1 0.27 0.34 0.75 110 -0.76 8 118
FOXM1C/SP1 0.49 0.45 1 99 -1 7 106
AURKB 0.2 0.31 0.66 60 -0.81 21 81
CENPF 0.68 0.53 1.2 171 -1 2 173
CDK4 0.09 0.06 0.24 10 -10000 0 10
MYC 0.31 0.44 0.96 80 -0.88 9 89
CHEK2 0.16 0.13 0.35 108 -10000 0 108
ONECUT1 0.49 0.48 1.1 126 -0.9 6 132
CDKN2A -0.016 0.076 -10000 0 -0.21 21 21
LAMA4 0.55 0.48 1.1 112 -1.2 3 115
FOXM1B/HNF6 0.49 0.5 1.1 111 -1.1 6 117
FOS -0.13 0.65 1.1 44 -1 73 117
SP1 0.031 0.032 -10000 0 -0.22 4 4
CDC25B 0.57 0.47 1.1 123 -1.1 2 125
response to radiation 0.11 0.093 0.24 130 -10000 0 130
CENPB 0.56 0.46 1.1 108 -1.1 2 110
CENPA 0.63 0.5 1.2 141 -1.1 2 143
NEK2 0.69 0.52 1.3 159 -1.2 1 160
HIST1H2BA 0.56 0.46 1.1 112 -1.1 2 114
CCNA2 0.11 0.075 0.21 144 -10000 0 144
EP300 0.032 0.008 -10000 0 -10000 0 0
CCNB1/CDK1 0.59 0.52 1.2 127 -1.1 3 130
CCNB2 0.62 0.51 1.2 141 -1.1 2 143
CCNB1 0.63 0.54 1.3 138 -1 3 141
ETV5 0.53 0.52 1.1 120 -1.2 9 129
ESR1 0.36 0.61 1.2 97 -0.98 15 112
CCND1 0.49 0.51 1.1 134 -0.93 8 142
GSK3A 0.14 0.1 0.3 82 -10000 0 82
Cyclin A-E1/CDK1-2 0.2 0.13 0.37 131 -10000 0 131
CDK2 0.069 0.036 0.23 6 -10000 0 6
G2/M transition of mitotic cell cycle 0.14 0.12 0.27 169 -10000 0 169
FOXM1B/Cbp/p300 0.3 0.38 0.86 17 -1 3 20
GAS1 0.27 0.71 1.1 93 -1.1 55 148
MMP2 0.55 0.48 1.1 118 -1.2 5 123
RB1/FOXM1C 0.44 0.46 0.98 127 -0.95 7 134
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
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 -0.044 0.13 -10000 0 -0.3 90 90
GNAO1 0.029 0.012 -10000 0 -10000 0 0
HRAS 0.031 0.013 -10000 0 -10000 0 0
SHBG/T-DHT 0.02 0.007 -10000 0 -10000 0 0
PELP1 0.029 0.01 -10000 0 -10000 0 0
AKT1 0.011 0.014 -10000 0 -10000 0 0
MAP2K1 -0.11 0.11 -10000 0 -0.36 61 61
T-DHT/AR -0.034 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 -0.007 356 356
GNAI2 0.032 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 -0.47 68 68
cell proliferation -0.3 0.21 -10000 0 -0.44 317 317
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
FOS -0.57 0.37 -10000 0 -0.8 361 361
mol:Ca2+ -0.038 0.037 -10000 0 -0.075 229 229
MAPK3 -0.21 0.16 -10000 0 -0.37 162 162
MAPK1 -0.16 0.15 -10000 0 -0.39 81 81
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 -0.003 0.002 -10000 0 -0.004 333 333
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 -0.004 333 333
HRAS/GTP -0.059 0.12 -10000 0 -0.33 64 64
actin cytoskeleton reorganization 0.015 0.093 -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 -0.004 333 333
PI3K 0.008 0.11 -10000 0 -0.34 42 42
apoptosis 0.3 0.21 0.43 348 -10000 0 348
T-DHT/AR/PELP1 -0.015 0.13 -10000 0 -0.35 66 66
HRAS/GDP -0.07 0.17 -10000 0 -0.46 66 66
CREB1 -0.32 0.23 -10000 0 -0.46 347 347
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 0.033 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 -0.47 77 77
mol:T-DHT -0.001 0.002 -10000 0 -0.005 72 72
RAC1 0.033 0.005 -10000 0 -10000 0 0
GNRH1 0 0.051 -10000 0 -0.4 8 8
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) 0.07 0.067 0.28 24 -10000 0 24
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 0.33 44 -0.36 4 48
PRL -0.061 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.52 177 -10000 0 177
RELA -0.095 0.11 0.27 3 -0.26 30 33
FGG 0.24 0.23 0.46 208 -10000 0 208
GR beta/TIF2 0.11 0.14 0.3 96 -0.35 3 99
IFNG -0.39 0.34 -10000 0 -0.69 227 227
apoptosis -0.25 0.18 -10000 0 -0.59 23 23
CREB1 0.057 0.04 -10000 0 -10000 0 0
histone acetylation 0.035 0.14 0.4 36 -0.33 10 46
BGLAP -0.094 0.14 -10000 0 -0.44 17 17
GR/PKAc 0.15 0.14 0.35 41 -0.31 3 44
NF kappa B1 p50/RelA -0.16 0.2 0.47 3 -0.33 150 153
SMARCD1 0.034 0.004 -10000 0 -10000 0 0
MDM2 0.12 0.099 0.22 193 -10000 0 193
GATA3 0.039 0.17 -10000 0 -0.54 34 34
AKT1 0.027 0.024 -10000 0 -10000 0 0
CSF2 -0.008 0.11 0.4 3 -10000 0 3
GSK3B 0.001 0.027 -10000 0 -10000 0 0
NR1I3 -0.19 0.16 -10000 0 -0.59 5 5
CSN2 0.19 0.19 0.37 206 -10000 0 206
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 0.032 0.04 -10000 0 -0.54 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.14 0.14 0.35 29 -0.36 3 32
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.65 0.33 -10000 0 -0.8 420 420
JUN -0.21 0.24 0.38 2 -0.48 163 165
IL4 -0.12 0.15 -10000 0 -0.51 11 11
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 -0.49 327 327
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.15 0.14 0.36 29 -0.4 2 31
cortisol/GR alpha (monomer) 0.29 0.31 0.58 227 -10000 0 227
NCOA2 0.028 0.013 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.42 0.26 -10000 0 -0.58 357 357
AP-1/NFAT1-c-4 -0.58 0.41 -10000 0 -0.82 342 342
AFP -0.18 0.2 -10000 0 -0.63 15 15
SUV420H1 0.031 0.01 -10000 0 -10000 0 0
IRF1 0.2 0.18 0.44 91 -10000 0 91
TP53 0.046 0.034 -10000 0 -0.51 1 1
PPP5C 0.035 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 0.028 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 -0.83 342 342
MAPK14 0.009 0.023 -10000 0 -10000 0 0
MAPK10 -0.012 0.082 -10000 0 -0.55 10 10
MAPK11 -0.001 0.025 -10000 0 -10000 0 0
KRT5 -0.95 0.63 -10000 0 -1.4 350 350
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 0.067 0.28 24 -10000 0 24
CGA -0.085 0.16 -10000 0 -0.49 10 10
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.18 0.34 192 -0.35 2 194
MAPK3 -0.002 0.024 -10000 0 -10000 0 0
MAPK1 0.007 0.023 -10000 0 -10000 0 0
ICAM1 -0.26 0.25 0.59 2 -0.52 154 156
NFKB1 -0.095 0.11 0.27 3 -0.25 29 32
MAPK8 -0.15 0.19 0.57 1 -0.36 154 155
MAPK9 0.008 0.025 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.19 -10000 0 -0.62 24 24
BAX 0.029 0.074 -10000 0 -10000 0 0
POMC -0.14 0.19 0.57 1 -0.79 9 10
EP300 0.18 0.14 0.29 271 -10000 0 271
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.52 187 -10000 0 187
proteasomal ubiquitin-dependent protein catabolic process 0.091 0.11 0.29 65 -10000 0 65
SGK1 0.23 0.17 0.36 299 -0.43 1 300
IL13 -0.3 0.25 -10000 0 -0.66 78 78
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 -0.64 36 36
IL2 -0.42 0.32 -10000 0 -0.68 271 271
CDK5 0.03 0.021 -10000 0 -10000 0 0
PRKACB 0.035 0.083 -10000 0 -0.54 8 8
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
IL8 -0.24 0.26 0.51 4 -0.53 139 143
CDK5R1/CDK5 0.036 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.096 0.18 0.42 3 -0.41 27 30
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.26 0.25 0.5 208 -10000 0 208
SMARCA4 0.034 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.17 0.16 0.34 167 -10000 0 167
NF kappa B1 p50/RelA/Cbp -0.004 0.2 0.48 26 -0.37 4 30
JUN (dimer) -0.21 0.24 0.38 2 -0.48 163 165
YWHAH 0.033 0.014 -10000 0 -10000 0 0
VIPR1 -0.11 0.17 -10000 0 -0.55 27 27
NR3C1 0.19 0.2 0.39 177 -0.44 5 182
NR4A1 0.017 0.12 -10000 0 -0.55 21 21
TIF2/SUV420H1 0.038 0.022 -10000 0 -10000 0 0
MAPKKK cascade -0.25 0.18 -10000 0 -0.59 23 23
cortisol/GR alpha (dimer)/Src-1 0.27 0.26 0.52 225 -10000 0 225
PBX1 0.042 0.04 -10000 0 -10000 0 0
POU1F1 0.038 0.026 -10000 0 -0.54 1 1
SELE -0.26 0.35 0.51 4 -0.67 137 141
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.16 0.34 167 -10000 0 167
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.26 0.25 0.5 208 -10000 0 208
mol:cortisol 0.18 0.17 0.33 238 -10000 0 238
MMP1 -0.02 0.34 -10000 0 -0.94 50 50
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 0.005 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.24 0.21 -10000 0 -0.41 237 237
PTP1B/AKT1 -0.16 0.15 0.24 1 -0.29 201 202
FYN 0.029 0.037 -10000 0 -0.54 2 2
p210 bcr-abl/PTP1B -0.19 0.16 0.25 1 -0.31 257 258
EGFR -0.28 0.28 -10000 0 -0.56 261 261
EGF/EGFR -0.35 0.26 -10000 0 -0.5 352 352
CSF1 0.034 0.008 -10000 0 -10000 0 0
AKT1 0.034 0.016 -10000 0 -10000 0 0
INSR 0.033 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.16 0.17 0.33 1 -0.32 186 187
Insulin Receptor/Insulin -0.11 0.13 -10000 0 -0.39 29 29
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 -0.31 217 219
EGF -0.18 0.26 -10000 0 -0.56 161 161
YES1 0.031 0.027 -10000 0 -0.54 1 1
CAV1 -0.36 0.23 -10000 0 -0.49 357 357
TXN 0.028 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.19 0.18 -10000 0 -0.34 230 230
cell migration 0.19 0.16 0.31 257 -0.25 1 258
STAT3 0.031 0.007 -10000 0 -10000 0 0
PRLR 0.072 0.062 -10000 0 -10000 0 0
ITGA2B 0.032 0.013 -10000 0 -10000 0 0
CSF1R 0.033 0.005 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.08 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 -0.31 233 234
Crk/p130 Cas -0.16 0.16 -10000 0 -0.31 180 180
DOK1 -0.15 0.14 0.27 1 -0.34 91 92
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 -0.31 258 259
LYN 0.03 0.015 -10000 0 -10000 0 0
CDH2 0.056 0.054 -10000 0 -10000 0 0
SRC -0.051 0.12 -10000 0 -0.68 15 15
ITGB3 0.033 0.018 -10000 0 -10000 0 0
CAT1/PTP1B -0.14 0.18 0.36 1 -0.44 81 82
CAPN1 0.031 0.013 -10000 0 -10000 0 0
CSK 0.033 0.011 -10000 0 -10000 0 0
PI3K -0.12 0.16 -10000 0 -0.43 55 55
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 0.038 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 -0.3 208 208
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 -0.4 71 72
STAT5A -0.14 0.16 0.26 1 -0.36 95 96
GRB2 0.033 0.017 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.17 0.16 0.24 1 -0.31 215 216
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 0.043 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 0.05 0.053 -10000 0 -10000 0 0
S1P1 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
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 0.33 5 -0.49 297 302
GNAO1 0.004 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.25 0.26 0.41 3 -0.45 278 281
PLCG1 -0.26 0.27 0.32 7 -0.47 285 292
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.007 -10000 0 -10000 0 0
GNAI2 0.004 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 0.28 7 -0.66 10 17
negative regulation of cAMP metabolic process -0.28 0.28 0.33 5 -0.48 297 302
MAPK3 -0.37 0.35 0.35 9 -0.63 306 315
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 0.005 -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 0.033 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 0.43 3 -1 308 311
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 -0.48 297 302
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 -0.67 308 313
S1P1/S1P/PDGFB-D/PDGFRB -0.078 0.14 0.33 8 -0.63 10 18
ABCC1 0.031 0.023 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.008 0.057 0.26 9 -0.35 2 11
NFATC2 0.009 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 0.68 10 -0.51 180 190
PTGS2 -0.32 0.36 0.66 9 -0.62 258 267
JUNB 0.03 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.031 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.031 -10000 0 -10000 0 0
CALM1 0.033 0.018 -10000 0 -10000 0 0
JUN -0.065 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 0.66 16 -0.51 176 192
AP-1/NFAT1-c-4 -0.25 0.34 0.7 11 -0.59 191 202
FASLG -0.19 0.29 0.65 16 -0.49 169 185
NFAT1-c-4/ICER1 0.016 0.097 0.4 9 -0.28 1 10
IL2RA -0.21 0.3 0.62 16 -0.51 181 197
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSF2 -0.22 0.3 0.61 16 -0.51 188 204
JunB/Fra1/NFAT1-c-4 0.039 0.11 0.41 9 -0.29 4 13
IL4 -0.22 0.29 0.65 10 -0.51 182 192
IL2 -0.009 0.15 -10000 0 -0.97 11 11
IL3 -0.009 0.13 -10000 0 -0.74 13 13
FKBP1A 0.033 0.011 -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
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.091 0.18 -10000 0 -0.58 61 61
PDGF/PDGFRA/CRKL -0.055 0.14 -10000 0 -0.41 63 63
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 62 62
AP1 -0.7 0.45 -10000 0 -0.97 362 362
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 -0.41 65 65
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.085 0.13 -10000 0 -0.45 56 56
CAV3 0.031 0.037 -10000 0 -0.54 2 2
CAV1 -0.38 0.26 -10000 0 -0.54 359 359
SHC/Grb2/SOS1 0.016 0.12 -10000 0 -0.33 44 44
PDGF/PDGFRA/Shf -0.054 0.14 -10000 0 -0.4 64 64
FOS -0.69 0.44 -10000 0 -0.95 362 362
JUN -0.13 0.16 -10000 0 -0.46 85 85
oligodendrocyte development -0.056 0.14 -10000 0 -0.41 65 65
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 -0.4 64 64
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 -0.41 62 62
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 62 62
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 -0.4 64 64
PDGF/PDGFRA/Caveolin-1 -0.34 0.24 -10000 0 -0.46 370 370
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 -0.41 63 63
JAK-STAT cascade -0.065 0.13 -10000 0 -0.4 62 62
cell proliferation -0.054 0.14 -10000 0 -0.4 64 64
HIF-1-alpha transcription factor network

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
PKM2 0.007 0.42 0.81 1 -0.72 76 77
HDAC7 0.007 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.007 0.37 0.82 4 -0.68 50 54
SMAD4 0.032 0.027 -10000 0 -0.54 1 1
ID2 0.005 0.42 -10000 0 -0.72 75 75
AP1 -0.33 0.27 -10000 0 -0.48 349 349
ABCG2 -0.011 0.43 -10000 0 -0.72 85 85
HIF1A 0.023 0.13 0.32 4 -0.31 13 17
TFF3 -0.047 0.43 -10000 0 -0.73 91 91
GATA2 0.021 0.047 -10000 0 -10000 0 0
AKT1 0.021 0.13 0.33 3 -0.21 13 16
response to hypoxia -0.003 0.11 0.25 13 -0.16 65 78
MCL1 -0.026 0.39 -10000 0 -0.7 78 78
NDRG1 -0.014 0.39 0.88 1 -0.72 69 70
SERPINE1 0.014 0.43 0.82 10 -0.71 78 88
FECH 0.001 0.42 -10000 0 -0.71 79 79
FURIN 0.009 0.42 -10000 0 -0.71 80 80
NCOA2 0.034 0.022 -10000 0 -10000 0 0
EP300 0.035 0.17 0.45 15 -0.3 31 46
HMOX1 0.012 0.43 0.82 7 -0.72 75 82
BHLHE40 -0.052 0.39 0.72 4 -0.72 77 81
BHLHE41 -0.052 0.39 0.72 4 -0.72 77 81
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.043 0.16 -10000 0 -0.39 3 3
ENG 0.045 0.14 0.43 3 -0.41 2 5
JUN -0.073 0.22 -10000 0 -0.55 86 86
RORA -0.004 0.43 -10000 0 -0.71 86 86
ABCB1 -0.29 0.47 -10000 0 -0.94 159 159
TFRC 0.009 0.43 0.84 6 -0.72 74 80
CXCR4 0.013 0.43 0.8 4 -0.7 80 84
TF -0.004 0.44 -10000 0 -0.73 82 82
CITED2 -0.003 0.43 -10000 0 -0.72 78 78
HIF1A/ARNT -0.067 0.44 0.9 3 -0.81 72 75
LDHA -0.011 0.13 -10000 0 -0.72 14 14
ETS1 0.001 0.42 0.77 1 -0.72 76 77
PGK1 0.009 0.43 0.82 4 -0.71 79 83
NOS2 -0.052 0.39 0.72 4 -0.72 77 81
ITGB2 0.009 0.43 0.81 8 -0.72 75 83
ALDOA 0.007 0.42 -10000 0 -0.71 77 77
Cbp/p300/CITED2 -0.011 0.42 0.81 2 -0.77 65 67
FOS -0.36 0.27 -10000 0 -0.55 342 342
HK2 0.006 0.42 -10000 0 -0.72 75 75
SP1 -0.018 0.093 -10000 0 -0.22 48 48
GCK 0.066 0.22 0.67 3 -0.52 2 5
HK1 0.007 0.43 -10000 0 -0.72 75 75
NPM1 0.004 0.42 -10000 0 -0.71 79 79
EGLN1 -0.02 0.4 -10000 0 -0.71 75 75
CREB1 0.04 0.01 -10000 0 -10000 0 0
PGM1 0.002 0.42 -10000 0 -0.71 78 78
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 -0.73 75 75
VEGFA 0.071 0.36 0.8 19 -0.59 47 66
HIF1A/JAB1 0.04 0.1 0.3 6 -0.41 4 10
CP -0.061 0.5 0.82 6 -0.78 118 124
CXCL12 -0.083 0.48 -10000 0 -0.79 115 115
COPS5 0.033 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4 0.047 0.028 -10000 0 -0.4 1 1
BNIP3 0.002 0.43 0.84 1 -0.72 80 81
EGLN3 0.024 0.44 0.82 13 -0.72 75 88
CA9 0.017 0.44 0.84 7 -0.7 80 87
TERT -0.008 0.41 -10000 0 -0.71 79 79
ENO1 0.006 0.42 -10000 0 -0.71 78 78
PFKL 0.004 0.42 -10000 0 -0.71 78 78
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 0.097 0.29 3 -0.16 1 4
HNF4A 0.035 0.009 -10000 0 -10000 0 0
ADFP -0.052 0.39 0.72 4 -0.72 77 81
SLC2A1 0.072 0.36 0.8 16 -0.58 49 65
LEP -0.14 0.48 -10000 0 -0.79 131 131
HIF1A/ARNT/Cbp/p300 -0.016 0.36 0.81 2 -0.69 52 54
EPO 0.071 0.31 0.79 12 -0.61 22 34
CREBBP 0.042 0.16 0.44 16 -0.28 12 28
HIF1A/ARNT/Cbp/p300/HDAC7 -0.009 0.35 0.79 5 -0.67 49 54
PFKFB3 -0.003 0.42 -10000 0 -0.73 74 74
NT5E -0.002 0.43 -10000 0 -0.74 77 77
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.11 0.078 -9999 0 -0.28 4 4
SMAD6-7/SMURF1 0.063 0.02 -9999 0 -10000 0 0
NOG 0.03 0.03 -9999 0 -0.54 1 1
SMAD9 -0.088 0.24 -9999 0 -0.68 62 62
SMAD4 0.031 0.027 -9999 0 -0.54 1 1
SMAD5 -0.1 0.19 -9999 0 -0.43 86 86
BMP7/USAG1 -0.23 0.2 -9999 0 -0.36 344 344
SMAD5/SKI -0.093 0.19 -9999 0 -0.43 79 79
SMAD1 0.004 0.09 -9999 0 -0.44 10 10
BMP2 -0.22 0.29 -9999 0 -0.54 226 226
SMAD1/SMAD1/SMAD4 0.029 0.087 -9999 0 -0.43 6 6
BMPR1A 0.03 0.044 -9999 0 -0.54 3 3
BMPR1B 0.085 0.069 -9999 0 -10000 0 0
BMPR1A-1B/BAMBI 0.079 0.12 -9999 0 -0.3 38 38
AHSG 0.033 0.006 -9999 0 -10000 0 0
CER1 0.032 0.011 -9999 0 -10000 0 0
BMP2-4/CER1 -0.16 0.23 -9999 0 -0.38 256 256
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.18 -9999 0 -0.4 89 89
BMP2-4 (homodimer) -0.21 0.25 -9999 0 -0.44 261 261
RGMB 0.033 0.007 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.022 0.19 -9999 0 -0.28 167 167
RGMA -0.049 0.2 -9999 0 -0.54 72 72
SMURF1 0.034 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.18 -9999 0 -0.4 108 108
BMP2-4/USAG1 -0.4 0.27 -9999 0 -0.51 401 401
SMAD6/SMURF1/SMAD5 -0.095 0.19 -9999 0 -0.43 77 77
SOSTDC1 -0.37 0.26 -9999 0 -0.54 352 352
BMP7/BMPR2/BMPR1A-1B 0.1 0.071 -9999 0 -0.32 3 3
SKI 0.033 0.007 -9999 0 -10000 0 0
BMP6 (homodimer) -0.16 0.27 -9999 0 -0.54 167 167
HFE2 0.031 0.038 -9999 0 -0.54 2 2
ZFYVE16 0.033 0.007 -9999 0 -10000 0 0
MAP3K7 0.032 0.009 -9999 0 -10000 0 0
BMP2-4/CHRD -0.16 0.23 -9999 0 -0.38 257 257
SMAD5/SMAD5/SMAD4 -0.095 0.19 -9999 0 -0.44 77 77
MAPK1 0.032 0.008 -9999 0 -10000 0 0
TAK1/TAB family -0.087 0.17 -9999 0 -0.36 97 97
BMP7 (homodimer) 0.042 0.042 -9999 0 -10000 0 0
NUP214 0.033 0.005 -9999 0 -10000 0 0
BMP6/FETUA -0.099 0.21 -9999 0 -0.39 170 170
SMAD1/SKI 0.014 0.095 -9999 0 -0.41 10 10
SMAD6 0.033 0.007 -9999 0 -10000 0 0
CTDSP2 0.033 0.006 -9999 0 -10000 0 0
BMP2-4/FETUA -0.16 0.23 -9999 0 -0.38 256 256
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 0.047 0.044 -9999 0 -10000 0 0
BMPR2 (homodimer) 0.033 0.005 -9999 0 -10000 0 0
GADD34/PP1CA 0.059 0.037 -9999 0 -0.34 2 2
BMPR1A-1B (homodimer) 0.081 0.062 -9999 0 -0.4 3 3
CHRDL1 -0.3 0.28 -9999 0 -0.54 298 298
ENDOFIN/SMAD1 0.014 0.097 -9999 0 -0.44 9 9
SMAD6-7/SMURF1/SMAD1 0.046 0.1 -9999 0 -0.47 6 6
SMAD6/SMURF1 0.033 0.005 -9999 0 -10000 0 0
BAMBI 0.016 0.16 -9999 0 -0.54 36 36
SMURF2 0.031 0.012 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.35 0.31 -9999 0 -0.54 349 349
BMP2-4/GREM1 -0.16 0.23 -9999 0 -0.37 261 261
SMAD7 0.033 0.007 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.079 0.23 -9999 0 -0.63 65 65
SMAD1/SMAD6 0.014 0.098 -9999 0 -0.5 6 6
TAK1/SMAD6 0.046 0.014 -9999 0 -10000 0 0
BMP7 0.042 0.042 -9999 0 -10000 0 0
BMP6 -0.16 0.27 -9999 0 -0.54 167 167
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.18 -9999 0 -0.4 106 106
PPM1A 0.033 0.006 -9999 0 -10000 0 0
SMAD1/SMURF2 0.012 0.093 -9999 0 -0.46 8 8
SMAD7/SMURF1 0.047 0.013 -9999 0 -10000 0 0
CTDSPL 0.031 0.037 -9999 0 -0.54 2 2
PPP1CA 0.033 0.02 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.033 0.005 -9999 0 -10000 0 0
PPP1R15A 0.031 0.036 -9999 0 -0.54 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.1 0.18 -9999 0 -0.38 110 110
CHRD 0.036 0.021 -9999 0 -10000 0 0
BMPR2 0.033 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.21 -9999 0 -0.45 110 110
BMP4 -0.039 0.19 -9999 0 -0.54 65 65
FST 0.032 0.039 -9999 0 -0.54 2 2
BMP2-4/NOG -0.16 0.22 -9999 0 -0.38 241 241
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.11 0.073 -9999 0 -0.3 3 3
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 -0.28 176 176
Ephrin B2/EPHB1-2 -0.075 0.19 -10000 0 -0.31 187 187
neuron projection morphogenesis -0.06 0.16 -10000 0 -0.27 176 176
Ephrin B1/EPHB1-2/Tiam1 -0.058 0.18 -10000 0 -0.3 182 182
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 0.25 -10000 0 -0.79 55 55
Ephrin B1/EPHB1-2/NCK2 -0.059 0.18 -10000 0 -0.3 184 184
PI3K -0.044 0.22 -10000 0 -0.55 68 68
mol:GDP -0.059 0.18 -10000 0 -0.29 182 182
ITGA2B 0.033 0.013 -10000 0 -10000 0 0
endothelial cell proliferation 0.037 0.046 -10000 0 -0.34 6 6
FYN -0.071 0.25 -10000 0 -0.79 55 55
MAP3K7 -0.058 0.19 -10000 0 -0.59 55 55
FGR -0.064 0.25 -10000 0 -0.78 55 55
TIAM1 0.034 0.012 0.17 3 -10000 0 3
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 -0.77 56 56
ITGB3 0.034 0.018 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 188 188
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
RAC1 0.033 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.038 0.046 -10000 0 -0.34 6 6
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 0.29 184 -10000 0 184
MAPK8 -0.055 0.18 -10000 0 -0.55 55 55
Ephrin B1/EPHB1-2/RGS3 -0.059 0.18 -10000 0 -0.3 179 179
endothelial cell migration -0.05 0.17 0.26 1 -0.5 58 59
NCK2 0.034 0.007 0.17 1 -10000 0 1
PTPN13 -0.027 0.2 -10000 0 -0.65 46 46
regulation of focal adhesion formation 0.06 0.18 0.29 184 -10000 0 184
chemotaxis 0.06 0.18 0.3 179 -10000 0 179
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.053 0.17 -10000 0 -0.28 176 176
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 -0.35 216 216
MAP3K8 -0.048 0.19 -9999 0 -0.55 64 64
FOS -0.099 0.12 -9999 0 -0.37 25 25
PRKCA -0.006 0.027 -9999 0 -10000 0 0
PTPN7 -0.002 0.044 -9999 0 -10000 0 0
HRAS 0.031 0.013 -9999 0 -10000 0 0
PRKCB -0.013 0.009 -9999 0 -0.018 357 357
NRAS 0.033 0.016 -9999 0 -10000 0 0
RAS family/GTP 0.028 0.037 -9999 0 -10000 0 0
MAPK3 -0.03 0.075 -9999 0 -0.61 3 3
MAP2K1 -0.055 0.089 -9999 0 -0.28 42 42
ELK1 -0.015 0.037 -9999 0 -10000 0 0
BRAF -0.016 0.037 -9999 0 -0.25 6 6
mol:GTP -0.004 0.003 -9999 0 -0.006 360 360
MAPK1 -0.053 0.11 -9999 0 -0.45 28 28
RAF1 -0.017 0.035 -9999 0 -0.25 5 5
KRAS 0.031 0.016 -9999 0 -10000 0 0
IL23-mediated signaling events

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.28 0.52 0.96 6 -1.2 63 69
IL23A -0.24 0.47 1.1 6 -1 51 57
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.46 0.76 2 -0.98 63 65
positive regulation of T cell mediated cytotoxicity -0.27 0.52 1.1 8 -0.89 119 127
ITGA3 -0.23 0.46 0.95 6 -0.98 57 63
IL17F -0.18 0.35 0.68 11 -0.66 68 79
IL12B 0.007 0.082 0.31 6 -10000 0 6
STAT1 (dimer) -0.26 0.5 0.88 6 -0.86 117 123
CD4 -0.24 0.46 0.95 5 -0.98 56 61
IL23 -0.24 0.45 0.92 6 -0.99 50 56
IL23R -0.019 0.21 0.74 4 -1.1 10 14
IL1B -0.25 0.48 1 8 -1 57 65
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.46 0.94 7 -0.98 51 58
TYK2 0.003 0.06 0.26 3 -10000 0 3
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 0.003 0.06 0.26 3 -10000 0 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.009 0.074 0.27 5 -10000 0 5
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 -0.89 119 127
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 0.89 7 -0.94 50 57
ALOX12B -0.24 0.46 0.95 5 -0.98 58 63
CXCL1 -0.64 0.73 1 8 -1.2 296 304
T cell proliferation -0.27 0.52 1.1 8 -0.89 119 127
NFKBIA 0.033 0.01 -10000 0 -10000 0 0
IL17A -0.12 0.3 0.64 13 -0.51 63 76
PI3K -0.28 0.47 0.78 2 -0.97 83 85
IFNG 0.022 0.074 0.17 65 -0.12 6 71
STAT3 (dimer) -0.26 0.46 0.76 2 -0.94 79 81
IL18R1 0.04 0.03 0.2 2 -0.54 1 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.33 0.76 11 -0.59 61 72
IL18/IL18R 0.064 0.14 0.28 24 -0.34 42 66
macrophage activation -0.013 0.029 0.075 21 -0.043 38 59
TNF -0.25 0.48 1.1 6 -1 56 62
STAT3/STAT4 -0.26 0.47 0.78 3 -1 66 69
STAT4 (dimer) -0.27 0.49 0.85 6 -0.89 113 119
IL18 0.047 0.044 -10000 0 -10000 0 0
IL19 -0.2 0.47 0.93 8 -0.98 51 59
STAT5A (dimer) -0.27 0.49 0.85 5 -0.85 125 130
STAT1 0.057 0.053 -10000 0 -10000 0 0
SOCS3 0.019 0.084 -10000 0 -0.54 11 11
CXCL9 -0.22 0.5 1.1 7 -1 56 63
MPO -0.23 0.46 0.99 5 -0.97 57 62
positive regulation of humoral immune response -0.27 0.52 1.1 8 -0.89 119 127
IL23/IL23R/JAK2/TYK2 -0.28 0.54 1.1 8 -1.1 66 74
IL6 -0.79 0.67 0.93 6 -1.2 364 370
STAT5A 0.031 0.027 -10000 0 -0.54 1 1
IL2 0.048 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 -0.98 57 62
keratinocyte proliferation -0.27 0.52 1.1 8 -0.89 119 127
NOS2 -0.25 0.46 0.88 8 -0.75 158 166
IL6-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 -0.024 0.3 0.66 3 -0.72 32 35
CRP 0 0.31 0.73 5 -0.75 27 32
cell cycle arrest -0.052 0.34 0.64 7 -0.75 53 60
TIMP1 -0.014 0.28 0.65 10 -0.62 32 42
IL6ST 0.038 0.08 -10000 0 -0.54 8 8
Rac1/GDP -0.088 0.22 0.41 8 -0.42 86 94
AP1 -0.16 0.24 0.49 4 -0.53 87 91
GAB2 0.033 0.015 -10000 0 -10000 0 0
TNFSF11 -0.007 0.31 0.69 7 -0.73 27 34
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 0.32 1 -0.53 60 61
AKT1 0.032 0.09 0.34 1 -0.4 9 10
FOXO1 0.007 0.13 0.32 3 -0.43 17 20
MAP2K6 -0.12 0.2 0.35 3 -0.44 87 90
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.056 0.24 0.46 11 -0.48 66 77
MITF -0.11 0.21 0.33 8 -0.42 98 106
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.033 0.005 -10000 0 -10000 0 0
A2M -0.16 0.49 -10000 0 -1.3 72 72
CEBPB 0.038 0.03 -10000 0 -0.54 1 1
GRB2/SOS1/GAB family/SHP2 -0.001 0.14 0.36 2 -0.48 21 23
STAT3 -0.071 0.36 0.64 7 -0.81 54 61
STAT1 0.033 0.12 -10000 0 -0.85 7 7
CEBPD -0.08 0.43 0.67 4 -1 70 74
PIK3CA 0.034 0.008 -10000 0 -10000 0 0
PI3K 0.008 0.13 -10000 0 -0.4 42 42
JUN -0.065 0.22 -10000 0 -0.54 86 86
PIAS3/MITF -0.1 0.2 0.35 4 -0.4 92 96
MAPK11 -0.12 0.2 0.32 1 -0.53 60 61
STAT3 (dimer)/FOXO1 -0.085 0.33 0.56 12 -0.65 74 86
GRB2/SOS1/GAB family -0.083 0.18 0.36 2 -0.44 47 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.19 0.31 4 -0.41 99 103
GRB2 0.035 0.018 -10000 0 -10000 0 0
JAK2 0.032 0.011 -10000 0 -10000 0 0
LBP 0.009 0.28 0.65 13 -0.62 23 36
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
JAK1 0.037 0.012 -10000 0 -10000 0 0
MYC -0.014 0.38 0.72 9 -0.95 42 51
FGG -0.026 0.3 0.69 3 -0.73 30 33
macrophage differentiation -0.052 0.34 0.64 7 -0.75 53 60
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.19 -10000 0 -0.3 269 269
JUNB -0.031 0.3 0.64 3 -0.74 31 34
FOS -0.36 0.27 -10000 0 -0.54 342 342
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.35 11 -0.43 100 111
STAT1/PIAS1 -0.073 0.22 0.4 13 -0.43 81 94
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.094 -10000 0 -0.41 10 10
STAT3 (dimer) -0.068 0.35 0.64 7 -0.8 53 60
PRKCD -0.034 0.26 0.52 13 -0.53 54 67
IL6R 0.03 0.031 -10000 0 -0.55 1 1
SOCS3 -0.15 0.24 -10000 0 -0.89 27 27
gp130 (dimer)/JAK1/JAK1/LMO4 0.072 0.12 0.31 2 -0.33 29 31
Rac1/GTP -0.077 0.23 0.42 10 -0.43 85 95
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 0.69 7 -0.69 27 34
IRF1 -0.024 0.3 0.66 7 -0.71 33 40
mol:GDP -0.1 0.21 0.38 11 -0.42 96 107
SOS1 0.037 0.009 -10000 0 -10000 0 0
VAV1 -0.1 0.22 0.38 11 -0.42 97 108
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.2 -10000 0 -0.56 61 61
PTPN11 0.02 0.094 -10000 0 -0.81 5 5
IL6/IL6RA -0.23 0.2 -10000 0 -0.38 307 307
gp130 (dimer)/TYK2/TYK2/LMO4 0.067 0.11 0.28 1 -0.33 26 27
gp130 (dimer)/JAK2/JAK2/LMO4 0.062 0.11 0.28 1 -0.33 29 30
IL6 -0.37 0.27 0.22 1 -0.54 361 362
PIAS3 0.032 0.008 -10000 0 -10000 0 0
PTPRE 0.003 0.043 -10000 0 -0.52 1 1
PIAS1 0.033 0.006 -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 -0.3 190 193
LMO4 0.028 0.12 0.24 3 -0.54 21 24
STAT3 (dimer)/PIAS3 -0.066 0.33 0.62 6 -0.72 58 64
MCL1 0.07 0.12 0.52 2 -0.47 1 3
Plasma membrane estrogen receptor signaling

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.79 130 130
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.18 0.38 -10000 0 -0.8 130 130
mol:Ca2+ -0.033 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 -0.02 0.17 0.22 1 -0.34 104 105
SHC1 0.027 0.014 -10000 0 -10000 0 0
apoptosis 0.17 0.35 0.74 132 -10000 0 132
RhoA/GTP -0.025 0.12 -10000 0 -0.27 82 82
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.14 0.23 0.31 1 -0.45 136 137
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 -0.34 106 106
KRAS 0.034 0.016 -10000 0 -10000 0 0
G13/GTP -0.02 0.15 -10000 0 -0.31 99 99
pseudopodium formation -0.017 0.12 0.25 19 -10000 0 19
E2/ER alpha (dimer)/PELP1 -0.025 0.17 -10000 0 -0.34 106 106
GRB2 0.033 0.017 -10000 0 -10000 0 0
GNG2 0.032 0.026 -10000 0 -0.54 1 1
GNAO1 0.029 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 -0.5 138 138
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 -0.5 138 138
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 -0.037 0.12 -10000 0 -0.32 45 45
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 -0.5 138 138
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 -10000 0 -0.54 106 106
Gq family/GDP/Gbeta gamma 0.008 0.15 -10000 0 -0.83 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.031 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 0.18 -10000 0 -0.39 110 110
STRN 0.033 0.027 -10000 0 -0.54 1 1
GNAL 0.029 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 0.033 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 -0.42 145 149
PI3K 0.006 0.12 -10000 0 -0.38 46 46
GNB1 0.033 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 -0.43 206 206
Gs family/GTP -0.013 0.14 -10000 0 -0.28 102 102
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.06 0.024 -10000 0 -10000 0 0
vasodilation -0.14 0.24 -10000 0 -0.48 138 138
mol:DAG -0.037 0.12 -10000 0 -0.32 45 45
Gs family/GDP/Gbeta gamma -0.041 0.16 -10000 0 -0.35 86 86
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 -0.76 130 130
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 0.48 138 -10000 0 138
GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
RhoA/GDP -0.028 0.19 -10000 0 -0.38 95 95
NOS3 -0.15 0.26 -10000 0 -0.53 137 137
GNA11 0.033 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.13 0.27 -10000 0 -0.57 129 129
E2/ER alpha (dimer)/PELP1/Src -0.14 0.24 0.31 3 -0.47 137 140
ruffle organization -0.017 0.12 0.25 19 -10000 0 19
ROCK2 -0.017 0.13 0.35 5 -10000 0 5
GNA14 0.042 0.066 -10000 0 -0.54 4 4
GNA15 0.035 0.017 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MMP9 -0.099 0.22 0.4 7 -0.55 55 62
MMP2 -0.14 0.22 0.3 6 -0.53 64 70
FAS signaling pathway (CD95)

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
SPTAN1 0.016 0.089 0.21 72 -10000 0 72
RFC1 0.016 0.085 0.21 72 -10000 0 72
PRKDC 0.037 0.11 0.23 108 -10000 0 108
RIPK1 0.04 0.009 -10000 0 -10000 0 0
CASP7 -0.041 0.11 -10000 0 -0.75 9 9
FASLG/FAS/FADD/FAF1 -0.023 0.09 0.26 9 -0.31 16 25
MAP2K4 -0.18 0.19 -10000 0 -0.44 91 91
mol:ceramide -0.075 0.12 0.26 1 -0.37 30 31
GSN -0.059 0.17 0.22 59 -0.34 104 163
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 0.27 2 -0.43 29 31
MAP3K7 0.025 0.01 -10000 0 -10000 0 0
RB1 0.017 0.083 0.21 71 -10000 0 71
CFLAR 0.039 0.026 -10000 0 -0.52 1 1
HGF/MET -0.01 0.17 -10000 0 -0.36 89 89
ARHGDIB 0.019 0.094 0.22 73 -10000 0 73
FADD -0.008 0.028 -10000 0 -10000 0 0
actin filament polymerization 0.056 0.17 0.34 104 -0.21 66 170
NFKB1 -0.1 0.12 -10000 0 -0.65 8 8
MAPK8 -0.31 0.25 -10000 0 -0.45 365 365
DFFA 0.016 0.085 0.21 68 -10000 0 68
DNA fragmentation during apoptosis 0.02 0.09 0.21 68 -10000 0 68
FAS/FADD/MET -0.034 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 74 -10000 0 74
DFFB 0.015 0.086 0.21 68 -10000 0 68
CHUK -0.098 0.12 -10000 0 -0.61 8 8
FASLG 0.001 0.061 -10000 0 -0.55 1 1
FAS/FADD -0.033 0.1 -10000 0 -0.4 30 30
HGF 0.034 0.01 -10000 0 -10000 0 0
LMNA 0.023 0.1 0.42 15 -10000 0 15
CASP6 0.017 0.086 0.21 69 -10000 0 69
CASP10 -0.012 0.029 -10000 0 -10000 0 0
CASP3 0.021 0.1 0.26 68 -0.22 16 84
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 -0.38 30 31
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
IL4-mediated signaling events

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
BCL2L1 -0.14 0.62 0.93 3 -1.1 98 101
STAT6 (cleaved dimer) -0.23 0.54 -10000 0 -1.1 105 105
IGHG1 0.024 0.29 0.62 15 -0.66 8 23
IGHG3 -0.15 0.58 0.78 3 -1.1 107 110
AKT1 -0.026 0.35 0.65 1 -0.72 34 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.028 0.28 0.61 2 -0.88 12 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.026 0.37 0.64 6 -0.77 36 42
THY1 -0.14 0.62 1 5 -1.1 99 104
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 -0.005 0.4 0.73 12 -0.64 60 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.001 0.34 0.63 6 -0.82 17 23
SP1 0.056 0.044 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.007 0.056 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.16 0.59 0.83 1 -1.1 103 104
SOCS1 -0.06 0.41 0.76 1 -0.72 79 80
SOCS3 -0.014 0.38 0.69 1 -1.1 20 21
FCER2 -0.14 0.52 0.87 6 -0.87 88 94
PARP14 0.042 0.031 -10000 0 -10000 0 0
CCL17 -0.12 0.64 1 9 -1.1 100 109
GRB2 0.033 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.029 0.29 0.59 8 -0.71 13 21
T cell proliferation -0.19 0.62 -10000 0 -1.2 104 104
IL4R/JAK1 -0.15 0.6 -10000 0 -1.2 95 95
EGR2 -0.52 0.86 0.98 4 -1.3 250 254
JAK2 0.029 0.088 0.27 1 -10000 0 1
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 0.037 0.31 0.66 9 -1.1 10 19
CCL26 -0.14 0.62 1.1 4 -1.1 99 103
IL4R -0.14 0.68 1.1 6 -1.2 96 102
PTPN6 0.015 0.044 0.2 1 -10000 0 1
IL13RA2 -0.15 0.63 0.96 4 -1.1 107 111
IL13RA1 0.031 0.091 0.26 4 -10000 0 4
IRF4 0.063 0.2 0.7 3 -0.68 7 10
ARG1 0.047 0.26 0.73 3 -1 5 8
CBL -0.016 0.36 0.65 6 -0.61 57 63
GTF3A 0.099 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 0.028 0.21 -10000 0 -0.66 9 9
CD40LG 0.048 0.032 0.31 2 -10000 0 2
MAPK14 -0.014 0.38 0.66 6 -0.66 52 58
mitosis -0.02 0.34 0.62 2 -0.67 34 36
STAT6 -0.16 0.75 1.2 14 -1.3 105 119
SPI1 0.043 0.033 -10000 0 -0.24 1 1
RPS6KB1 -0.003 0.33 0.64 5 -0.69 26 31
STAT6 (dimer) -0.15 0.75 1.2 14 -1.3 105 119
STAT6 (dimer)/PARP14 -0.17 0.64 -10000 0 -1.2 105 105
mast cell activation -0.006 0.026 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.017 0.36 0.62 7 -0.73 39 46
FRAP1 -0.026 0.35 0.65 1 -0.72 34 35
LTA -0.14 0.62 0.93 3 -1.1 103 106
FES 0.03 0.037 -10000 0 -0.54 2 2
T-helper 1 cell differentiation 0.14 0.73 1.3 105 -1.1 14 119
CCL11 -0.11 0.6 0.88 5 -1.1 100 105
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.01 0.34 0.62 5 -0.89 16 21
IL2RG 0.044 0.041 0.21 10 -10000 0 10
IL10 -0.11 0.62 1 11 -1.1 93 104
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 116 116
IL4 0.042 0.3 0.8 6 -1 14 20
IL5 -0.14 0.62 1 3 -1.1 100 103
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.061 0.54 0.97 13 -0.87 92 105
COL1A1 0.12 0.4 0.75 41 -0.93 24 65
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.16 0.62 -10000 0 -1.2 87 87
IL2R gamma/JAK3 0.062 0.039 -10000 0 -10000 0 0
TFF3 -0.27 0.73 0.93 3 -1.3 139 142
ALOX15 -0.14 0.62 0.93 3 -1.1 99 102
MYBL1 0.048 0.053 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.096 0.53 0.81 7 -0.9 103 110
SHC1 0.027 0.014 -10000 0 -10000 0 0
CEBPB 0.034 0.034 -10000 0 -0.39 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.044 0.36 0.62 5 -0.7 42 47
mol:PI-3-4-5-P3 -0.025 0.35 0.65 1 -0.72 34 35
PI3K -0.032 0.37 0.66 1 -0.78 34 35
DOK2 0.025 0.039 -10000 0 -0.54 2 2
ETS1 0.002 0.059 -10000 0 -0.51 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.038 0.28 0.57 8 -0.69 11 19
ITGB3 -0.14 0.62 0.96 4 -1.1 99 103
PIGR -0.39 0.84 1 11 -1.3 205 216
IGHE -0.041 0.1 0.17 16 -0.26 25 41
MAPKKK cascade 0.039 0.27 0.57 9 -0.67 11 20
BCL6 -0.023 0.17 -10000 0 -0.54 48 48
OPRM1 -0.14 0.62 0.93 3 -1.1 98 101
RETNLB -0.14 0.62 0.93 3 -1.1 98 101
SELP -0.29 0.82 0.97 10 -1.4 157 167
AICDA -0.14 0.59 0.94 1 -1.1 99 100
Integrins in angiogenesis

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
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 0.39 2 -0.47 7 9
IGF1R 0.01 0.12 -10000 0 -0.54 21 21
PI4KB 0.027 0.014 -10000 0 -10000 0 0
MFGE8 0.008 0.12 -10000 0 -0.54 24 24
SRC 0.032 0.008 -10000 0 -10000 0 0
CDKN1B -0.099 0.13 -10000 0 -0.57 26 26
VEGFA 0.049 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 -0.3 273 274
CBL 0.03 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.063 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 0.038 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 -0.49 270 270
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 0.098 0.067 0.25 8 -0.34 4 12
RPS6KB1 -0.28 0.23 0.6 1 -0.51 200 201
TLN1 0.033 0.006 -10000 0 -10000 0 0
MAPK3 -0.36 0.29 -10000 0 -0.55 337 337
GPR124 0.008 0.1 -10000 0 -0.54 17 17
MAPK1 -0.38 0.29 -10000 0 -0.55 350 350
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 0.091 -10000 0 -0.3 29 29
ANGPTL3 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.071 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 0.034 0.018 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 250 250
RAC1 0.033 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 0.17 2 -0.54 1 3
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 0.095 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 -0.27 244 244
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 -0.38 7 9
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 0.17 2 -0.54 375 377
F11R -0.23 0.2 -10000 0 -0.4 293 293
alphaV/beta3 Integrin/Lactadherin 0.047 0.088 0.25 1 -0.34 21 22
alphaV/beta3 Integrin/TGFBR2 0.038 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 0.071 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 0.38 3 -0.38 7 10
cell migration -0.033 0.1 0.36 3 -0.35 7 10
ITGAV 0.033 0.028 0.17 2 -0.54 1 3
PI3K -0.16 0.18 -10000 0 -0.31 268 268
SPP1 0.089 0.085 -10000 0 -0.54 3 3
KDR 0.033 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 0.17 2 -0.54 1 3
COL4A3 0.033 0.006 -10000 0 -10000 0 0
angiogenesis -0.37 0.28 -10000 0 -0.55 339 339
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
Visual signal transduction: Rods

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
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 -0.34 1 1
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 -0.09 0.17 -10000 0 -0.28 207 207
mol:Na + -0.089 0.17 -10000 0 -0.28 215 215
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 0.18 -10000 0 -0.29 215 215
CNGB1 0.029 0.012 -10000 0 -10000 0 0
RDH5 -0.43 0.23 -10000 0 -0.54 409 409
SAG 0.054 0.058 -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 -0.27 212 212
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 0.056 0.092 -10000 0 -0.27 28 28
GUCY2D 0.03 0.011 -10000 0 -10000 0 0
GNGT1 0.065 0.059 -10000 0 -10000 0 0
GUCY2F 0.032 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 0.033 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 0.037 0.071 -10000 0 -0.37 14 14
mol:Pi 0.047 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 0.17 5 -0.54 12 17
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 0.032 0.027 -10000 0 -0.54 1 1
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.037 0.19 -10000 0 -0.54 61 61
LAT2 -0.03 0.13 -10000 0 -0.35 50 50
AP1 -0.19 0.23 -10000 0 -0.45 164 164
mol:PIP3 0.004 0.19 0.34 29 -0.41 49 78
IKBKB 0.02 0.14 0.28 47 -0.25 41 88
AKT1 -0.007 0.2 0.34 72 -0.46 28 100
IKBKG 0.003 0.13 0.26 26 -0.25 43 69
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 0.009 0.15 0.35 12 -0.38 30 42
mol:Ca2+ 0.012 0.16 0.31 31 -0.31 48 79
LYN 0.031 0.017 -10000 0 -10000 0 0
CBLB -0.03 0.13 -10000 0 -0.36 46 46
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 -0.013 0.2 0.34 63 -0.34 90 153
PTPN13 -0.039 0.19 -10000 0 -0.59 27 27
PTPN11 0.032 0.021 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.001 0.16 0.36 19 -0.35 29 48
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 -0.38 67 67
LAT -0.026 0.12 0.21 2 -0.34 49 51
PAK2 0.007 0.16 0.36 12 -0.42 28 40
NFATC2 -0.012 0.057 -10000 0 -0.69 1 1
HRAS 0.003 0.16 0.3 12 -0.43 32 44
GAB2 0.029 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 -0.42 94 94
Antigen/IgE/Fc epsilon R1 -0.032 0.18 0.23 1 -0.38 94 95
mol:GDP -0.024 0.15 0.28 2 -0.44 30 32
JUN -0.065 0.22 -10000 0 -0.54 86 86
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.019 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 53 53
CHUK 0.002 0.13 0.26 26 -0.25 44 70
KLRG1 -0.025 0.12 -10000 0 -0.32 45 45
VAV1 -0.029 0.13 0.21 2 -0.34 51 53
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 -0.34 31 31
BTK -0.024 0.15 -10000 0 -0.46 30 30
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.047 0.17 -10000 0 -0.37 87 87
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 -0.36 49 49
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 -0.6 35 35
DUSP1 -0.2 0.28 -10000 0 -0.54 208 208
NF-kappa-B/RelA 0.012 0.081 0.19 8 -0.18 22 30
actin cytoskeleton reorganization -0.015 0.18 -10000 0 -0.58 23 23
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.012 0.17 -10000 0 -0.45 38 38
FER -0.029 0.13 -10000 0 -0.35 48 48
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 -0.002 0.17 0.32 7 -0.43 33 40
cytokine secretion -0.006 0.047 -10000 0 -10000 0 0
SPHK1 -0.026 0.12 -10000 0 -0.35 45 45
PTK2 -0.017 0.18 -10000 0 -0.61 23 23
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.04 0.16 -10000 0 -0.39 73 73
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.032 0.22 0.34 21 -0.45 70 91
MAP2K2 0.004 0.11 -10000 0 -0.85 7 7
MAP2K1 0.004 0.11 -10000 0 -0.85 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 -0.074 0.32 -10000 0 -0.86 68 68
Fc epsilon R1/FcgammaRIIB -0.02 0.19 -10000 0 -0.38 94 94
mol:Choline -0.013 0.2 0.34 63 -0.34 90 153
SHC/Grb2/SOS1 0.009 0.14 -10000 0 -0.39 26 26
FYN 0.029 0.037 -10000 0 -0.54 2 2
DOK1 0.035 0.016 -10000 0 -10000 0 0
PXN -0.016 0.17 -10000 0 -0.56 22 22
HCLS1 -0.028 0.13 0.21 1 -0.35 46 47
PRKCB -0.005 0.16 0.3 26 -0.32 62 88
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 -0.34 31 31
LCP2 0.036 0.023 -10000 0 -10000 0 0
PLA2G4A -0.15 0.2 -10000 0 -0.35 215 215
RASA1 0.033 0.011 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.013 0.2 0.34 63 -0.34 90 153
IKK complex 0.021 0.12 0.27 37 -0.21 28 65
WIPF1 0.037 0.022 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.048 0.033 0.22 2 -0.34 1 3
cell-cell adhesion 0.1 0.12 0.27 162 -10000 0 162
Ephrin B/EPHB2/RasGAP 0.081 0.064 -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 -0.098 0.19 -10000 0 -0.34 187 187
HRAS/GDP -0.081 0.16 -10000 0 -0.37 45 45
Ephrin B/EPHB1/GRB7 -0.055 0.18 -10000 0 -0.31 156 156
Endophilin/SYNJ1 0.018 0.048 0.26 1 -0.28 6 7
KRAS 0.034 0.016 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.055 0.19 -10000 0 -0.31 169 169
endothelial cell migration 0.027 0.11 -10000 0 -0.3 45 45
GRB2 0.033 0.017 -10000 0 -10000 0 0
GRB7 0.028 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 0.017 0.047 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 -0.29 186 188
lamellipodium assembly -0.1 0.12 -10000 0 -0.27 162 162
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.061 0.14 -10000 0 -0.28 123 123
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
EPHB2 0.042 0.036 -10000 0 -10000 0 0
EPHB3 0.034 0.015 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 188 188
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
mol:GDP -0.081 0.14 -10000 0 -0.39 41 41
Ephrin B/EPHB2 0.067 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 -0.3 179 183
Ephrin B/EPHB1 -0.069 0.18 -10000 0 -0.3 186 186
RAP1/GDP -0.059 0.14 -10000 0 -0.36 35 35
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 -0.32 187 187
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.033 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.061 0.17 -10000 0 -0.34 41 41
Rap1/GTP -0.074 0.14 -10000 0 -0.47 6 6
axon guidance 0.047 0.032 0.22 2 -0.34 1 3
MAPK3 -0.056 0.13 0.26 1 -0.38 29 30
MAPK1 -0.062 0.13 -10000 0 -0.38 30 30
Rac1/GDP -0.073 0.14 -10000 0 -0.37 39 39
actin cytoskeleton reorganization -0.078 0.11 -10000 0 -0.3 31 31
CDC42/GDP -0.072 0.14 -10000 0 -0.37 39 39
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 -0.34 6 6
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 -0.075 0.14 -10000 0 -0.27 151 151
PTK2 0.14 0.27 0.67 101 -10000 0 101
MAP4K4 -0.091 0.16 0.39 4 -0.3 179 183
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 -0.35 11 16
MAP2K1 -0.057 0.13 -10000 0 -0.4 30 30
WASL 0.032 0.026 -10000 0 -0.54 1 1
Ephrin B1/EPHB1-2/NCK1 -0.061 0.2 -10000 0 -0.31 187 187
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 0.048 0.26 1 -0.28 6 7
PXN 0.034 0.003 -10000 0 -10000 0 0
TF -0.014 0.067 0.25 1 -0.28 21 22
HRAS/GTP -0.06 0.16 -10000 0 -0.28 174 174
Ephrin B1/EPHB1-2 -0.072 0.18 -10000 0 -0.31 187 187
cell adhesion mediated by integrin -0.009 0.047 0.27 6 -0.2 10 16
RAC1 0.033 0.005 -10000 0 -10000 0 0
mol:GTP -0.061 0.18 -10000 0 -0.29 177 177
RAC1-CDC42/GTP -0.086 0.14 -10000 0 -0.46 6 6
RASA1 0.033 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.062 0.14 -10000 0 -0.36 38 38
ruffle organization -0.095 0.14 0.41 3 -0.47 7 10
NCK1 0.033 0.005 -10000 0 -10000 0 0
receptor internalization -0.006 0.048 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 0.093 -10000 0 -0.31 25 25
Rac1/GTP -0.087 0.14 -10000 0 -0.28 162 162
Ephrin B/EPHB1/Src/Paxillin -0.085 0.16 -10000 0 -0.41 42 42
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.035 0.043 0.12 4 -0.12 27 31
BUB1B 0.093 0.062 0.17 110 -10000 0 110
PLK1 0.046 0.035 0.11 62 -10000 0 62
PLK1S1 0.023 0.019 0.059 47 -10000 0 47
KIF2A 0.038 0.037 0.27 4 -10000 0 4
regulation of mitotic centrosome separation 0.046 0.035 0.11 62 -10000 0 62
GOLGA2 0.034 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.1 0.061 0.16 218 -10000 0 218
WEE1 0.049 0.077 0.22 1 -0.32 15 16
cytokinesis 0.13 0.081 0.21 155 -0.39 1 156
PP2A-alpha B56 0.14 0.11 -10000 0 -0.47 5 5
AURKA 0.05 0.039 0.13 18 -0.16 2 20
PICH/PLK1 0.13 0.093 0.24 168 -10000 0 168
CENPE 0.083 0.066 0.17 123 -10000 0 123
RhoA/GTP 0.024 0.005 -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 0.033 0.009 -10000 0 -10000 0 0
TPX2 0.08 0.037 0.12 96 -10000 0 96
PAK1 0.042 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 0.14 21 -0.2 12 33
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 47 -10000 0 47
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 62 -10000 0 62
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 0.065 0.17 7 -0.21 10 17
CDC25B 0.047 0.04 -10000 0 -10000 0 0
SGOL1 0.035 0.043 0.12 27 -0.12 4 31
RHOA 0.033 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.09 0.065 0.24 26 -0.21 1 27
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 0.14 171 -10000 0 171
mitosis -0.001 0.003 0.033 2 -10000 0 2
FBXO5 0.038 0.043 0.16 20 -10000 0 20
CDC2 0.005 0.004 0.015 31 -10000 0 31
NDC80 0.11 0.072 -10000 0 -10000 0 0
metaphase plate congression 0.028 0.055 -10000 0 -0.21 22 22
ERCC6L 0.12 0.093 0.23 158 -10000 0 158
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 0.034 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.013 11 -10000 0 11
PLK1/PRC1-2 0.17 0.096 0.26 222 -10000 0 222
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 0.093 77 -10000 0 77
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 0.17 259 -10000 0 259
Golgi organization 0.046 0.035 0.11 62 -10000 0 62
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 0.18 148 -10000 0 148
PPP2R1A 0.033 0.005 -10000 0 -10000 0 0
chromosome segregation 0.072 0.053 0.13 171 -10000 0 171
PRC1 0.099 0.072 -10000 0 -10000 0 0
ECT2 0.071 0.073 0.2 88 -10000 0 88
C13orf34 0.039 0.03 0.092 62 -10000 0 62
NUDC 0.028 0.055 -10000 0 -0.21 22 22
regulation of attachment of spindle microtubules to kinetochore 0.092 0.062 0.16 150 -10000 0 150
spindle assembly 0.036 0.029 0.099 34 -10000 0 34
spindle stabilization 0.023 0.019 0.059 47 -10000 0 47
APC/C/HCDH1 0.021 0.06 -10000 0 -0.34 13 13
MKLP2/PLK1 0.12 0.064 0.17 259 -10000 0 259
CCNB1 0.085 0.068 -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 -0.31 5 6
TUBG1 0.026 0.039 0.11 6 -0.15 17 23
G2/M transition of mitotic cell cycle 0.061 0.063 0.21 25 -0.21 1 26
MLF1IP 0.07 0.065 0.14 19 -10000 0 19
INCENP 0.047 0.039 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.043 0.24 0.58 2 -0.55 75 77
IHH 0.021 0.075 -10000 0 -10000 0 0
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 -0.002 0.18 0.41 2 -0.47 30 32
SMO -0.016 0.18 0.44 2 -0.48 33 35
AKT1 -0.019 0.19 0.3 1 -0.59 35 36
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 -0.015 0.18 0.44 2 -0.47 33 35
STIL 0.041 0.15 0.34 31 -0.34 7 38
DHH N/PTCH2 0.049 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 0.006 0.16 0.38 2 -0.32 84 86
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 -0.89 93 99
determination of left/right symmetry -0.015 0.18 0.44 2 -0.47 33 35
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
skeletal system development -0.11 0.38 0.52 6 -0.88 93 99
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 -0.015 0.18 0.44 2 -0.47 33 35
pancreas development 0.034 0.012 -10000 0 -10000 0 0
HHAT 0.023 0.059 -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 -0.015 0.18 0.44 2 -0.47 33 35
SHH Np/Cholesterol/PTCH1 -0.009 0.12 -10000 0 -0.27 61 61
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 -0.009 0.18 0.46 2 -0.36 85 87
SMO/Vitamin D3 0.01 0.17 0.41 15 -0.36 28 43
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 -0.062 0.2 0.35 8 -0.5 40 48
SHH Np/Cholesterol/BOC -0.038 0.13 -10000 0 -0.31 85 85
SHH Np/Cholesterol/CDO 0.019 0.049 -10000 0 -0.35 7 7
mesenchymal cell differentiation -0.024 0.038 0.31 5 -10000 0 5
mol:Vitamin D3 0.027 0.16 0.41 16 -0.33 15 31
IHH N/PTCH2 0.037 0.051 -10000 0 -10000 0 0
CDON 0.027 0.045 -10000 0 -0.54 3 3
IHH N/PTCH1 -0.001 0.18 0.46 2 -0.36 85 87
Megalin/LRPAP1 -0.073 0.2 -10000 0 -0.4 136 136
PTCH2 0.033 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.014 0.034 -10000 0 -0.31 5 5
PTCH1 -0.009 0.18 0.46 2 -0.36 85 87
HHIP 0.034 0.012 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.024 0.12 0.24 1 -0.32 44 45
adherens junction organization -0.024 0.12 0.23 1 -0.32 52 53
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 0.32 3 -0.38 98 101
FMN1 -0.024 0.11 -10000 0 -0.3 52 52
mol:IP3 -0.023 0.097 -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 44 44
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.026 0.17 -10000 0 -0.51 39 39
CTNND1 0.033 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.02 0.1 -10000 0 -0.31 40 40
VASP -0.019 0.12 -10000 0 -0.37 23 23
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 -0.41 113 113
E-cadherin/beta catenin-gamma catenin 0.035 0.089 -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 -0.005 0.12 -10000 0 -0.3 49 49
FYN -0.024 0.11 0.24 1 -0.39 21 22
mol:Ca2+ -0.022 0.095 -10000 0 -0.28 41 41
JUP 0.033 0.011 -10000 0 -10000 0 0
PIK3R1 -0.017 0.16 -10000 0 -0.54 45 45
mol:DAG -0.023 0.097 -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 98 101
establishment of polarity of embryonic epithelium -0.019 0.11 -10000 0 -0.37 23 23
SRC 0.032 0.008 -10000 0 -10000 0 0
RAC1 0.033 0.005 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
EGFR -0.26 0.29 -10000 0 -0.54 261 261
CASR -0.022 0.096 0.23 2 -0.31 15 17
RhoA/GTP -0.005 0.1 -10000 0 -0.3 15 15
AKT2 -0.02 0.11 -10000 0 -0.29 44 44
actin cable formation -0.02 0.11 0.26 2 -0.36 23 25
apoptosis 0.017 0.12 0.31 45 -0.26 4 49
CTNNA1 0.033 0.007 -10000 0 -10000 0 0
mol:GDP -0.15 0.18 -10000 0 -0.4 99 99
PIP5K1A -0.021 0.1 -10000 0 -0.32 40 40
PLCG1 -0.024 0.099 -10000 0 -0.29 41 41
Rac1/GTP -0.14 0.18 -10000 0 -0.39 110 110
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.049 0.076 0.25 32 -10000 0 32
STMN1 0.054 0.083 0.28 44 -10000 0 44
Aurora B/RasGAP/Survivin 0.11 0.075 0.26 1 -10000 0 1
Chromosomal passenger complex/Cul3 protein complex -0.07 0.13 0.21 19 -0.32 28 47
BIRC5 0.12 0.074 -10000 0 -10000 0 0
DES -0.01 0.13 -10000 0 -0.55 24 24
Aurora C/Aurora B/INCENP 0.075 0.051 0.23 2 -10000 0 2
Aurora B/TACC1 0.025 0.088 -10000 0 -0.3 27 27
Aurora B/PP2A 0.057 0.04 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.019 0.021 0.14 2 -10000 0 2
mitotic metaphase/anaphase transition -0.002 0.004 -10000 0 -10000 0 0
NDC80 0.099 0.1 0.28 83 -10000 0 83
Cul3 protein complex -0.23 0.18 -10000 0 -0.34 358 358
KIF2C 0.13 0.1 0.22 259 -10000 0 259
PEBP1 0.038 0.027 -10000 0 -0.54 1 1
KIF20A 0.12 0.068 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.056 0.04 -10000 0 -10000 0 0
SEPT1 0.034 0.023 -10000 0 -10000 0 0
SMC2 0.04 0.029 -10000 0 -10000 0 0
SMC4 0.045 0.04 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.064 0.16 0.31 12 -0.41 32 44
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 0.03 0.036 -10000 0 -10000 0 0
AURKB 0.05 0.052 0.2 1 -10000 0 1
AURKC 0.035 0.019 -10000 0 -10000 0 0
CDCA8 0.1 0.072 -10000 0 -10000 0 0
cytokinesis 0.18 0.15 0.35 194 -10000 0 194
Aurora B/Septin1 0.17 0.15 0.37 127 -10000 0 127
AURKA 0.076 0.066 -10000 0 -10000 0 0
INCENP 0.053 0.039 -10000 0 -10000 0 0
KLHL13 -0.38 0.26 -10000 0 -0.54 364 364
BUB1 0.15 0.052 0.21 1 -10000 0 1
hSgo1/Aurora B/Survivin 0.12 0.097 0.3 64 -10000 0 64
EVI5 0.036 0.026 -10000 0 -0.53 1 1
RhoA/GTP 0.21 0.14 0.35 198 -10000 0 198
SGOL1 0.072 0.063 -10000 0 -10000 0 0
CENPA 0.14 0.12 0.27 190 -10000 0 190
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.057 0.04 -10000 0 -10000 0 0
NCAPD2 0.035 0.021 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.058 0.04 -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 0.026 0.098 -10000 0 -0.4 11 11
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 0.04 -10000 0 -10000 0 0
PPP1CC 0.034 0.004 -10000 0 -10000 0 0
Centraspindlin 0.23 0.15 0.38 219 -10000 0 219
RhoA/GDP 0.024 0.005 -10000 0 -10000 0 0
NSUN2 0.026 0.091 -10000 0 -0.75 2 2
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 0.079 0.064 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.025 0.11 -10000 0 -0.39 18 18
Chromosomal passenger complex 0.16 0.12 0.28 224 -10000 0 224
Chromosomal passenger complex/EVI5 0.14 0.1 0.36 24 -10000 0 24
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
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 0.032 0.01 -10000 0 -10000 0 0
PRNP 0.019 0.088 -10000 0 -0.54 12 12
GPC1/SLIT2 -0.009 0.15 -10000 0 -0.39 65 65
SMAD2 -0.001 0.084 0.28 1 -0.31 32 33
GPC1/PrPc/Cu2+ 0.034 0.06 -10000 0 -0.34 12 12
GPC1/Laminin alpha1 0.047 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 0.045 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 -0.001 0.13 -10000 0 -0.4 42 42
NRG1 -0.019 0.16 -10000 0 -0.54 42 42
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.069 0.038 -10000 0 -10000 0 0
LYN 0.018 0.014 -10000 0 -10000 0 0
mol:Spermine 0.009 0.01 -10000 0 -10000 0 0
cell growth -0.22 0.18 -10000 0 -0.35 322 322
BMP signaling pathway -0.034 0.012 -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 -0.033 0.2 -10000 0 -0.54 65 65
GPC1 0.034 0.012 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.035 0.016 -10000 0 -10000 0 0
VEGFA 0.049 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 0.17 2 -0.54 375 377
FGFR1 0.017 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 0.045 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 65 65
LCK 0.031 0.033 -10000 0 -10000 0 0
neuron differentiation -0.001 0.13 -10000 0 -0.4 42 42
PrPc/Cu2+ 0.014 0.064 -10000 0 -0.4 12 12
APP 0.03 0.055 -10000 0 -0.54 4 4
TGFBR2 (dimer) -0.005 0.14 -10000 0 -0.54 34 34
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.067 0.14 0.31 58 -10000 0 58
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 0.029 0.012 -10000 0 -10000 0 0
RhoA/GTP -0.067 0.14 -10000 0 -0.32 58 58
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 0.033 0.005 -10000 0 -10000 0 0
GNA12 0.033 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 0.005 -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 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
CBL/APS/CAP -0.16 0.2 -10000 0 -0.32 276 276
TC10/GTP -0.13 0.16 -10000 0 -0.28 269 269
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 -0.002 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 0.09 0.072 0.46 6 -10000 0 6
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 -0.54 274 274
CRK 0.031 0.01 -10000 0 -10000 0 0
PTPN1 0.019 0.053 0.28 17 -10000 0 17
CAV1 -0.23 0.18 -10000 0 -0.33 362 362
CBL/APS/CAP/Crk-II/C3G -0.13 0.18 -10000 0 -0.3 273 273
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 0.14 -10000 0 -0.3 90 90
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.016 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 0.018 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 0.26 1 -0.42 20 21
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 -0.32 108 108
SHC1 0.027 0.014 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.057 0.052 -10000 0 -0.47 4 4
PI3K 0.008 0.15 -10000 0 -0.3 90 90
NCK2 0.034 0.007 0.17 1 -10000 0 1
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 0.045 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 0.035 -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 0.075 0.054 -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 0.033 0.005 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.14 0.18 -10000 0 -0.31 274 274
TC10/GDP 0.024 0.019 -10000 0 -0.4 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.068 0.056 -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 0.038 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 0.021 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
Nectin adhesion 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
PDGFRB 0.033 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.048 0.027 -10000 0 -0.4 1 1
PTK2 -0.052 0.17 -10000 0 -0.44 66 66
positive regulation of JNK cascade -0.024 0.15 -10000 0 -0.32 81 81
CDC42/GDP -0.018 0.2 0.46 1 -0.43 83 84
Rac1/GDP -0.018 0.2 -10000 0 -0.42 82 82
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.033 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 74 74
nectin-3/I-afadin -0.024 0.16 -10000 0 -0.41 77 77
RAPGEF1 -0.042 0.2 0.47 1 -0.46 77 78
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.22 -10000 0 -0.52 78 78
PDGFB-D/PDGFRB 0.033 0.005 -10000 0 -10000 0 0
TLN1 -0.04 0.12 -10000 0 -0.47 22 22
Rap1/GTP -0.03 0.14 -10000 0 -0.34 65 65
IQGAP1 0.032 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 0.16 -10000 0 -0.41 77 77
PVR 0.035 0.015 -10000 0 -10000 0 0
Necl-5(dimer) 0.035 0.015 -10000 0 -10000 0 0
mol:GDP -0.044 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 -0.003 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 -0.4 3 3
positive regulation of lamellipodium assembly -0.02 0.15 -10000 0 -0.33 82 82
PVRL1 0.031 0.014 -10000 0 -10000 0 0
PVRL3 -0.052 0.2 -10000 0 -0.54 75 75
PVRL2 0.038 0.025 -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 79 79
SRC -0.073 0.24 -10000 0 -0.56 82 82
ITGB3 0.034 0.018 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.4 3 3
FARP2 -0.044 0.24 0.47 1 -0.54 76 77
RAC1 0.033 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 77 77
nectin-1/I-afadin 0.038 0.046 -10000 0 -0.4 3 3
nectin-2/I-afadin 0.044 0.048 -10000 0 -0.25 9 9
RAC1/GTP/IQGAP1/filamentous actin 0.043 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.004 0.15 -10000 0 -0.35 77 77
CDC42/GTP/IQGAP1/filamentous actin 0.042 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 -0.32 81 81
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 0.044 0.048 -10000 0 -0.25 9 9
nectin-2(dimer)/I-afadin/I-afadin 0.044 0.048 -10000 0 -0.25 9 9
PIP5K1C -0.037 0.12 -10000 0 -0.27 82 82
VAV2 -0.042 0.24 0.45 1 -0.53 81 82
RAP1/GDP -0.014 0.19 -10000 0 -0.4 71 71
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 77 77
nectin-3(dimer)/I-afadin/I-afadin -0.024 0.16 -10000 0 -0.41 77 77
Rac1/GTP -0.022 0.19 -10000 0 -0.4 82 82
PTPRM -0.034 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
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 -0.045 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 -0.006 0.14 -10000 0 -0.33 74 74
NT-4/5 (dimer)/p75(NTR) -0.041 0.15 -10000 0 -0.38 78 78
IKBKB 0.028 0.013 -10000 0 -10000 0 0
AKT1 -0.031 0.16 0.33 3 -0.32 94 97
IKBKG 0.034 0.003 -10000 0 -10000 0 0
BDNF 0.037 0.047 -10000 0 -0.54 2 2
MGDIs/NGR/p75(NTR)/LINGO1 0.013 0.15 -10000 0 -0.33 72 72
FURIN 0.036 0.023 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.001 0.14 -10000 0 -0.34 74 74
LINGO1 0.054 0.05 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.033 0.029 -10000 0 -0.28 1 1
proBDNF (dimer) 0.037 0.047 -10000 0 -0.54 2 2
NTRK1 0.03 0.021 -10000 0 -10000 0 0
RTN4R 0.04 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 0.005 -10000 0 -10000 0 0
Gamma Secretase 0.074 0.053 -10000 0 -0.3 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.008 0.14 -10000 0 -0.33 81 81
MAGEH1 0.018 0.095 -10000 0 -0.54 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.077 0.2 -10000 0 -0.38 146 146
Mammalian IAPs/DIABLO 0.046 0.076 -10000 0 -0.31 16 16
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.043 0.035 -10000 0 -10000 0 0
APP 0.03 0.055 -10000 0 -0.54 4 4
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.033 0.006 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.01 0.12 -10000 0 -0.29 72 72
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.036 0.11 0.21 31 -0.27 73 104
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.015 0.094 -10000 0 -0.25 57 57
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.018 0.14 -10000 0 -0.34 74 74
NCSTN 0.028 0.014 -10000 0 -10000 0 0
mol:GTP -0.018 0.15 -10000 0 -0.35 77 77
PSENEN 0.035 0.015 -10000 0 -10000 0 0
mol:ceramide -0.022 0.13 -10000 0 -0.31 73 73
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 75 75
BEX1 0.053 0.048 -10000 0 -10000 0 0
mol:GDP -0.053 0.12 -10000 0 -0.34 74 74
NGF (dimer) 0.004 0.13 -10000 0 -0.31 64 64
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.027 0.14 -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 73 73
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 -0.017 0.15 -10000 0 -0.36 77 77
RHOB 0.032 0.037 -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 -0.54 129 129
TP53 -0.028 0.13 0.37 8 -10000 0 8
PRDM4 -0.018 0.13 -10000 0 -0.31 73 73
BDNF (dimer) 0.054 0.17 -10000 0 -0.31 69 69
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
SORT1 0.033 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.14 -10000 0 -0.31 89 89
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0 0.13 -10000 0 -0.31 73 73
RHOC 0.033 0.005 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.028 0.14 0.31 5 -0.33 66 71
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 -0.022 0.13 -10000 0 -0.31 73 73
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 -0.017 0.14 -10000 0 -0.34 73 73
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) -0.12 0.23 -10000 0 -0.44 166 166
MAPK8 -0.025 0.14 0.3 6 -0.32 65 71
MAPK9 -0.024 0.13 0.29 5 -0.32 64 69
APAF1 0.034 0.003 -10000 0 -10000 0 0
NTF3 -0.11 0.25 -10000 0 -0.54 129 129
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 0.009 0.14 -10000 0 -0.3 70 70
p75 CTF/Sortilin/TRAF6/NRIF 0.079 0.026 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.018 0.15 -10000 0 -0.35 77 77
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.026 0.14 -10000 0 -0.3 70 70
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.017 0.14 -10000 0 -0.31 74 74
PRKACB 0.035 0.083 -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 0.017 0.1 -10000 0 -0.54 16 16
BIRC2 0.03 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.16 -10000 0 -0.4 94 94
BAD -0.024 0.15 0.46 6 -0.33 65 71
RIPK2 0.029 0.021 -10000 0 -10000 0 0
NGFR -0.054 0.2 -10000 0 -0.54 74 74
CYCS -0.008 0.13 0.26 7 -0.3 67 74
ADAM17 0.033 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.003 0.12 -10000 0 -0.31 60 60
BCL2L11 -0.024 0.15 0.44 7 -0.33 65 72
BDNF (dimer)/p75(NTR) -0.02 0.16 -10000 0 -0.38 79 79
PI3K -0.029 0.16 -10000 0 -0.34 96 96
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.001 0.13 -10000 0 -0.31 73 73
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 78 78
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.005 0.13 -10000 0 -0.31 73 73
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.033 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 -0.027 0.13 -10000 0 -0.33 73 73
SQSTM1 0.034 0.008 -10000 0 -10000 0 0
NGFRAP1 0.009 0.12 -10000 0 -0.54 22 22
CASP3 -0.022 0.14 0.43 7 -0.31 66 73
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 0.012 0.13 -10000 0 -0.3 72 72
MMP3 0.092 0.098 -10000 0 -0.54 5 5
APAF-1/Caspase 9 -0.032 0.1 -10000 0 -0.41 6 6
TCGA08_retinoblastoma

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
CDKN2B 0.034 0.032 -10000 0 -10000 0 0
CDKN2C -0.024 0.15 -10000 0 -0.52 42 42
CDKN2A 0.057 0.054 0.2 3 -10000 0 3
CCND2 -0.006 0.062 0.18 29 -0.19 14 43
RB1 0.003 0.073 0.23 12 -0.21 31 43
CDK4 -0.002 0.075 0.22 35 -0.21 12 47
CDK6 -0.004 0.074 0.21 33 -0.22 15 48
G1/S progression 0.003 0.086 0.21 52 -0.23 14 66
Presenilin action in Notch and Wnt signaling

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
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 0.032 0.008 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
DTX1 0.03 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 -0.34 330 330
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 0.092 -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 0.015 0.07 -10000 0 -0.6 4 4
CtBP/CBP/TCF1/TLE1/AES 0.001 0.079 0.27 2 -0.32 12 14
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 0.09 -10000 0 -0.42 10 10
MAPK3 0.032 0.009 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.099 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 -0.05 0.32 -10000 0 -1.3 30 30
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 0.054 0.095 -10000 0 -0.41 14 14
apoptosis -0.22 0.19 -10000 0 -0.34 331 331
Delta 1/NOTCHprecursor 0.052 0.092 -10000 0 -0.41 14 14
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 0.053 -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 0.37 1 -0.48 13 14
DKK2 0.031 0.054 -10000 0 -0.54 4 4
NOTCH1 precursor/DVL1 -0.014 0.12 -10000 0 -0.66 11 11
GSK3B 0.033 0.008 -10000 0 -10000 0 0
FRAT1 0.033 0.008 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.036 0.087 -10000 0 -0.41 14 14
PPP2R5D -0.003 0.065 -10000 0 -0.39 9 9
MAPK1 0.032 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.2 0.18 -10000 0 -0.31 350 350
RBPJ 0.032 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 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
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 0.07 0.28 5 -0.32 1 6
EGFR -0.26 0.29 -10000 0 -0.54 261 261
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 0.072 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 -0.54 161 161
NCKAP1 0.033 0.005 -10000 0 -10000 0 0
AQP3 -0.051 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 -0.27 24 24
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
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.001 0.069 -10000 0 -0.42 1 1
PVRL2 0.038 0.025 -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 -0.35 348 348
RhoA/GDP 0.041 0.083 -10000 0 -0.28 24 24
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 6 6
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 0.027 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 25 25
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 -0.003 0.088 -10000 0 -0.26 45 45
actin cable formation 0.054 0.11 0.34 17 -0.29 1 18
KIAA1543 -0.021 0.064 -10000 0 -0.27 24 24
KIFC3 0.001 0.069 -10000 0 -0.28 24 24
NCK1 0.033 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 0.033 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 -0.65 11 12
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 0.044 0.048 -10000 0 -0.25 9 9
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 -0.003 0.088 -10000 0 -0.26 45 45
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.046 0.035 -10000 0 -0.25 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.06 0.28 3 -0.24 2 5
AP1 -0.21 0.19 -10000 0 -0.33 341 341
mol:PIP3 -0.15 0.16 -10000 0 -0.28 269 269
AKT1 0.005 0.09 -10000 0 -0.33 7 7
PTK2B -0.014 0.079 -10000 0 -0.18 83 83
RHOA 0.009 0.066 -10000 0 -0.28 17 17
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 0.13 2 -0.19 5 7
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.013 0.078 0.25 3 -0.28 6 9
NF kappa B1 p50/RelA 0.021 0.04 -10000 0 -0.31 1 1
endothelial cell migration 0.016 0.053 0.26 2 -0.47 5 7
ADCY4 -0.048 0.096 -10000 0 -0.23 45 45
ADCY5 -0.047 0.094 -10000 0 -0.22 44 44
ADCY6 -0.047 0.094 -10000 0 -0.22 44 44
ADCY7 -0.037 0.091 -10000 0 -0.27 19 19
ADCY1 -0.046 0.094 -10000 0 -0.22 44 44
ADCY2 -0.049 0.098 -10000 0 -0.31 17 17
ADCY3 -0.046 0.094 -10000 0 -0.22 43 43
ADCY8 -0.041 0.087 -10000 0 -0.23 30 30
ADCY9 -0.043 0.091 -10000 0 -0.22 36 36
GSK3B -0.014 0.078 0.25 4 -0.22 17 21
arachidonic acid secretion -0.053 0.1 -10000 0 -0.24 61 61
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 0.027 0.06 0.27 3 -0.25 3 6
GAB1 0.032 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 -0.11 3 3
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 -0.24 61 61
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 -0.28 7 7
GNAZ 0.015 0.045 -10000 0 -0.28 10 10
EGFR/PI3K-beta/Gab1 -0.15 0.17 -10000 0 -0.3 269 269
positive regulation of dendritic cell cytokine production 0.007 0.02 -10000 0 -0.18 5 5
LPA/LPA2/MAGI-3 0.028 0.03 -10000 0 -0.2 3 3
ARHGEF1 0.037 0.054 -10000 0 -0.22 2 2
GNAI2 0.019 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 -0.094 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 -0.31 241 241
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 -0.28 26 27
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 0.056 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 0.36 9 -0.39 245 254
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 0.13 2 -0.19 5 7
EGFR -0.26 0.29 -10000 0 -0.54 261 261
PLCG1 0.016 0.017 -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 -0.37 8 8
cell migration 0.028 0.042 -10000 0 -0.25 6 6
SLC9A3R2 0.032 0.015 -10000 0 -10000 0 0
PXN 0.016 0.059 -10000 0 -0.28 7 7
HRAS/GTP -0.054 0.1 -10000 0 -0.25 61 61
RAC1 0.033 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 0.21 9 -0.26 1 10
Gi(beta/gamma) -0.051 0.11 -10000 0 -0.25 56 56
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 4 4
MAPKKK cascade -0.053 0.1 -10000 0 -0.24 61 61
contractile ring contraction involved in cytokinesis 0.008 0.068 -10000 0 -0.27 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.02 0.039 -10000 0 -0.31 4 4
GNA15 0.016 0.014 0.1 3 -0.087 2 5
GNA12 0.033 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MAPT -0.014 0.079 0.25 3 -0.29 6 9
GNA11 0.015 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.052 0.11 -10000 0 -0.92 6 6
MMP2 0.016 0.053 0.27 2 -0.47 5 7
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 0.004 0.13 -10000 0 -0.4 48 48
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 0.39 11 -10000 0 11
PTK2B 0.027 0.014 -10000 0 -10000 0 0
RAPGEF1 -0.003 0.11 0.35 1 -0.43 10 11
RANBP10 0.029 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 0.036 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 -0.77 363 363
STAT3 (dimer) -0.007 0.11 -10000 0 -0.42 16 16
GAB1/CRKL/SHP2/PI3K 0.01 0.14 -10000 0 -0.44 15 15
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.013 0.11 0.36 1 -0.41 11 12
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 0.28 11 -0.21 7 18
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.007 0.063 -10000 0 -0.25 6 6
PAK1 0.046 0.099 0.42 14 -10000 0 14
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 -0.38 17 19
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 -0.024 0.18 -10000 0 -0.53 55 55
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 0.27 11 -0.21 8 19
HGF/MET/MUC20 0.007 0.12 -10000 0 -0.34 50 50
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 -0.4 50 50
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.011 0.097 -10000 0 -0.38 14 14
MET/MUC20 -0.017 0.13 -10000 0 -0.39 52 52
RAP1B 0.002 0.11 0.31 3 -0.4 10 13
RAP1A -0.004 0.1 0.51 1 -0.41 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 37 48
RPS6KB1 0.001 0.061 -10000 0 -0.32 10 10
MAPK3 -0.037 0.081 0.5 5 -10000 0 5
MAPK1 -0.003 0.17 0.66 28 -10000 0 28
RANBP9 0.033 0.009 -10000 0 -10000 0 0
MAPK8 -0.004 0.12 0.44 1 -0.38 21 22
SRC -0.006 0.096 -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 -0.023 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 -0.41 18 19
PTK2 0.027 0.014 -10000 0 -10000 0 0
MAP2K2 -0.023 0.18 0.48 1 -0.52 56 57
BAD 0.018 0.074 0.38 8 -10000 0 8
MAP2K4 -0.012 0.12 0.35 1 -0.38 22 23
SHP2/GRB2/SOS1/GAB1 0.019 0.14 -10000 0 -0.36 51 51
INPPL1 0.031 0.009 -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 0.033 0.005 -10000 0 -10000 0 0
PTPRJ 0.035 0.016 -10000 0 -10000 0 0
NCK/PLCgamma1 0.025 0.093 -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 50 50
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 -9999 0 -10000 0 0
GNAO1 0.029 0.012 -9999 0 -10000 0 0
CDC42/GTP -0.067 0.14 -9999 0 -0.32 58 58
PLCG1 -0.073 0.13 -9999 0 -0.33 54 54
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.033 0.01 -9999 0 -10000 0 0
GNAI3 0.033 0.005 -9999 0 -10000 0 0
G12/G13 0.045 0.016 -9999 0 -10000 0 0
cell migration -0.067 0.14 -9999 0 -0.31 58 58
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 -0.07 0.13 -9999 0 -0.34 49 49
MAPK1 -0.077 0.13 -9999 0 -0.33 56 56
S1P/S1P5/Gi -0.081 0.14 -9999 0 -0.25 184 184
GNAI1 -0.17 0.28 -9999 0 -0.54 181 181
CDC42/GDP 0.024 0.005 -9999 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -9999 0 -10000 0 0
RHOA 0.033 0.05 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.081 0.14 -9999 0 -0.25 184 184
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.025 0.063 -9999 0 -0.54 6 6
S1P/S1P4/G12/G13 0.039 0.014 -9999 0 -10000 0 0
GNA12 0.033 0.005 -9999 0 -10000 0 0
GNA13 0.031 0.01 -9999 0 -10000 0 0
CDC42 0.033 0.007 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.005 0.015 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.1 -10000 0 -0.28 18 18
NFATC4 -0.027 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 -0.035 0.087 -10000 0 -0.3 28 28
JUN -0.054 0.072 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
DOCK7 -0.035 0.09 0.26 2 -0.29 27 29
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.097 -10000 0 -0.3 25 25
AKT1 0.007 0.016 0.14 3 -10000 0 3
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 -0.036 0.094 -10000 0 -0.32 27 27
RAF1 -0.037 0.095 -10000 0 -0.29 20 20
ErbB2/ErbB3/neuregulin 2 -0.18 0.17 -10000 0 -0.33 269 269
STAT3 0.009 0.16 -10000 0 -0.84 18 18
cell migration -0.014 0.071 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 -0.65 120 120
FOS -0.33 0.26 -10000 0 -0.49 362 362
NRAS 0.034 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.035 0.087 -10000 0 -0.3 28 28
MAPK3 -0.16 0.21 -10000 0 -0.5 91 91
MAPK1 -0.18 0.24 -10000 0 -0.55 106 106
JAK2 -0.032 0.09 0.26 2 -0.29 27 29
NF2 0.004 0.061 -10000 0 -0.67 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.081 -10000 0 -0.27 27 27
NRG1 -0.02 0.16 -10000 0 -0.55 42 42
GRB2/SOS1 0.046 0.018 -10000 0 -10000 0 0
MAPK8 -0.037 0.1 -10000 0 -0.29 31 31
MAPK9 -0.019 0.064 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 0.013 -10000 0 -10000 0 0
RAC1 0.033 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 5 -10000 0 5
RAC1-CDC42/GTP -0.036 0.06 -10000 0 -0.22 27 27
ErbB2/ErbB2/HSP90 (dimer) -0.008 0.023 -10000 0 -10000 0 0
CHRNA1 -0.12 0.16 -10000 0 -0.38 85 85
myelination -0.021 0.089 0.33 6 -10000 0 6
PPP3CB -0.032 0.086 0.25 2 -0.27 26 28
KRAS 0.033 0.016 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.036 0.1 -10000 0 -0.25 22 22
NRG2 -0.35 0.27 -10000 0 -0.54 334 334
mol:GDP 0 0.08 0.2 1 -0.27 27 28
SOS1 0.033 0.004 -10000 0 -10000 0 0
MAP2K2 -0.053 0.1 -10000 0 -0.31 25 25
SRC 0.032 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.032 0.092 0.27 2 -0.29 27 29
MAP2K1 -0.17 0.21 -10000 0 -0.59 54 54
heart morphogenesis -0.035 0.087 -10000 0 -0.3 28 28
RAS family/GDP 0.029 0.1 -10000 0 -0.27 15 15
GRB2 0.032 0.017 -10000 0 -10000 0 0
PRKACA 0.006 0.074 -10000 0 -0.67 6 6
CHRNE -0.005 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 -0.14 3 3
nervous system development -0.035 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 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
CRKL 0.032 0.008 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.026 0.093 -10000 0 -0.26 16 16
NT3 (dimer)/TRKC -0.079 0.21 -10000 0 -0.4 140 140
NT3 (dimer)/TRKB -0.24 0.29 -10000 0 -0.47 276 276
SHC/Grb2/SOS1/GAB1/PI3K 0.003 0.072 -10000 0 -0.24 26 26
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
BDNF 0.037 0.047 0.17 23 -0.54 2 25
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 0.016 0.098 -10000 0 -0.54 15 15
NT-4/5 (dimer)/TRKB -0.17 0.23 -10000 0 -0.41 220 220
neuron apoptosis 0.12 0.21 0.44 110 -10000 0 110
SHC 2-3/Grb2 -0.13 0.23 -10000 0 -0.49 109 109
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 -0.14 0.24 -10000 0 -0.53 115 115
SHC3 -0.12 0.21 -10000 0 -0.52 79 79
STAT3 (dimer) 0.053 0.076 -10000 0 -0.36 10 10
NT3 (dimer)/TRKA -0.082 0.2 -10000 0 -0.38 131 131
RIN/GDP 0.006 0.11 0.25 4 -0.29 14 18
GIPC1 0.034 0.01 -10000 0 -10000 0 0
KRAS 0.034 0.016 -10000 0 -10000 0 0
DNAJA3 -0.053 0.13 -10000 0 -0.34 70 70
RIN/GTP 0.023 0.019 -10000 0 -0.4 1 1
CCND1 0.014 0.12 -10000 0 -0.77 10 10
MAGED1 0.043 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 0.031 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 -0.34 3 3
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 0.029 0.012 -10000 0 -10000 0 0
RIT2 0.031 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 -0.034 0.15 -10000 0 -0.36 60 60
mol:GDP -0.007 0.15 0.32 6 -0.43 18 24
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 0.23 2 -0.28 16 18
TIAM1 0.034 0.012 0.17 3 -10000 0 3
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 0.063 0.028 -10000 0 -0.34 1 1
SHC/GRB2/SOS1/GAB1 0.062 0.042 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.01 -10000 0 -10000 0 0
NT3 (dimer) -0.11 0.25 -10000 0 -0.54 129 129
RAP1/GDP 0.003 0.089 -10000 0 -0.25 13 13
KIDINS220/CRKL 0.032 0.008 -10000 0 -10000 0 0
BDNF (dimer) 0.037 0.047 0.17 23 -0.54 2 25
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 0.026 0.066 -10000 0 -0.3 6 6
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.033 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.22 -10000 0 -0.35 266 266
ABL1 0.033 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 0.068 0.28 5 -10000 0 5
CDC42/GDP 0.008 0.11 0.27 7 -0.28 16 23
NTF3 -0.11 0.25 -10000 0 -0.54 129 129
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.038 0.021 -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 0.032 0.027 -10000 0 -0.54 1 1
RASGRF1 -0.052 0.14 -10000 0 -0.35 73 73
SOS1 0.034 0.004 -10000 0 -10000 0 0
MCF2L -0.08 0.17 -10000 0 -0.35 134 134
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 0.098 0.36 1 -0.43 5 6
Rac1/GDP 0.007 0.11 0.26 6 -0.29 14 20
NGF (dimer)/TRKA/GRIT 0.02 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis -0.026 0.22 0.42 1 -0.73 28 29
NGF (dimer)/TRKA/NEDD4-2 0.029 0.057 -10000 0 -0.34 9 9
MAP2K1 0.063 0.087 0.36 13 -10000 0 13
NGFR -0.054 0.2 -10000 0 -0.54 74 74
NGF (dimer)/TRKA/GIPC/GAIP 0.024 0.024 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.003 0.082 -10000 0 -0.26 38 38
FRS2 family/SHP2/GRB2/SOS1 0.086 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 0.033 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.018 0.071 -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 0.048 0.029 -10000 0 -10000 0 0
MATK 0.038 0.027 -10000 0 -10000 0 0
NEDD4L 0.017 0.095 -10000 0 -0.54 14 14
RAS family/GDP -0.032 0.057 -10000 0 -0.22 17 17
NGF (dimer)/TRKA -0.058 0.14 -10000 0 -0.36 77 77
Rac1/GTP -0.05 0.097 -10000 0 -0.29 38 38
FRS2 family/SHP2/CRK family 0.081 0.045 -10000 0 -0.3 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.027 0.081 -10000 0 -0.49 7 7
Crk/p130 Cas/Paxillin -0.083 0.14 -10000 0 -0.37 76 76
JUN -0.002 0.15 0.26 6 -0.35 37 43
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 0.033 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 0.34 3 -0.3 57 60
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 0.24 1 -0.31 60 61
RHOA 0.033 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.074 0.15 -10000 0 -0.28 47 47
GRB7 0.028 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.11 0.17 -10000 0 -0.3 58 58
MAPKKK cascade 0.056 0.13 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 92 92
lamellipodium assembly -0.045 0.16 -10000 0 -0.34 78 78
RET51/GFRalpha1/GDNF/SHC 0.089 0.16 -10000 0 -0.3 44 44
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.043 0.13 -10000 0 -0.31 45 45
RET9/GFRalpha1/GDNF/Shank3 0.047 0.14 -10000 0 -0.31 61 61
MAPK3 0.041 0.13 0.26 9 -0.28 46 55
DOK1 0.035 0.016 -10000 0 -10000 0 0
DOK6 0.032 0.049 -10000 0 -0.54 3 3
PXN 0.034 0.003 -10000 0 -10000 0 0
neurite development 0.042 0.12 0.33 1 -0.33 2 3
DOK5 0.011 0.11 -10000 0 -0.54 18 18
GFRA1 0.025 0.23 -10000 0 -0.54 64 64
MAPK8 0.051 0.12 0.23 7 -0.37 8 15
HRAS/GTP 0.09 0.16 0.3 4 -0.3 55 59
tube development 0.054 0.14 0.31 12 -0.3 57 69
MAPK1 0.043 0.13 0.28 9 -0.28 46 55
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.02 0.11 -10000 0 -0.26 58 58
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 0.34 2 -0.28 57 59
SHC1 0.027 0.014 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.088 0.17 -10000 0 -0.3 59 59
RET51/GFRalpha1/GDNF/Dok5 0.084 0.17 -10000 0 -0.3 64 64
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 0.018 0.096 -10000 0 -0.25 40 40
RET51/GFRalpha1/GDNF/Grb7 0.096 0.16 -10000 0 -0.3 44 44
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.071 -10000 0 -10000 0 0
DOK4 0.029 0.012 -10000 0 -10000 0 0
JNK cascade -0.001 0.15 0.26 6 -0.35 37 43
RET9/GFRalpha1/GDNF/FRS2 0.048 0.14 -10000 0 -0.31 62 62
SHANK3 0.032 0.009 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
NCK1 0.033 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.019 0.097 -10000 0 -0.25 40 40
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.052 0.13 0.24 5 -0.38 5 10
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.059 0.13 0.24 4 -0.27 47 51
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.046 0.11 0.24 5 -0.38 3 8
PI3K -0.042 0.25 0.3 7 -0.53 78 85
SOS1 0.034 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.056 0.14 -10000 0 -0.3 57 57
GRB10 0.029 0.051 -10000 0 -0.54 4 4
activation of MAPKK activity 0.055 0.12 0.26 6 -0.34 3 9
RET51/GFRalpha1/GDNF/FRS2 0.1 0.17 0.34 1 -0.3 60 61
GAB1 0.032 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 -0.54 116 116
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.045 0.11 0.24 5 -0.25 33 38
RET51/GFRalpha1/GDNF/PKC alpha 0.095 0.17 -10000 0 -0.3 56 56
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 0.033 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.068 0.23 -10000 0 -0.38 86 86
Rac1/GTP -0.034 0.2 0.25 3 -0.42 74 77
RET9/GFRalpha1/GDNF 0.036 0.15 -10000 0 -0.33 65 65
GFRalpha1/GDNF 0.037 0.17 -10000 0 -0.38 65 65
TCGA08_p53

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
CDKN2A 0.027 0.045 0.13 77 -10000 0 77
TP53 0 0.05 -10000 0 -0.19 29 29
Senescence -0.005 0.059 -10000 0 -0.19 44 44
Apoptosis -0.005 0.059 -10000 0 -0.19 44 44
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.009 0.067 0.3 18 -10000 0 18
MDM4 0.028 0.016 -10000 0 -10000 0 0
IL27-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
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 0.21 0.71 22 -0.52 8 30
IL27/IL27R/JAK1 0.033 0.28 0.64 17 -1 18 35
TBX21 0.025 0.26 0.53 40 -0.59 38 78
IL12B 0.042 0.026 -10000 0 -10000 0 0
IL12A 0.005 0.059 0.14 6 -0.4 10 16
IL6ST 0.034 0.075 0.24 1 -0.54 7 8
IL27RA/JAK1 0.004 0.23 0.49 4 -1.2 17 21
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 -0.55 6 6
T-helper 2 cell differentiation -0.011 0.21 0.71 22 -0.52 8 30
T cell proliferation during immune response -0.011 0.21 0.71 22 -0.52 8 30
MAPKKK cascade 0.011 0.21 0.52 8 -0.71 22 30
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT2 0.034 0.004 -10000 0 -10000 0 0
STAT1 0.059 0.055 0.21 3 -10000 0 3
IL12RB1 0.036 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 0.55 46 -0.63 22 68
IL27/IL27R/JAK2/TYK2 0.01 0.22 0.52 8 -0.73 22 30
positive regulation of T cell mediated cytotoxicity 0.011 0.21 0.52 8 -0.71 22 30
STAT1 (dimer) 0.039 0.32 0.69 35 -1 21 56
JAK2 0.038 0.022 0.23 1 -10000 0 1
JAK1 0.035 0.013 -10000 0 -10000 0 0
STAT2 (dimer) 0.025 0.21 0.46 8 -0.68 22 30
T cell proliferation -0.18 0.25 0.5 5 -0.57 80 85
IL12/IL12R/TYK2/JAK2 0.068 0.19 0.52 2 -0.75 14 16
IL17A -0.19 0.14 -10000 0 -0.55 6 6
mast cell activation -0.011 0.21 0.71 22 -0.52 8 30
IFNG 0.033 0.065 0.14 100 -0.11 9 109
T cell differentiation 0 0.009 0.019 29 -0.024 19 48
STAT3 (dimer) 0.024 0.2 0.46 7 -0.69 21 28
STAT5A (dimer) 0.023 0.2 0.46 7 -0.66 23 30
STAT4 (dimer) 0.021 0.21 0.48 7 -0.68 23 30
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 0.054 0.24 0.54 3 -1.1 17 20
GATA3 -0.017 0.38 0.68 16 -1.3 34 50
IL18 0.019 0.036 0.14 27 -10000 0 27
positive regulation of mast cell cytokine production 0.024 0.2 0.46 7 -0.67 21 28
IL27/EBI3 0.014 0.14 0.3 5 -0.39 51 56
IL27RA -0.014 0.24 0.51 5 -1.3 17 22
IL6 -0.37 0.26 -10000 0 -0.54 361 361
STAT5A 0.031 0.027 -10000 0 -0.54 1 1
monocyte differentiation 0.002 0.003 -10000 0 -10000 0 0
IL2 -0.009 0.11 0.47 17 -0.82 2 19
IL1B 0.009 0.04 0.14 10 -0.4 4 14
EBI3 0.04 0.025 0.22 2 -10000 0 2
TNF 0.013 0.02 0.14 4 -10000 0 4
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.033 0.11 0.31 5 -0.34 6 11
epithelial cell differentiation 0.085 0.09 -10000 0 -10000 0 0
ITCH 0.046 0.025 -10000 0 -10000 0 0
WWP1 0.048 0.15 0.52 28 -10000 0 28
FYN 0.029 0.037 -10000 0 -0.54 2 2
EGFR -0.26 0.29 -10000 0 -0.54 261 261
PRL 0.033 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis 0.026 0.12 0.37 10 -0.37 4 14
PTPRZ1 -0.36 0.27 -10000 0 -0.54 347 347
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.016 0.1 -10000 0 -0.38 6 6
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.012 0.11 0.28 1 -0.32 33 34
ADAM17 0.047 0.025 -10000 0 -10000 0 0
ErbB4/ErbB4 0.029 0.12 0.42 24 -0.38 3 27
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.034 0.11 0.35 1 -0.34 3 4
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 -0.39 7 7
GRIN2B -0.018 0.1 -10000 0 -0.37 7 7
ErbB4/ErbB2/betacellulin 0.027 0.096 -10000 0 -0.36 4 4
STAT1 0.057 0.053 -10000 0 -10000 0 0
HBEGF 0.029 0.051 -10000 0 -0.54 4 4
PRLR 0.069 0.062 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.006 0.14 -10000 0 -0.39 41 41
axon guidance 0.12 0.14 0.45 30 -10000 0 30
NEDD4 0.039 0.06 -10000 0 -0.51 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.072 0.046 -10000 0 -10000 0 0
CBFA2T3 -0.023 0.17 -10000 0 -0.54 47 47
ErbB4/ErbB2/HBEGF 0.035 0.085 -10000 0 -0.33 3 3
MAPK3 0.029 0.12 0.37 8 -0.37 5 13
STAT1 (dimer) 0.052 0.11 0.35 9 -0.36 2 11
MAPK1 0.033 0.12 0.39 11 -0.37 5 16
JAK2 0.032 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.003 0.11 -10000 0 -0.38 7 7
NRG1 -0.014 0.12 -10000 0 -0.4 40 40
NRG3 0.034 0.043 -10000 0 -0.54 2 2
NRG2 -0.35 0.27 -10000 0 -0.54 334 334
NRG4 0.034 0.012 -10000 0 -10000 0 0
heart development 0.12 0.14 0.45 30 -10000 0 30
neural crest cell migration 0.003 0.11 -10000 0 -0.38 7 7
ERBB2 0.02 0.028 0.3 1 -0.37 1 2
WWOX/E4ICDs 0.027 0.1 0.35 5 -0.36 2 7
SHC1 0.027 0.014 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.12 0.16 -10000 0 -0.36 21 21
apoptosis -0.035 0.093 0.32 2 -0.33 9 11
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.19 0.17 -10000 0 -0.32 252 252
ErbB4/ErbB2/epiregulin 0.045 0.092 0.35 4 -0.34 1 5
ErbB4/ErbB4/betacellulin/betacellulin 0.02 0.12 -10000 0 -0.35 16 16
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.085 0.12 0.38 9 -0.33 1 10
MDM2 0.027 0.11 0.35 27 -0.36 2 29
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.002 0.1 -10000 0 -0.3 33 33
STAT5A 0.11 0.12 0.41 31 -10000 0 31
ErbB4/EGFR/neuregulin 1 beta -0.15 0.18 -10000 0 -0.46 59 59
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 -10000 0 -0.33 2 2
STAT5A (dimer) 0.13 0.12 0.4 18 -10000 0 18
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.12 0.12 0.4 27 -0.36 1 28
LRIG1 0.014 0.1 -10000 0 -0.54 16 16
EREG 0.044 0.048 -10000 0 -0.54 1 1
BTC 0.01 0.12 -10000 0 -0.54 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.11 0.13 0.46 28 -10000 0 28
ERBB4 0.029 0.12 0.42 24 -0.38 3 27
STAT5B 0.033 0.009 -10000 0 -10000 0 0
YAP1 0 0.12 0.26 6 -0.38 36 42
GRB2 0.033 0.017 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.037 0.08 -10000 0 -10000 0 0
glial cell differentiation -0.023 0.089 0.33 2 -10000 0 2
WWOX 0.034 0.03 -10000 0 -10000 0 0
cell proliferation 0.051 0.14 0.41 12 -0.41 6 18
Syndecan-3-mediated signaling events

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
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 0.042 0.1 -9999 0 -0.47 16 16
POMC 0.035 0.031 -9999 0 -0.54 1 1
EGFR -0.26 0.29 -9999 0 -0.54 261 261
Syndecan-3/EGFR -0.12 0.18 -9999 0 -0.3 186 186
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 0.04 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 0.033 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 0.033 0.1 -9999 0 -0.47 16 16
Syndecan-3/AgRP/MC4R 0.049 0.1 -9999 0 -0.46 15 15
Fyn/Cortactin 0.037 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 0.047 0.11 -9999 0 -0.46 16 16
IL8 0.047 0.052 -9999 0 -0.54 1 1
Syndecan-3/Fyn/Cortactin 0.042 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 0.053 -9999 0 -0.3 1 1
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.036 0.19 -10000 0 -0.54 61 61
HRAS 0.034 0.013 -10000 0 -10000 0 0
EGFR -0.26 0.29 -10000 0 -0.54 261 261
AKT -0.018 0.12 0.36 5 -0.26 38 43
FOXO3 0.031 0.01 -10000 0 -10000 0 0
AKT1 0.035 0.016 -10000 0 -10000 0 0
FOXO1 -0.022 0.16 -10000 0 -0.54 46 46
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 0.008 -10000 0 -10000 0 0
RAS -0.075 0.14 0.23 1 -0.33 85 86
ERBB2 0.028 0.029 -10000 0 -0.54 1 1
proliferation/survival/translation -0.017 0.096 0.3 22 -0.28 2 24
PI3K -0.067 0.16 0.31 9 -0.31 101 110
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
KRAS 0.034 0.016 -10000 0 -10000 0 0
FOXO 0.035 0.08 0.31 7 -0.17 9 16
AKT2 0.033 0.006 -10000 0 -10000 0 0
PTEN 0.025 0.068 -10000 0 -0.54 7 7
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.069 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 0.032 0.01 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.056 0.17 -10000 0 -0.32 133 133
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 0.48 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 -0.54 314 314
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 0.078 -10000 0 -0.37 17 17
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 0.005 -10000 0 -10000 0 0
MAPK3 0.041 0.093 0.2 84 -0.3 16 100
MAPK1 0.046 0.096 0.2 98 -0.3 16 114
Syndecan-2/RACK1 0.03 0.062 -10000 0 -0.28 16 16
NF1 0.032 0.008 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0 0.071 -10000 0 -0.39 16 16
ITGA2 0.015 0.1 -10000 0 -0.54 16 16
MAPK8 0.001 0.068 0.34 3 -0.33 17 20
Syndecan-2/alpha2/beta1 Integrin 0.035 0.089 -10000 0 -0.33 22 22
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 -0.32 235 235
Syndecan-2/Laminin alpha3 -0.081 0.16 -10000 0 -0.35 130 130
Syndecan-2/RasGAP 0.042 0.066 -10000 0 -0.27 16 16
alpha5/beta1 Integrin 0.049 0.011 -10000 0 -10000 0 0
PRKCD 0.034 0.016 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.07 -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 0.031 0.014 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.078 -10000 0 -0.37 17 17
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 0.2 89 -0.3 16 105
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 0.006 -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 0.038 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 0.073 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
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.09 0.16 0.33 68 -0.38 13 81
FYN 0.062 0.16 0.41 24 -0.4 18 42
LAT/GRAP2/SLP76 0.071 0.16 0.41 28 -0.4 12 40
IKBKB 0.028 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 48 -10000 0 48
MAP3K8 -0.04 0.19 -10000 0 -0.54 64 64
mol:Ca2+ -0.011 0.017 0.032 9 -0.089 12 21
integrin-mediated signaling pathway 0.037 0.022 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.053 0.18 0.5 21 -0.41 28 49
TRPV6 0.013 0.22 1.3 10 -0.54 17 27
CD28 0.028 0.08 -10000 0 -0.55 9 9
SHC1 0.073 0.18 0.34 73 -0.4 22 95
receptor internalization 0.025 0.18 0.35 25 -0.4 61 86
PRF1 0.038 0.16 0.54 9 -0.79 6 15
KRAS 0.034 0.016 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
COT/AKT1 0.036 0.16 0.35 40 -0.31 34 74
LAT 0.055 0.17 0.4 28 -0.41 21 49
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D 0.04 0.035 0.21 8 -10000 0 8
CD3E 0.034 0.016 0.21 1 -10000 0 1
CD3G 0.038 0.072 -10000 0 -0.54 5 5
RASGRP2 0.009 0.048 0.16 10 -0.16 26 36
RASGRP1 0.064 0.16 0.44 29 -0.33 15 44
HLA-A 0.04 0.024 -10000 0 -10000 0 0
RASSF5 0.029 0.022 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.037 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.066 0.097 0.22 86 -0.13 2 88
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.009 0.047 -10000 0 -0.18 15 15
PRKCA 0.041 0.1 0.32 25 -0.22 6 31
GRAP2 0.034 0.018 -10000 0 -10000 0 0
mol:IP3 0.003 0.089 0.29 10 -0.31 12 22
EntrezGene:6957 0.003 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.025 0.13 0.32 19 -0.31 44 63
ORAI1 -0.02 0.17 -10000 0 -1.1 10 10
CSK 0.047 0.15 0.41 18 -0.4 21 39
B7 family/CD28 0.082 0.17 0.47 22 -0.44 13 35
CHUK 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.042 0.17 0.4 21 -0.37 42 63
PTPN6 0.045 0.15 0.37 24 -0.39 21 45
VAV1 0.044 0.16 0.45 17 -0.4 23 40
Monovalent TCR/CD3 0.022 0.1 0.27 22 -0.36 21 43
CBL 0.03 0.011 -10000 0 -10000 0 0
LCK 0.062 0.15 0.39 28 -0.41 14 42
PAG1 0.062 0.16 0.4 27 -0.41 19 46
RAP1A 0.033 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.041 0.16 0.37 25 -0.36 42 67
CD80 0.044 0.036 -10000 0 -10000 0 0
CD86 0.035 0.012 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 0.01 0.066 -10000 0 -0.21 15 15
HRAS 0.034 0.013 -10000 0 -10000 0 0
GO:0035030 0.043 0.14 0.38 25 -0.38 13 38
CD8A 0.003 0.006 0.047 1 -10000 0 1
CD8B 0.04 0.025 0.21 5 -10000 0 5
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDK1/PKC theta 0.071 0.18 0.42 54 -0.37 22 76
CSK/PAG1 0.065 0.16 0.39 27 -0.44 13 40
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 0.16 0.46 18 -0.41 18 36
STIM1 0.004 0.1 1.2 3 -10000 0 3
RAS family/GTP 0.076 0.11 0.28 52 -0.18 11 63
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.023 0.19 0.35 26 -0.41 61 87
mol:DAG -0.015 0.067 0.13 2 -0.26 15 17
RAP1A/GDP 0.035 0.047 0.13 48 -10000 0 48
PLCG1 0.032 0.008 -10000 0 -10000 0 0
CD247 0.022 0.11 0.2 10 -0.55 15 25
cytotoxic T cell degranulation 0.038 0.16 0.54 9 -0.75 6 15
RAP1A/GTP 0.002 0.015 -10000 0 -0.061 23 23
mol:PI-3-4-5-P3 0.055 0.17 0.46 24 -0.36 27 51
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.025 0.12 0.32 10 -0.39 11 21
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 -0.38 13 25
MALT1 0.033 0.009 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
CD8 heterodimer 0.033 0.021 0.18 5 -10000 0 5
CARD11 0.038 0.026 0.17 17 -10000 0 17
PRKCB -0.011 0.05 0.15 5 -0.18 22 27
PRKCE 0.046 0.1 0.31 29 -0.22 9 38
PRKCQ 0.06 0.18 0.47 27 -0.39 25 52
LCP2 0.036 0.022 -10000 0 -10000 0 0
BCL10 0.033 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression 0.059 0.15 0.34 51 -0.27 27 78
IKK complex 0.055 0.092 0.24 67 -10000 0 67
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 0.029 0.13 0.29 44 -0.25 27 71
PDPK1 0.063 0.16 0.38 52 -0.3 25 77
TCR/CD3/MHC I/CD8/Fyn 0.015 0.17 0.39 13 -0.47 27 40
Regulation of nuclear SMAD2/3 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
EP300 0.035 0.016 -10000 0 -10000 0 0
HSPA8 0.029 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.076 0.19 0.33 1 -0.4 107 108
AKT1 0.038 0.019 -10000 0 -10000 0 0
GSC -0.094 0.39 -10000 0 -1.3 45 45
NKX2-5 0.045 0.049 -10000 0 -10000 0 0
muscle cell differentiation 0 0.12 0.48 16 -10000 0 16
SMAD2-3/SMAD4/SP1 0.053 0.12 -10000 0 -0.33 10 10
SMAD4 -0.028 0.084 -10000 0 -0.27 22 22
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 0.051 0.095 -10000 0 -0.35 6 6
MYC -0.006 0.12 -10000 0 -0.55 24 24
CDKN2B -0.047 0.19 -10000 0 -0.69 19 19
AP1 -0.26 0.29 -10000 0 -0.64 133 133
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 -0.008 0.11 0.25 1 -0.36 22 23
SP3 0.035 0.008 -10000 0 -10000 0 0
CREB1 0.033 0.006 -10000 0 -10000 0 0
FOXH1 0.018 0.041 -10000 0 -0.17 4 4
SMAD3/SMAD4/GR -0.046 0.14 -10000 0 -0.39 50 50
GATA3 0.034 0.16 -10000 0 -0.53 34 34
SKI/SIN3/HDAC complex/NCoR1 0.016 0.083 -10000 0 -0.38 15 15
MEF2C/TIF2 0.007 0.15 -10000 0 -0.55 24 24
endothelial cell migration -0.058 0.11 0.57 7 -10000 0 7
MAX 0.025 0.024 -10000 0 -10000 0 0
RBBP7 0.036 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 -0.006 0.15 -10000 0 -0.54 35 35
RUNX1 0.018 0.095 -10000 0 -0.54 14 14
CTBP1 0.032 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 0.004 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 -0.33 29 29
DCP1A 0.032 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 15 15
SMAD3/SMAD4/ATF3 -0.089 0.2 -10000 0 -0.41 129 129
SAP30 0.033 0.009 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.062 0.039 -10000 0 -10000 0 0
JUN -0.26 0.28 -10000 0 -0.64 131 131
SMAD3/SMAD4/IRF7 0.021 0.093 -10000 0 -0.29 9 9
TFE3 0.03 0.045 -10000 0 -0.18 7 7
COL1A2 0.075 0.13 0.39 10 -0.71 5 15
mesenchymal cell differentiation -0.004 0.092 0.26 16 -10000 0 16
DLX1 0.043 0.035 -10000 0 -10000 0 0
TCF3 0.034 0.017 -10000 0 -10000 0 0
FOS -0.37 0.28 -10000 0 -0.56 342 342
SMAD3/SMAD4/Max -0.019 0.089 -10000 0 -0.29 9 9
Cbp/p300/SNIP1 0.06 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 -0.6 26 26
TGIF2/HDAC complex/SMAD3/SMAD4 0.005 0.091 -10000 0 -0.26 16 16
IRF7 0.039 0.023 0.22 1 -10000 0 1
ESR1 -0.071 0.25 0.23 1 -0.55 106 107
HNF4A 0.032 0.008 -10000 0 -10000 0 0
MEF2C 0.014 0.17 0.42 9 -0.55 28 37
SMAD2-3/SMAD4 0.009 0.11 -10000 0 -0.31 21 21
Cbp/p300/Src-1 0.062 0.039 -10000 0 -0.32 2 2
IGHV3OR16-13 -0.007 0.07 -10000 0 -0.45 10 10
TGIF2/HDAC complex 0.032 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 0.032 0.006 -10000 0 -10000 0 0
GCN5L2 0.003 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.019 0.13 -10000 0 -0.38 30 30
MSG1/HSC70 -0.21 0.22 -10000 0 -0.4 294 294
SMAD2 0.02 0.052 -10000 0 -10000 0 0
SMAD3 -0.015 0.063 -10000 0 -0.21 6 6
SMAD3/E2F4-5/DP1/p107/SMAD4 0.004 0.07 -10000 0 -0.29 9 9
SMAD2/SMAD2/SMAD4 0.01 0.053 0.22 6 -0.22 5 11
NCOR1 0.03 0.011 -10000 0 -10000 0 0
NCOA2 0.028 0.013 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
MYOD/E2A 0.049 0.029 -10000 0 -0.4 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.074 0.12 -10000 0 -0.33 6 6
IFNB1 -0.012 0.071 0.32 2 -0.3 1 3
SMAD3/SMAD4/MEF2C 0.021 0.18 0.41 1 -0.55 30 31
CITED1 -0.3 0.29 -10000 0 -0.54 293 293
SMAD2-3/SMAD4/ARC105 0.024 0.11 -10000 0 -0.3 15 15
RBL1 0.039 0.031 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.001 0.11 -10000 0 -0.4 15 15
RUNX1-3/PEBPB2 0.022 0.12 -10000 0 -0.35 47 47
SMAD7 -0.18 0.22 -10000 0 -0.51 97 97
MYC/MIZ-1 0.009 0.096 -10000 0 -0.4 24 24
SMAD3/SMAD4 0.031 0.097 0.34 8 -0.37 3 11
IL10 -0.006 0.12 0.36 2 -0.37 29 31
PIASy/HDAC complex 0.026 0.027 -10000 0 -10000 0 0
PIAS3 0.033 0.009 -10000 0 -10000 0 0
CDK2 0.039 0.023 -10000 0 -10000 0 0
IL5 -0.004 0.12 0.4 1 -0.36 32 33
CDK4 0.036 0.011 -10000 0 -10000 0 0
PIAS4 0.026 0.027 -10000 0 -10000 0 0
ATF3 -0.12 0.24 -10000 0 -0.54 125 125
SMAD3/SMAD4/SP1 0.039 0.1 -10000 0 -0.3 10 10
FOXG1 0.041 0.036 -10000 0 -10000 0 0
FOXO3 0.021 0.019 -10000 0 -10000 0 0
FOXO1 -0.017 0.12 -10000 0 -0.39 46 46
FOXO4 0.022 0.018 -10000 0 -10000 0 0
heart looping 0.015 0.17 0.42 9 -0.55 28 37
CEBPB 0.031 0.028 -10000 0 -0.54 1 1
SMAD3/SMAD4/DLX1 0.012 0.093 -10000 0 -0.26 12 12
MYOD1 0.034 0.032 -10000 0 -0.54 1 1
SMAD3/SMAD4/HNF4 0.005 0.091 -10000 0 -0.27 14 14
SMAD3/SMAD4/GATA3 0.024 0.15 -10000 0 -0.4 34 34
SnoN/SIN3/HDAC complex/NCoR1 0.044 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.007 0.15 -10000 0 -0.36 47 47
SMAD3/SMAD4/SP1-3 0.06 0.1 -10000 0 -0.34 4 4
MED15 0.032 0.008 -10000 0 -10000 0 0
SP1 0.046 0.024 -10000 0 -10000 0 0
SIN3B 0.034 0.013 -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 24 24
ITGB5 -0.003 0.084 0.33 1 -0.45 3 4
TGIF/SIN3/HDAC complex/CtBP 0.023 0.07 -10000 0 -0.33 12 12
SMAD3/SMAD4/AR -0.045 0.16 -10000 0 -0.39 72 72
AR -0.041 0.2 -10000 0 -0.54 66 66
negative regulation of cell growth -0.024 0.12 -10000 0 -0.38 22 22
SMAD3/SMAD4/MYOD 0.005 0.094 -10000 0 -0.27 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 -0.37 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 -0.005 0.1 -10000 0 -0.37 19 19
TFDP1 0.033 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.25 0.3 -10000 0 -0.64 132 132
SMAD3/SMAD4/RUNX2 0.005 0.093 -10000 0 -0.26 16 16
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
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 -0.012 0.1 0.34 1 -0.48 17 18
AKT1 -0.04 0.12 0.25 5 -0.28 69 74
INSR 0.033 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.043 0.011 -10000 0 -10000 0 0
mol:GTP -0.003 0.11 0.27 3 -0.28 31 34
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.055 -10000 0 -0.21 9 9
TSC2 0.031 0.01 -10000 0 -10000 0 0
RHEB/GDP -0.013 0.092 -10000 0 -0.26 30 30
TSC1 0.033 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 -0.32 21 25
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 -0.007 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 13 13
eIF4E/eIF4G1/eIF4A1 -0.001 0.066 -10000 0 -0.31 13 13
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 0.25 11 -0.2 11 22
FKBP1A 0.033 0.011 -10000 0 -10000 0 0
RHEB/GTP 0.004 0.1 0.25 2 -0.33 9 11
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 8 -0.29 86 94
EIF4E 0.033 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 -0.24 15 15
TSC1/TSC2 -0.002 0.12 0.29 3 -0.3 30 33
tumor necrosis factor receptor activity 0 0.001 0.002 61 -0.001 2 63
RPS6 0.031 0.027 -10000 0 -0.54 1 1
PPP5C 0.035 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 0.23 6 -0.29 72 78
EIF4EBP1 -0.034 0.25 -10000 0 -1 29 29
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
PPP2R5D -0.011 0.098 0.4 2 -0.43 17 19
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 16 -0.003 5 21
EEF2 0.019 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.017 0.24 -10000 0 -0.97 29 29
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.05 -10000 0 -0.38 2 2
RAP1A 0.033 0.005 -10000 0 -10000 0 0
SELPLG 0.033 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 0.06 0.086 -10000 0 -0.37 6 6
RHOA 0.033 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.1 0.24 -10000 0 -0.54 116 116
MYH2 0.063 0.093 0.32 3 -0.5 4 7
MST1R 0.042 0.036 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.013 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 -0.01 0.15 -10000 0 -0.54 35 35
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 0.048 0.082 0.25 2 -0.36 8 10
JAM3 homodimer -0.01 0.14 -10000 0 -0.54 35 35
ICAM2 0.02 0.076 -10000 0 -0.54 9 9
ICAM1 0.039 0.027 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor 0.046 0.086 0.24 2 -0.36 9 11
cell adhesion -0.016 0.078 0.26 3 -10000 0 3
NFKB1 -0.22 0.19 0.39 1 -0.36 297 298
THY1 0.034 0.024 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.005 -10000 0 -10000 0 0
Lipoprotein(a) 0.042 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.063 0.13 -10000 0 -0.32 82 82
IL6 -0.52 0.36 0.38 1 -0.74 369 370
ITGB2 -0.022 0.062 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.031 0.11 0.3 8 -10000 0 8
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.2 -10000 0 -0.42 121 121
JAM2 -0.12 0.25 -10000 0 -0.54 131 131
alphaM/beta2 Integrin/ICAM1 0.007 0.091 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA/Plg 0.01 0.09 -10000 0 -0.36 1 1
RhoA/GTP 0.043 0.1 -10000 0 -0.44 10 10
positive regulation of phagocytosis 0.037 0.083 0.28 3 -0.39 2 5
Ron/MSP 0.055 0.027 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.033 0.11 0.31 8 -10000 0 8
alphaM/beta2 Integrin/uPAR 0.01 0.095 0.26 12 -10000 0 12
PLAU 0.055 0.051 -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 -0.44 5 13
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 0.002 0.084 0.25 1 -10000 0 1
fibrinolysis 0.008 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 2 -0.36 9 11
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 0.09 0.27 2 -0.36 2 4
FN1 0.13 0.066 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.017 0.074 0.25 1 -10000 0 1
MPO 0.031 0.016 -10000 0 -10000 0 0
KNG1 0.033 0.006 -10000 0 -10000 0 0
RAP1/GDP 0.043 0.011 -10000 0 -10000 0 0
ROCK1 0.063 0.11 0.28 5 -0.42 10 15
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 -0.073 0.16 -10000 0 -0.36 99 99
HP 0.029 0.012 -10000 0 -10000 0 0
leukocyte adhesion -0.17 0.2 -10000 0 -0.47 119 119
SELP -0.1 0.24 -10000 0 -0.54 116 116
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.015 0.18 -10000 0 -0.75 3 3
PCK1 -0.75 0.54 -10000 0 -1 384 384
HNF4A 0.031 0.2 0.72 1 -0.74 3 4
KCNJ11 0.036 0.24 0.89 1 -0.75 3 4
AKT1 0.01 0.15 -10000 0 -0.49 4 4
response to starvation 0.005 0.002 -10000 0 -10000 0 0
DLK1 0.025 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 -0.057 0.2 -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 -10000 0 -0.67 35 35
PKLR 0.032 0.19 -10000 0 -0.79 2 2
APOA1 0.02 0.22 -10000 0 -0.88 3 3
CPT1C 0.025 0.2 0.71 1 -0.75 3 4
ALAS1 0.029 0.14 -10000 0 -10000 0 0
TFRC -0.019 0.2 0.7 2 -10000 0 2
FOXF1 0.025 0.021 -10000 0 -10000 0 0
NF1 0.037 0.01 -10000 0 -10000 0 0
HNF1A (dimer) 0.05 0.022 -10000 0 -0.22 1 1
CPT1A 0.022 0.2 0.72 3 -0.7 3 6
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 0.04 0.015 -10000 0 -10000 0 0
GCK 0.02 0.19 -10000 0 -0.75 3 3
CREB1 -0.18 0.14 -10000 0 -0.26 369 369
IGFBP1 0.015 0.14 -10000 0 -1.1 1 1
PDX1 0.04 0.16 -10000 0 -1.1 2 2
UCP2 0.022 0.2 0.68 1 -0.7 3 4
ALDOB 0.02 0.22 -10000 0 -0.81 3 3
AFP -0.054 0.14 -10000 0 -10000 0 0
BDH1 0.022 0.19 0.67 2 -0.75 3 5
HADH 0.016 0.23 -10000 0 -0.93 5 5
F2 0.035 0.22 -10000 0 -0.82 3 3
HNF1A 0.05 0.022 -10000 0 -0.22 1 1
G6PC -0.098 0.12 -10000 0 -10000 0 0
SLC2A2 0.045 0.16 -10000 0 -0.84 2 2
INS 0.022 0.015 0.25 1 -10000 0 1
FOXA1 -0.008 0.23 0.38 3 -0.53 75 78
FOXA3 -0.11 0.14 -10000 0 -0.32 27 27
FOXA2 0.027 0.26 -10000 0 -0.92 3 3
ABCC8 -0.071 0.43 0.89 1 -0.93 86 87
ALB -0.056 0.15 -10000 0 -1.1 2 2
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 0.012 0.092 0.35 8 -0.28 7 15
TBX21 -0.13 0.37 0.73 5 -1.3 36 41
B2M 0.038 0.013 -10000 0 -10000 0 0
TYK2 0.017 0.035 -10000 0 -10000 0 0
IL12RB1 0.017 0.035 -10000 0 -10000 0 0
GADD45B -0.07 0.28 0.6 7 -0.74 46 53
IL12RB2 0.029 0.074 0.25 6 -0.55 1 7
GADD45G -0.06 0.26 0.69 2 -0.74 33 35
natural killer cell activation -0.008 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 0.044 0.23 1 -10000 0 1
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 0.57 9 -0.61 41 50
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 0.55 4 -0.59 59 63
CD4 -0.008 0.031 -10000 0 -10000 0 0
SOCS1 0.031 0.012 -10000 0 -10000 0 0
EntrezGene:6955 -0.014 0.015 -10000 0 -10000 0 0
CD3D 0.003 0.049 0.2 5 -10000 0 5
CD3E -0.001 0.033 0.2 1 -10000 0 1
CD3G 0.003 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 0.78 1 -0.8 18 19
CCL4 -0.085 0.25 0.78 1 -0.8 18 19
HLA-A 0.042 0.026 -10000 0 -10000 0 0
IL18/IL18R 0.057 0.14 0.36 14 -0.36 42 56
NOS2 -0.085 0.25 0.59 8 -0.6 62 70
IL12/IL12R/TYK2/JAK2/SPHK2 0.009 0.096 0.35 8 -0.3 7 15
IL1R1 -0.17 0.43 0.78 1 -1.2 59 60
IL4 0.038 0.029 -10000 0 -10000 0 0
JAK2 0.016 0.037 0.24 1 -10000 0 1
EntrezGene:6957 -0.011 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.001 0.14 0.35 18 -0.46 13 31
RAB7A -0.044 0.24 0.67 2 -0.71 24 26
lysosomal transport -0.04 0.23 0.64 3 -0.67 24 27
FOS -0.83 0.6 0.56 1 -1.2 364 365
STAT4 (dimer) -0.034 0.27 0.61 9 -0.67 40 49
STAT5A (dimer) -0.061 0.26 0.57 7 -0.61 53 60
GZMA -0.092 0.24 0.57 7 -0.59 62 69
GZMB -0.09 0.26 0.72 5 -0.87 18 23
HLX 0.025 0.038 -10000 0 -0.54 2 2
LCK -0.084 0.27 0.7 8 -0.62 61 69
TCR/CD3/MHC II/CD4 -0.12 0.16 0.28 5 -0.43 61 66
IL2/IL2R 0.087 0.055 0.37 4 -0.32 1 5
MAPK14 -0.058 0.28 0.62 7 -0.72 45 52
CCR5 -0.066 0.28 0.7 9 -0.74 40 49
IL1B 0.015 0.066 0.25 1 -0.55 4 5
STAT6 -0.04 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 0.057 0.053 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
NFKB2 0.034 0.012 -10000 0 -10000 0 0
IL12B 0.009 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 0.092 0.28 7 -0.34 8 15
IL2RB 0.035 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.25 0.61 9 -0.62 40 49
IL2RG 0.043 0.034 -10000 0 -10000 0 0
IL12 0.007 0.086 0.29 3 -0.41 10 13
STAT5A 0.031 0.027 -10000 0 -0.54 1 1
CD247 -0.004 0.11 0.2 8 -0.55 15 23
IL2 0.032 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 0.089 -10000 0 -0.56 10 10
IL12/IL12R/TYK2/JAK2 -0.1 0.27 0.69 7 -0.66 61 68
MAP2K3 -0.069 0.28 0.61 7 -0.75 48 55
RIPK2 0.029 0.021 -10000 0 -10000 0 0
MAP2K6 -0.062 0.27 0.62 7 -0.71 45 52
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.013 0.033 -10000 0 -10000 0 0
IL18RAP -0.01 0.16 0.21 2 -0.55 42 44
IL12Rbeta1/TYK2 0.029 0.046 0.25 1 -10000 0 1
EOMES 0.042 0.1 -10000 0 -0.61 3 3
STAT1 (dimer) -0.014 0.26 0.65 15 -0.59 37 52
T cell proliferation -0.031 0.22 0.52 9 -0.54 41 50
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 0.42 2 -0.62 37 39
ATF2 -0.055 0.26 0.59 7 -0.7 41 48
Syndecan-1-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
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 32 -0.36 7 39
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 18 -0.34 9 27
Syndecan-1/Syntenin 0.072 0.14 0.3 25 -0.34 8 33
MAPK3 0.071 0.13 0.28 28 -0.33 7 35
HGF/MET 0.005 0.14 -10000 0 -0.4 50 50
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 0.28 18 -0.34 9 27
Syndecan-1/RANTES 0.076 0.15 0.3 32 -0.38 10 42
Syndecan-1/CD147 0.093 0.15 0.35 14 -0.35 7 21
Syndecan-1/Syntenin/PIP2 0.067 0.13 0.28 25 -0.33 8 33
LAMA5 0.031 0.012 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.065 0.13 0.27 25 -0.33 8 33
MMP7 -0.041 0.19 -10000 0 -0.54 63 63
HGF 0.034 0.01 -10000 0 -10000 0 0
Syndecan-1/CASK 0.059 0.13 0.25 25 -0.34 9 34
Syndecan-1/HGF/MET 0.063 0.18 0.33 11 -0.38 31 42
regulation of cell adhesion 0.062 0.12 0.3 10 -0.33 6 16
HPSE 0.045 0.039 -10000 0 -10000 0 0
positive regulation of cell migration 0.087 0.14 0.32 32 -0.36 7 39
SDC1 0.086 0.13 0.26 91 -0.35 3 94
Syndecan-1/Collagen 0.087 0.14 0.32 32 -0.36 7 39
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 0.28 30 -0.34 6 36
homophilic cell adhesion 0.086 0.14 0.32 32 -0.35 7 39
MMP1 0.11 0.074 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.049 0.021 -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 0.028 -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 -0.054 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 0.069 0.084 0.24 2 -0.29 20 22
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 57 57
long-term memory 0.079 0.11 -10000 0 -0.32 21 21
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 0.031 0.012 -10000 0 -10000 0 0
CDK5R1 0.033 0.014 -10000 0 -10000 0 0
RELN 0.011 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 0.25 1 -0.32 22 23
GRIN2A/RELN/LRP8/DAB1/Fyn 0.082 0.095 -10000 0 -0.28 20 20
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 92 97
RELN/LRP8 0.068 0.091 0.25 1 -0.32 20 21
GRIN2B/RELN/LRP8/DAB1/Fyn 0.078 0.11 -10000 0 -0.31 30 30
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 0.031 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 0.019 0.089 -10000 0 -0.54 12 12
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 -0.051 0.16 -10000 0 -0.31 111 111
CDK5 0.036 0.02 -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 -0.38 35 39
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.048 0.068 -10000 0 -0.55 1 1
RELN/VLDLR 0.028 0.16 -10000 0 -0.31 79 79
IL1-mediated signaling events

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
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 -0.37 21 21
IRAK/TOLLIP 0.038 0.014 -10000 0 -10000 0 0
IKBKB 0.028 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 -10000 0 -10000 0 0
IL1B -0.018 0.12 -10000 0 -0.42 41 41
IRAK/TRAF6/p62/Atypical PKCs 0.064 0.026 -10000 0 -10000 0 0
IL1R2 0.038 0.055 -10000 0 -0.54 3 3
IL1R1 -0.029 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 0.03 0.011 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.021 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.038 0.067 -10000 0 -0.35 1 1
JUN -0.049 0.1 -10000 0 -0.27 80 80
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.023 0.19 -10000 0 -0.36 109 109
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 -0.022 0.16 -10000 0 -0.35 88 88
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.01 0.05 -10000 0 -0.27 11 11
IRAK1 0.019 0.011 -10000 0 -10000 0 0
IL1RN/IL1R1 0.015 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 -0.022 0.16 -10000 0 -0.35 88 88
IL1 beta/IL1R2 0.007 0.12 -10000 0 -0.36 44 44
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 -0.007 0.15 -10000 0 -0.32 86 86
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 -0.022 0.12 -10000 0 -0.29 80 80
CASP1 -0.014 0.15 -10000 0 -0.54 39 39
IL1RN/IL1R2 0.066 0.056 0.25 7 -0.4 3 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.004 0.16 -10000 0 -0.34 86 86
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 58 58
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
IL1RN 0.053 0.048 -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 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
PDGFRB 0.033 0.005 -10000 0 -10000 0 0
mol:S1P 0.001 0.003 0.03 6 -10000 0 6
S1P1/S1P/Gi -0.09 0.16 -10000 0 -0.28 184 184
GNAO1 0.031 0.013 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.041 0.016 -10000 0 -10000 0 0
AKT1 -0.011 0.1 -10000 0 -0.49 17 17
AKT3 -0.015 0.12 0.43 1 -0.58 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.033 0.005 -10000 0 -10000 0 0
GNAI2 0.034 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 0.24 2 -0.34 58 60
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 60 61
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 0.005 -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 -0.071 0.14 0.24 2 -0.34 58 60
RAC1 0.033 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.058 0.14 -10000 0 -0.32 57 57
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 0.016 -10000 0 -10000 0 0
GNA14 0.042 0.066 -10000 0 -0.54 4 4
GNA15 0.035 0.017 -10000 0 -10000 0 0
GNA12 0.033 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 -0.32 57 57
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.008 0.23 -10000 0 -0.9 24 24
NCK1/PAK1/Dok-R -0.033 0.093 -10000 0 -0.42 23 23
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 -0.002 0.19 -10000 0 -0.54 52 52
ELK1 0.005 0.22 -10000 0 -0.94 23 23
GRB7 0.028 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 -0.68 19 19
ITGA5 0.034 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.017 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 -0.004 0.23 -10000 0 -1 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.001 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 -0.71 26 26
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 0.007 -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 0.011 -10000 0 -10000 0 0
FGF2 -0.39 0.25 0.18 2 -0.54 375 377
STAT5A (dimer) -0.001 0.23 -10000 0 -0.86 20 20
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 -1.1 25 25
Tie2/SHP2 0.001 0.21 -10000 0 -1 15 15
TEK -0.003 0.22 -10000 0 -1.1 15 15
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 -0.004 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 -0.005 0.23 -10000 0 -1 23 23
PI3K -0.004 0.26 -10000 0 -1 24 24
FES -0.01 0.26 -10000 0 -1.1 24 24
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 0.014 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 -0.84 23 23
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 -0.83 24 24
ELF1 0.035 0.027 -10000 0 -10000 0 0
ELF2 0.002 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 -0.017 0.22 -10000 0 -0.84 21 21
DOK2 0.025 0.039 -10000 0 -0.54 2 2
negative regulation of cell cycle 0.003 0.17 -10000 0 -0.61 19 19
ETS1 0.031 0.056 -10000 0 -0.29 11 11
PXN 0.038 0.2 -10000 0 -0.69 23 23
ITGB1 0.033 0.006 -10000 0 -10000 0 0
NOS3 0.013 0.2 -10000 0 -0.74 24 24
RAC1 0.033 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 22 22
NCK1 0.033 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 -0.003 0.24 -10000 0 -1 23 23
Osteopontin-mediated events

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
IKK alpha homodimer 0.097 0.076 0.3 7 -0.28 4 11
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.1 0.38 10 -10000 0 10
alphaV/beta3 Integrin/Osteopontin/Src 0.097 0.071 0.26 2 -0.39 4 6
AP1 -0.14 0.22 0.49 1 -0.46 88 89
ILK 0.076 0.072 0.31 6 -0.3 4 10
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 0.088 0.33 1 -0.28 4 5
ITGAV 0.039 0.029 0.18 2 -0.54 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.047 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 0.094 0.34 17 -0.28 3 20
MAPK1 0.076 0.091 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 0.29 9 -0.29 6 15
ITGB3 0.041 0.021 -10000 0 -10000 0 0
NFKBIA 0.076 0.098 0.34 21 -0.27 3 24
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 0.082 0.15 0.5 8 -0.53 1 9
NF kappa B1 p50/RelA 0.13 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 0.06 0.033 -10000 0 -0.39 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.079 0.074 0.3 10 -0.3 4 14
VAV3 0.062 0.095 0.29 14 -0.29 12 26
MAP3K14 0.085 0.082 0.3 13 -0.3 4 17
ROCK2 0.032 0.026 -10000 0 -0.54 1 1
SPP1 0.094 0.086 -10000 0 -0.54 3 3
RAC1 0.033 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.071 0.087 0.27 10 -0.27 10 20
MMP2 -0.13 0.17 0.47 1 -0.41 72 73
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.021 0.12 -10000 0 -0.4 45 45
MAP4K4 0.005 0.08 -10000 0 -0.39 6 6
BAG4 0.027 0.015 -10000 0 -10000 0 0
PKC zeta/ceramide -0.012 0.067 0.14 10 -0.28 8 18
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.017 0.1 -10000 0 -0.54 16 16
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 0.26 5 -0.25 10 15
RB1 -0.012 0.067 0.16 2 -0.34 5 7
FADD/Caspase 8 0.033 0.12 0.29 9 -0.42 8 17
MAP2K4 -0.013 0.07 0.19 1 -0.35 6 7
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 0.23 9 -0.35 4 13
EGF -0.15 0.27 -10000 0 -0.54 161 161
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 -0.34 5 7
cell proliferation -0.11 0.14 -10000 0 -0.27 139 139
BID -0.014 0.19 -10000 0 -0.66 35 35
MAP3K1 -0.011 0.073 0.18 2 -0.29 9 11
EIF2A -0.004 0.073 0.25 11 -0.25 5 16
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 0.18 2 -0.27 7 9
FADD 0.03 0.1 0.28 2 -0.42 4 6
KSR1 -0.006 0.073 0.21 6 -0.36 4 10
MAPK8 -0.008 0.069 -10000 0 -0.27 10 10
PRKRA -0.012 0.07 0.17 4 -0.3 7 11
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 -0.32 86 86
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 0.029 -10000 0 -0.54 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.009 0.089 -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 0.19 59 -0.23 7 66
TNFRSF1A 0.032 0.008 -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 0.21 7 -0.3 5 12
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 0.037 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 0.23 188 -0.22 3 191
NF kappa B1/RelA/I kappa B alpha 0.074 0.03 -10000 0 -0.3 1 1
AIFM1 0.026 0.082 0.19 58 -0.24 7 65
BCL2 -0.074 0.22 -10000 0 -0.54 94 94
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.038 0.11 1 1 -10000 0 1
VDR 0.032 0.037 0.17 1 -0.54 2 3
FAM120B 0.032 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.062 0.077 -10000 0 -10000 0 0
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 7 7
RXRs/NUR77 0.071 0.09 -10000 0 -0.3 16 16
RXRs/PPAR -0.15 0.14 -10000 0 -0.41 39 39
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.027 -10000 0 -0.4 2 2
RARs/VDR/DNA/Vit D3 0.015 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 0.17 1 -0.54 2 3
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 0.16 0.56 50 -10000 0 50
RARs/THRs/DNA/SMRT -0.03 0.13 -10000 0 -0.27 98 98
THRA -0.001 0.13 -10000 0 -0.54 27 27
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.027 -10000 0 -0.4 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.074 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 0.042 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 0.01 0.12 -10000 0 -0.54 21 21
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 76 76
SREBF1 0.083 0.1 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.075 0.069 -10000 0 -0.3 4 4
ABCA1 0.076 0.1 -10000 0 -1 2 2
RARs/THRs 0.006 0.16 -10000 0 -0.31 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 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
MMP14 0.036 0.1 0.46 2 -0.63 5 7
oxygen homeostasis 0.025 0.029 0.19 3 -10000 0 3
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 0.43 25 -0.32 5 30
EPO 0.22 0.24 0.68 56 -0.46 3 59
FIH (dimer) 0.055 0.031 0.26 1 -10000 0 1
APEX1 0.057 0.038 0.23 2 -10000 0 2
SERPINE1 0.25 0.24 0.72 43 -0.5 4 47
FLT1 -0.014 0.17 -10000 0 -0.68 19 19
ADORA2A 0.26 0.25 0.66 72 -0.48 4 76
germ cell development 0.24 0.23 0.69 36 -0.49 3 39
SLC11A2 0.25 0.24 0.7 39 -0.5 4 43
BHLHE40 0.18 0.23 0.67 35 -0.49 4 39
HIF1AN 0.055 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 -0.68 14 14
PGK1 0.26 0.24 0.72 38 -0.49 4 42
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 21 -0.56 4 25
EPAS1 0.16 0.18 0.47 64 -0.32 10 74
SP1 0.046 0.028 -10000 0 -10000 0 0
ABCG2 0.24 0.26 0.69 37 -0.62 10 47
EFNA1 0.18 0.22 0.67 17 -0.5 4 21
FXN 0.25 0.23 0.67 47 -0.48 3 50
POU5F1 0.25 0.23 0.7 36 -0.51 3 39
neuron apoptosis -0.22 0.26 0.55 4 -0.76 21 25
EP300 0.032 0.008 -10000 0 -10000 0 0
EGLN3 0.081 0.068 0.26 18 -10000 0 18
EGLN2 0.059 0.035 0.25 1 -10000 0 1
EGLN1 0.045 0.034 0.26 1 -10000 0 1
VHL/Elongin B/Elongin C 0.053 0.032 -10000 0 -10000 0 0
VHL 0.035 0.017 -10000 0 -10000 0 0
ARNT 0.044 0.038 0.21 1 -10000 0 1
SLC2A1 0.25 0.24 0.67 55 -0.48 4 59
TWIST1 0.21 0.28 0.67 42 -0.54 30 72
ELK1 0.039 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.14 0.18 0.54 21 -0.36 5 26
VEGFA 0.25 0.25 0.73 41 -0.5 4 45
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Canonical Wnt signaling pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.042 0.26 5 -10000 0 5
AES 0.026 0.035 0.22 2 -10000 0 2
FBXW11 0.033 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.047 0.024 -10000 0 -0.4 1 1
SMAD4 0.031 0.027 -10000 0 -0.54 1 1
DKK2 0.031 0.054 -10000 0 -0.54 4 4
TLE1 0.01 0.1 0.22 6 -0.55 15 21
MACF1 0.034 0.006 -10000 0 -10000 0 0
CTNNB1 0.15 0.11 0.34 31 -0.41 3 34
WIF1 -0.38 0.26 -10000 0 -0.54 363 363
beta catenin/RanBP3 0.041 0.15 0.49 40 -0.4 3 43
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 0.34 30 -0.38 3 33
FZD1 0.033 0.026 -10000 0 -0.54 1 1
AXIN2 0.027 0.28 0.64 46 -1.1 14 60
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 0.086 -10000 0 -0.54 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.09 0.15 0.41 4 -0.58 13 17
Axin1/APC/GSK3 0.065 0.058 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 0.037 0.24 4 -10000 0 4
MYC 0.096 0.44 0.63 117 -1.3 28 145
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 0.027 0.041 0.26 5 -10000 0 5
WNT1/LRP6/FZD1/Axin1 0.076 0.038 -10000 0 -0.32 1 1
Ran/GTP 0.025 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.001 0.2 0.54 32 -0.54 13 45
LEF1 0.053 0.066 0.26 8 -10000 0 8
DVL1 0.078 0.056 0.25 3 -10000 0 3
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.096 0.17 0.34 3 -0.6 14 17
DKK1/LRP6/Kremen 2 0.079 0.13 0.25 1 -0.29 42 43
LRP6 0.033 0.008 -10000 0 -10000 0 0
CSNK1A1 0.027 0.041 0.26 5 -10000 0 5
NLK 0.035 0.031 -10000 0 -10000 0 0
CCND1 0.11 0.38 0.75 91 -1.2 14 105
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 0.037 0.062 0.38 4 -0.3 1 5
WNT1/LRP6/FZD1 0.16 0.1 0.26 67 -0.29 1 68
CREBBP 0.023 0.043 0.25 3 -0.55 1 4
Coregulation of Androgen receptor activity

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
NRIP1 0.028 0.064 -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 -0.35 64 64
CARM1 0.035 0.013 -10000 0 -10000 0 0
PRDX1 0.034 0.014 -10000 0 -10000 0 0
PELP1 0.03 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 0.031 -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 -0.54 128 128
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 0.032 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 84 84
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 -0.38 68 68
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 0.036 0.02 -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 -0.22 170 170
KLK3 0.012 0.056 -10000 0 -10000 0 0
TMF1 0.033 0.007 -10000 0 -10000 0 0
HNRNPA1 0.032 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 -0.36 65 65
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 -0.35 66 66
LATS2 0.02 0.076 -10000 0 -0.54 9 9
T-DHT/AR/PRX1 -0.034 0.13 -10000 0 -0.33 66 66
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 -0.018 0.069 -10000 0 -0.42 1 1
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 0.087 -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 -0.35 71 71
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
Regulation of Telomerase

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
Telomerase catalytic core complex -0.002 0.18 -10000 0 -0.77 10 10
RAD9A 0.031 0.01 -10000 0 -10000 0 0
AP1 -0.31 0.26 -10000 0 -0.47 341 341
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 -0.54 161 161
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 -0.71 10 10
SAP18 0.032 0.01 -10000 0 -10000 0 0
MRN complex 0.049 0.032 -10000 0 -10000 0 0
WT1 0.085 0.068 -10000 0 -10000 0 0
WRN 0.028 0.015 -10000 0 -10000 0 0
SP1 0.04 0.016 -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 -0.64 10 10
Mad/Max 0.054 0.017 -10000 0 -10000 0 0
TERT -0.009 0.18 -10000 0 -0.8 10 10
CCND1 0.031 0.25 0.57 9 -1 14 23
MAX 0.035 0.009 -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 0.042 0.11 0.31 1 -0.61 10 11
RAD1 0.033 0.009 -10000 0 -10000 0 0
XRCC5 0.033 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 -0.064 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 0.082 0.28 4 -0.32 10 14
PARP2 0.033 0.006 -10000 0 -10000 0 0
BLM 0.072 0.065 -10000 0 -10000 0 0
Telomerase 0.005 0.092 -10000 0 -0.72 4 4
IRF1 0.045 0.047 -10000 0 -0.18 9 9
ESR1 -0.059 0.26 -10000 0 -0.54 106 106
KU/TER 0.047 0.014 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.032 -10000 0 -0.29 1 1
ubiquitin-dependent protein catabolic process 0.042 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 0.033 0.005 -10000 0 -10000 0 0
MXD1 0.037 0.008 -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 0.029 0.012 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.022 0.18 -10000 0 -0.73 11 11
NR2F2 0.008 0.094 -10000 0 -0.55 13 13
MAPK3 0.018 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 -0.26 0.29 -10000 0 -0.54 261 261
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.3 0.26 -10000 0 -0.46 347 347
MYC -0.001 0.12 -10000 0 -0.54 24 24
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 0.032 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 0.02 0.18 -10000 0 -0.72 10 10
SP1/HDAC2 0.06 0.031 -10000 0 -10000 0 0
PINX1 0.027 0.014 -10000 0 -10000 0 0
Telomerase/EST1A 0.02 0.16 -10000 0 -0.66 9 9
Smad3/Myc 0.006 0.08 -10000 0 -0.34 24 24
911 complex 0.061 0.025 -10000 0 -10000 0 0
IFNG 0.064 0.072 -10000 0 -0.22 9 9
Telomerase/PinX1 0.009 0.16 -10000 0 -0.69 8 8
Telomerase/AKT1/mTOR/p70S6K 0.021 0.12 -10000 0 -0.52 13 13
SIN3B 0.035 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 -0.68 8 8
response to DNA damage stimulus 0 0.029 -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 0.025 0.16 -10000 0 -0.64 10 10
E2F1 0.053 0.047 0.2 8 -10000 0 8
ZNFX1 0.033 0.015 -10000 0 -10000 0 0
PIF1 0.038 0.027 -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
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.12 0.11 0.28 7 -0.63 4 11
Syndecan-4/Syndesmos 0.13 0.12 0.4 4 -0.72 4 8
positive regulation of JNK cascade 0.063 0.18 0.38 2 -0.7 5 7
Syndecan-4/ADAM12 0.15 0.13 0.41 5 -0.76 4 9
CCL5 0.028 0.06 -10000 0 -0.54 5 5
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DNM2 0.033 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 0.012 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 0.031 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 0.4 2 -0.72 4 6
Syndecan-4/CXCL12/CXCR4 0.066 0.19 0.42 1 -0.76 5 6
Syndecan-4/Laminin alpha3 0.054 0.16 0.41 2 -0.75 5 7
MDK 0.043 0.036 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.062 0.17 0.39 2 -0.69 5 7
Syndecan-4/Midkine 0.14 0.12 0.4 4 -0.7 4 8
FZD7 -0.13 0.26 -10000 0 -0.54 140 140
Syndecan-4/FGFR1/FGF -0.067 0.16 0.39 1 -0.58 9 10
THBS1 0.037 0.025 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.14 0.12 0.39 3 -0.72 4 7
positive regulation of MAPKKK cascade 0.063 0.18 0.38 2 -0.7 5 7
Syndecan-4/TACI 0.13 0.12 0.4 3 -0.76 4 7
CXCR4 0.043 0.037 -10000 0 -10000 0 0
cell adhesion 0.09 0.071 0.26 49 -10000 0 49
Syndecan-4/Dynamin 0.14 0.12 0.4 2 -0.76 4 6
Syndecan-4/TSP1 0.14 0.12 0.42 4 -0.76 4 8
Syndecan-4/GIPC 0.14 0.12 0.41 4 -0.76 4 8
Syndecan-4/RANTES 0.13 0.12 0.39 2 -0.76 4 6
ITGB1 0.033 0.006 -10000 0 -10000 0 0
LAMA1 0.032 0.01 -10000 0 -10000 0 0
LAMA3 -0.15 0.27 -10000 0 -0.54 158 158
RAC1 0.033 0.005 -10000 0 -10000 0 0
PRKCA 0.029 0.22 0.71 47 -10000 0 47
Syndecan-4/alpha-Actinin 0.14 0.12 0.4 2 -0.76 4 6
TFPI -0.19 0.28 -10000 0 -0.54 196 196
F2 0.038 0.02 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.049 0.011 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.044 0.15 0.41 1 -0.69 5 6
ACTN1 0.033 0.007 -10000 0 -10000 0 0
TNC 0.036 0.035 -10000 0 -0.54 1 1
Syndecan-4/CXCL12 0.056 0.18 0.4 2 -0.73 6 8
FGF6 0.03 0.037 -10000 0 -0.54 2 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
CXCL12 -0.13 0.26 -10000 0 -0.54 147 147
TNFRSF13B 0.031 0.014 -10000 0 -10000 0 0
FGF2 -0.39 0.25 0.17 2 -0.54 375 377
FGFR1 0.017 0.077 -10000 0 -0.54 9 9
Syndecan-4/PI-4-5-P2 0.094 0.11 -10000 0 -0.76 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.074 0.2 7 -10000 0 7
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 0.41 4 -0.72 4 8
SDC4 0.11 0.12 -10000 0 -0.81 4 4
Syndecan-4/Tenascin C 0.14 0.12 0.4 3 -0.76 4 7
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.12 0.12 0.39 2 -0.76 4 6
MMP9 0.091 0.076 -10000 0 -10000 0 0
Rac1/GTP 0.09 0.071 0.27 49 -10000 0 49
cytoskeleton organization 0.12 0.12 0.39 4 -0.69 4 8
GIPC1 0.034 0.01 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.035 0.19 0.39 3 -0.63 8 11
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 -0.33 41 41
JUN -0.065 0.22 -10000 0 -0.54 86 86
EP300 0.032 0.008 -10000 0 -10000 0 0
KAT2B 0 0 0.004 1 -10000 0 1
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.003 0.063 -10000 0 -0.41 10 10
FOXO1 -0.022 0.16 -10000 0 -0.54 46 46
T-DHT/AR -0.027 0.14 -10000 0 -0.35 40 40
MAP2K6 0.008 0.084 -10000 0 -0.55 10 10
BRM/BAF57 0.046 0.017 -10000 0 -10000 0 0
MAP2K4 0.018 0.027 -10000 0 -10000 0 0
SMARCA2 0.032 0.009 -10000 0 -10000 0 0
PDE9A -0.06 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 0.036 0.15 0.43 13 -0.42 4 17
NR0B1 -0.093 0.25 0.17 24 -0.54 117 141
EGR1 -0.43 0.23 -10000 0 -0.54 409 409
RXRs/9cRA 0.05 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 0.098 -10000 0 -10000 0 0
APPBP2 0.018 0.026 -10000 0 -10000 0 0
TRIM24 0.035 0.012 -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 0.004 1 -10000 0 1
RXRA 0.033 0.006 -10000 0 -10000 0 0
RXRB 0.034 0.005 -10000 0 -10000 0 0
CARM1 0.035 0.013 -10000 0 -10000 0 0
NR2C2 0.034 0.014 -10000 0 -10000 0 0
KLK2 0.013 0.077 0.37 1 -10000 0 1
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 0.031 -10000 0 -10000 0 0
MYST2 0 0.001 -10000 0 -0.006 4 4
HOXB13 0.077 0.068 0.2 2 -10000 0 2
T-DHT/AR/RACK1/Src 0 0.1 0.36 5 -0.35 7 12
positive regulation of transcription 0.041 0.031 -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 0.098 0.36 2 -0.36 11 13
GSK3B 0.033 0.01 -10000 0 -10000 0 0
NR2C1 0.032 0.026 -10000 0 -0.54 1 1
mol:T-DHT -0.019 0.072 0.22 15 -0.36 10 25
SIRT1 0.033 0.005 -10000 0 -10000 0 0
ZMIZ2 0.032 0.008 -10000 0 -10000 0 0
POU2F1 0.003 0.065 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.072 0.16 0.36 2 -0.33 110 112
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
SMARCE1 0.032 0.009 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.045 0.041 -10000 0 -10000 0 0
GNB1/GNG2 -0.019 0.054 -10000 0 -0.18 47 47
AKT1 0.058 0.13 0.44 14 -0.35 4 18
EGF -0.15 0.27 -10000 0 -0.54 161 161
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 0.5 15 -0.33 14 29
LYN 0.026 0.051 0.26 3 -10000 0 3
RhoA/GTP 0.025 0.066 0.18 15 -0.15 1 16
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK 0.057 0.17 0.58 11 -0.34 41 52
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 0.013 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 40 49
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 0.031 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 0.12 0.38 13 -0.46 9 22
mol:NADP 0.033 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 -0.38 32 41
cell morphogenesis 0.043 0.012 -10000 0 -10000 0 0
PLCB2 0.05 0.22 0.7 8 -0.5 42 50
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.03 0.054 0.25 3 -10000 0 3
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 0.054 0.18 0.63 9 -0.37 43 52
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.033 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.052 0.22 0.72 8 -0.51 45 53
LCK 0.038 0.06 0.25 6 -10000 0 6
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 -0.41 20 20
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.04 0.041 -10000 0 -10000 0 0
MAPK14 0.051 0.13 0.43 16 -0.25 8 24
TGM2/GTP 0.055 0.2 0.67 9 -0.46 14 23
MAPK11 0.049 0.13 0.44 16 -0.25 11 27
ARHGEF1 0.043 0.11 0.36 15 -0.2 6 21
GNAI2 0.033 0.01 -10000 0 -10000 0 0
JNK cascade 0.058 0.18 0.62 10 -0.38 43 53
RAB11/GDP 0.031 0.01 -10000 0 -10000 0 0
ICAM1 0.057 0.15 0.52 13 -0.31 12 25
cAMP biosynthetic process 0.053 0.17 0.6 9 -0.38 14 23
Gq family/GTP/EBP50 0.033 0.047 0.16 1 -0.22 6 7
actin cytoskeleton reorganization 0.043 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 0.033 0.011 -10000 0 -10000 0 0
EGF/EGFR -0.062 0.11 0.26 3 -0.28 44 47
VCAM1 0.052 0.16 0.55 11 -0.32 39 50
TP beta/Gq family/GDP/G beta5/gamma2 0.013 0.12 -10000 0 -0.6 14 14
platelet activation 0.062 0.16 0.54 13 -0.32 13 26
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 -0.48 16 16
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 0.056 0.2 0.68 8 -0.42 43 51
EGFR -0.26 0.29 -10000 0 -0.54 261 261
TXA2/TP alpha 0.056 0.21 0.7 8 -0.47 35 43
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 0.039 -10000 0 -0.24 4 4
PGD2/DP 0.022 0.044 -10000 0 -0.4 5 5
SLC9A3R1 0.057 0.056 -10000 0 -10000 0 0
FYN 0.026 0.055 0.27 1 -0.29 2 3
mol:NO 0.033 0.006 -10000 0 -10000 0 0
GNA15 0.035 0.017 -10000 0 -10000 0 0
PGK/cGMP 0.045 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.01 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.066 0.055 0.28 1 -0.34 1 2
NOS3 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.033 0.005 -10000 0 -10000 0 0
PRKCA 0.062 0.18 0.6 10 -0.35 36 46
PRKCB 0.052 0.17 0.61 9 -0.35 45 54
PRKCE 0.054 0.17 0.6 10 -0.36 41 51
PRKCD 0.053 0.18 0.62 9 -0.38 44 53
PRKCG 0.055 0.18 0.6 10 -0.38 43 53
muscle contraction 0.053 0.21 0.71 8 -0.48 44 52
PRKCZ 0.055 0.17 0.53 13 -0.34 43 56
ARR3 0.034 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.044 0.048 -10000 0 -0.25 6 6
PRKCQ 0.059 0.18 0.58 12 -0.35 43 55
MAPKKK cascade 0.053 0.2 0.68 8 -0.45 39 47
SELE 0.048 0.18 0.51 14 -0.38 46 60
TP beta/GNAI2/GDP/G beta/gamma 0.061 0.048 0.28 1 -0.34 1 2
ROCK1 0.033 0.006 -10000 0 -10000 0 0
GNA14 0.042 0.066 -10000 0 -0.54 4 4
chemotaxis 0.048 0.25 0.75 8 -0.6 47 55
GNA12 0.033 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 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
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 0.03 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 -0.32 35 35
PRKG1 0.033 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 -0.37 21 21
apoptosis -0.038 0.088 -10000 0 -0.3 35 35
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 -0.54 208 208
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 0.033 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 0.043 0.011 -10000 0 -10000 0 0
MAPK11 0.002 0.13 0.4 2 -0.38 26 28
BLK 0.038 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 0.39 2 -0.37 29 31
positive regulation of innate immune response 0.002 0.15 0.47 2 -0.44 29 31
LCK 0.048 0.043 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.015 0.15 0.58 1 -0.42 29 30
p38alpha-beta/MKP5 0.01 0.15 0.58 1 -0.42 28 29
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 0.19 -10000 0 -0.44 63 63
CDC42 0.033 0.007 -10000 0 -10000 0 0
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.033 0.005 -10000 0 -10000 0 0
PAK3 -0.31 0.28 -10000 0 -0.54 305 305
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.006 0.029 0.35 1 -0.34 1 2
SNTA1 0.032 0.026 -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 23 62
CCND1 0.008 0.083 0.2 1 -0.5 10 11
p38 gamma/SNTA1 0.026 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 -0.28 23 62
MAP2K6 0.015 0.098 0.25 44 -0.3 24 68
MAPT 0.013 0.067 0.27 8 -0.26 9 17
MAPK13 0.017 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
IL2 signaling events mediated by PI3K

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
BCL2L1 0.02 0.089 -10000 0 -0.44 3 3
UGCG 0.028 0.11 -10000 0 -0.65 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT 0 0.18 0.33 1 -0.39 44 45
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.029 0.11 -10000 0 -0.64 11 11
mol:DAG 0.004 0.11 -10000 0 -0.85 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.22 -10000 0 -0.5 42 42
FRAP1 -0.036 0.24 0.38 1 -0.53 55 56
FOXO3 0.005 0.18 0.37 3 -0.5 30 33
AKT1 0.002 0.2 0.38 1 -0.54 31 32
GAB2 0.027 0.014 -10000 0 -10000 0 0
SMPD1 0.008 0.12 -10000 0 -0.66 15 15
SGMS1 0.018 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 0.42 1 -0.48 9 10
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 0.004 0.11 -10000 0 -0.85 7 7
natural killer cell activation -0.002 0.005 -10000 0 -0.019 5 5
JAK3 0.033 0.009 -10000 0 -10000 0 0
PIK3R1 -0.02 0.16 -10000 0 -0.54 45 45
JAK1 0.033 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MYC 0.023 0.27 0.54 1 -0.92 30 31
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 0.32 1 -0.38 13 14
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 0.12 0.32 1 -0.37 13 14
Rac1/GDP -0.011 0.094 -10000 0 -0.31 42 42
T cell proliferation 0.028 0.12 0.3 1 -0.35 13 14
SHC1 0.025 0.015 -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 0.3 1 -0.36 13 14
NF kappa B1 p50/RelA -0.009 0.22 -10000 0 -0.51 38 38
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.022 0.095 0.29 1 -0.36 10 11
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL2RA 0.038 0.035 -10000 0 -10000 0 0
IL2RB 0.034 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 0.031 0.01 -10000 0 -10000 0 0
RPS6 0.031 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 0.3 1 -0.35 13 14
GRB2 0.031 0.019 -10000 0 -10000 0 0
IL2 0.031 0.028 -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 0.044 -10000 0 -10000 0 0
BCL2 -0.12 0.38 0.52 1 -0.83 104 105
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.41 24 24
PLCG1 0.006 0.13 -10000 0 -0.43 24 24
YES1 -0.001 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 24 28
MAP3K7 -0.005 0.1 0.25 1 -0.37 20 21
mol:Ca2+ 0.007 0.12 -10000 0 -0.4 24 24
mol:IP3 0.006 0.13 -10000 0 -0.41 24 24
NLK 0.003 0.13 -10000 0 -0.8 12 12
GNB1 0.033 0.011 -10000 0 -10000 0 0
CAMK2A 0 0.12 0.26 1 -0.39 22 23
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.015 0.13 -10000 0 -0.38 43 43
CSNK1A1 0.033 0.005 -10000 0 -10000 0 0
GNAS -0.005 0.13 0.25 1 -0.45 23 24
GO:0007205 0 0.12 0.26 1 -0.41 24 25
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 -0.44 21 21
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 S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.033 0.005 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
GNB1/GNG2 0.048 0.086 -10000 0 -0.34 22 22
forebrain development -0.043 0.2 -10000 0 -0.53 56 56
GNAO1 0.03 0.012 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.029 0.091 -10000 0 -0.4 21 21
SMO 0.013 0.12 -10000 0 -0.54 21 21
ARRB2 0.032 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.029 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 0.033 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.076 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) -0.032 0.19 -10000 0 -0.64 28 28
SAP30 0.033 0.009 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 -10000 0 -0.54 21 21
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 -0.38 13 13
GLI3 0.015 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 0.031 0.009 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.03 0.027 -10000 0 -0.54 1 1
GNG2 0.032 0.026 -10000 0 -0.54 1 1
Gi family/GTP -0.082 0.16 -10000 0 -0.37 70 70
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 -0.45 15 15
GLI2/Su(fu) 0.019 0.11 -10000 0 -0.44 13 13
FOXA2 0.016 0.12 -10000 0 -0.72 10 10
neural tube patterning -0.043 0.2 -10000 0 -0.53 56 56
SPOP 0.03 0.011 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.027 0.064 -10000 0 -0.35 1 1
GNB1 0.033 0.011 -10000 0 -10000 0 0
CSNK1G2 0.033 0.006 -10000 0 -10000 0 0
CSNK1G3 0.033 0.006 -10000 0 -10000 0 0
MTSS1 0.033 0.029 0.31 1 -10000 0 1
embryonic limb morphogenesis -0.043 0.2 -10000 0 -0.53 56 56
SUFU 0.019 0.049 -10000 0 -0.26 3 3
LGALS3 -0.03 0.18 -10000 0 -0.54 55 55
catabolic process 0.037 0.13 -10000 0 -0.6 12 12
GLI3A/CBP 0.002 0.12 -10000 0 -0.36 48 48
KIF3A 0.033 0.006 -10000 0 -10000 0 0
GLI1 -0.044 0.21 -10000 0 -0.55 56 56
RAB23 0.034 0.014 -10000 0 -10000 0 0
CSNK1A1 0.033 0.005 -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 0.006 -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 -0.081 0.17 -10000 0 -0.39 68 68
PTCH1 -0.037 0.18 -10000 0 -0.62 24 24
MIM/GLI1 -0.023 0.18 -10000 0 -0.58 33 33
CREBBP 0.002 0.12 -10000 0 -0.36 48 48
Su(fu)/SIN3/HDAC complex 0.015 0.1 -10000 0 -0.45 17 17
Signaling events mediated by PRL

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
CCNE1 0.057 0.055 -10000 0 -10000 0 0
mol:Halofuginone 0.003 0.004 -10000 0 -10000 0 0
ITGA1 0.031 0.037 -10000 0 -0.54 2 2
CDKN1A -0.08 0.099 -10000 0 -0.53 16 16
PRL-3/alpha Tubulin 0.042 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.042 -10000 0 -10000 0 0
AGT 0.041 0.047 0.17 52 -10000 0 52
CCNA2 -0.18 0.12 -10000 0 -10000 0 0
TUBA1B 0.035 0.012 -10000 0 -10000 0 0
EGR1 -0.31 0.16 -10000 0 -0.39 407 407
CDK2/Cyclin E1 -0.042 0.11 -10000 0 -0.46 16 16
MAPK3 0.015 0.018 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.051 0.017 -10000 0 -10000 0 0
MAPK1 0.015 0.019 -10000 0 -10000 0 0
PTP4A1 -0.22 0.13 -10000 0 -10000 0 0
PTP4A3 0.03 0.025 -10000 0 -10000 0 0
PTP4A2 0.036 0.019 -10000 0 -10000 0 0
ITGB1 0.015 0.019 -10000 0 -10000 0 0
SRC 0.032 0.008 -10000 0 -10000 0 0
RAC1 -0.058 0.079 -10000 0 -0.49 8 8
Rab GGTase beta/Rab GGTase alpha 0.048 0.011 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.21 0.12 -10000 0 -10000 0 0
RABGGTA 0.033 0.006 -10000 0 -10000 0 0
BCAR1 -0.019 0.018 -10000 0 -10000 0 0
RHOC -0.059 0.084 -10000 0 -0.52 9 9
RHOA -0.065 0.1 -10000 0 -0.54 15 15
cell motility -0.084 0.095 0.27 1 -0.4 23 24
PRL-1/alpha Tubulin -0.21 0.12 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.04 0.034 -10000 0 -0.4 1 1
ROCK1 -0.082 0.095 0.27 1 -0.4 22 23
RABGGTB 0.033 0.006 -10000 0 -10000 0 0
CDK2 0.037 0.021 -10000 0 -10000 0 0
mitosis -0.22 0.13 -10000 0 -10000 0 0
ATF5 0.034 0.012 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.035 0.093 -9999 0 -0.34 24 24
E-cadherin/beta catenin 0.018 0.1 -9999 0 -0.33 35 35
CTNNB1 0.03 0.045 -9999 0 -0.54 3 3
JUP 0.032 0.01 -9999 0 -10000 0 0
CDH1 0.006 0.12 -9999 0 -0.54 22 22
Wnt signaling

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
Noncanonical Wnts/FZD -0.015 0.13 -9999 0 -0.38 43 43
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
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.036 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 0.34 4 -0.35 5 9
ENAH -0.031 0.14 -10000 0 -0.43 36 36
AP1M1 0.033 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 0.074 -10000 0 -0.29 2 2
ABI1/Sra1/Nap1 -0.016 0.04 -10000 0 -0.18 12 12
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.049 0.094 -10000 0 -0.31 25 25
RAPGEF1 -0.029 0.14 0.33 1 -0.4 37 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 50 50
CRK -0.027 0.14 0.34 1 -0.42 43 44
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 0.032 0.008 -10000 0 -10000 0 0
NCKAP1 0.033 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.054 0.041 -10000 0 -0.31 3 3
DLG1 -0.039 0.16 -10000 0 -0.42 51 51
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.02 0.06 -10000 0 -0.21 5 5
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GTP/NME1/Tiam1 0.057 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 -0.32 32 32
TIAM1 0.034 0.012 0.18 3 -10000 0 3
E-cadherin(dimer)/Ca2+ 0.046 0.088 -10000 0 -0.29 25 25
AKT1 -0.007 0.055 -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 0.32 4 -0.35 5 9
actin cytoskeleton organization 0.036 0.093 0.26 41 -0.19 13 54
CDC42/GDP 0.001 0.12 0.32 4 -0.35 5 9
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.004 0.067 -10000 0 -0.25 24 24
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 0.33 4 -0.35 24 28
CDC42/GTP/IQGAP1 0.042 0.013 -10000 0 -10000 0 0
JUP 0.032 0.01 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.007 0.12 0.36 2 -0.39 3 5
RAC1/GTP/IQGAP1 0.043 0.011 -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 0.033 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.067 0.22 19 -0.23 11 30
NME1 0.03 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 46 46
regulation of cell-cell adhesion 0 0.061 -10000 0 -0.25 2 2
WASF2 0.019 0.043 0.12 31 -0.12 2 33
Rap1/GTP 0.013 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 0.24 19 -0.28 11 30
VAV2 -0.019 0.19 0.41 1 -0.63 18 19
RAP1/GDP 0.01 0.099 0.32 2 -0.36 3 5
adherens junction assembly -0.034 0.15 -10000 0 -0.42 46 46
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.033 0.006 -10000 0 -10000 0 0
PIP5K1C 0.033 0.009 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.044 0.087 -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 -0.43 48 48
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 50 50
Cellular roles of Anthrax toxin

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
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 0.084 -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 -10000 0 -0.3 10 10
CYAA -0.01 0.043 -10000 0 -0.29 11 11
MAP2K4 -0.005 0.012 -10000 0 -0.18 1 1
IL1B -0.008 0.046 0.18 2 -0.21 14 16
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 </