Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNA expression and copy number data
(primary solid tumor cohort)
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 54 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 240
Signaling events mediated by Stem cell factor receptor (c-Kit) 218
Endothelins 149
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 149
EGFR-dependent Endothelin signaling events 143
Class IB PI3K non-lipid kinase events 125
IGF1 pathway 120
FOXM1 transcription factor network 112
Arf6 signaling events 109
Nongenotropic Androgen signaling 91
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 240 10598 44 -0.6 0.034 1000 -1000 -0.016 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 218 17080 78 -1 0.32 1000 -1000 -0.024 -1000
Endothelins 149 14380 96 -0.81 0.16 1000 -1000 -0.01 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 149 10134 68 -0.89 0.45 1000 -1000 -0.045 -1000
EGFR-dependent Endothelin signaling events 143 3006 21 -0.31 0.047 1000 -1000 -0.037 -1000
Class IB PI3K non-lipid kinase events 125 375 3 -0.11 -1000 1000 -1000 -0.024 -1000
IGF1 pathway 120 6852 57 -0.27 0.11 1000 -1000 -0.026 -1000
FOXM1 transcription factor network 112 5746 51 -0.13 0.69 1000 -1000 0.011 -1000
Arf6 signaling events 109 6789 62 -0.31 0.081 1000 -1000 -0.002 -1000
Nongenotropic Androgen signaling 91 4756 52 -0.57 0.3 1000 -1000 -0.023 -1000
Glucocorticoid receptor regulatory network 83 9485 114 -0.95 0.29 1000 -1000 -0.05 -1000
S1P1 pathway 76 2760 36 -0.62 0.045 1000 -1000 -0.019 -1000
Signaling events mediated by PTP1B 73 5607 76 -0.37 0.19 1000 -1000 -0.015 -1000
PDGFR-alpha signaling pathway 70 3085 44 -0.7 0.063 1000 -1000 -0.027 -1000
Calcium signaling in the CD4+ TCR pathway 69 2149 31 -0.36 0.039 1000 -1000 -0.032 -1000
HIF-1-alpha transcription factor network 68 5240 76 -0.39 0.072 1000 -1000 -0.011 -1000
BMP receptor signaling 68 5512 81 -0.4 0.11 1000 -1000 -0.037 -1000
Ephrin B reverse signaling 67 3243 48 -0.18 0.06 1000 -1000 -0.03 -1000
IL6-mediated signaling events 62 4655 75 -0.37 0.072 1000 -1000 -0.026 -1000
Ras signaling in the CD4+ TCR pathway 57 982 17 -0.2 0.033 1000 -1000 -0.008 -1000
Plasma membrane estrogen receptor signaling 56 4848 86 -0.25 0.17 1000 -1000 -0.048 -1000
FAS signaling pathway (CD95) 54 2560 47 -0.88 0.059 1000 -1000 -0.028 -1000
EPHB forward signaling 54 4601 85 -0.18 0.15 1000 -1000 -0.055 -1000
IL4-mediated signaling events 53 4909 91 -0.52 0.14 1000 -1000 -0.098 -1000
Integrins in angiogenesis 49 4138 84 -0.39 0.13 1000 -1000 -0.032 -1000
IL23-mediated signaling events 48 2889 60 -0.79 0.064 1000 -1000 -0.003 -1000
Visual signal transduction: Rods 48 2538 52 -0.43 0.073 1000 -1000 -0.014 -1000
Aurora B signaling 46 3110 67 -0.38 0.23 1000 -1000 -0.026 -1000
Fc-epsilon receptor I signaling in mast cells 45 4441 97 -0.36 0.04 1000 -1000 -0.042 -1000
PLK1 signaling events 44 3815 85 -0.036 0.17 1000 -1000 -0.029 -1000
S1P4 pathway 42 1070 25 -0.17 0.045 1000 -1000 -0.01 -1000
Signaling events mediated by the Hedgehog family 40 2109 52 -0.14 0.067 1000 -1000 -0.018 -1000
Glypican 1 network 40 1937 48 -0.39 0.07 1000 -1000 -0.024 -1000
S1P5 pathway 39 673 17 -0.17 0.067 1000 -1000 -0.008 -1000
Insulin Pathway 39 2906 74 -0.28 0.091 1000 -1000 -0.031 -1000
E-cadherin signaling in keratinocytes 39 1685 43 -0.27 0.036 1000 -1000 -0.022 -1000
p75(NTR)-mediated signaling 38 4802 125 -0.13 0.092 1000 -1000 -0.038 -1000
TCGA08_retinoblastoma 38 309 8 -0.024 0.057 1000 -1000 -0.007 -1000
Nectin adhesion pathway 36 2316 63 -0.074 0.054 1000 -1000 -0.037 -1000
Presenilin action in Notch and Wnt signaling 35 2180 61 -0.38 0.1 1000 -1000 -0.026 -1000
Stabilization and expansion of the E-cadherin adherens junction 35 2619 74 -0.27 0.073 1000 -1000 -0.059 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 33 2843 85 -0.54 0.046 1000 -1000 -0.03 -1000
LPA receptor mediated events 33 3417 102 -0.36 0.092 1000 -1000 -0.083 -1000
IL27-mediated signaling events 31 1610 51 -0.37 0.067 1000 -1000 -0.024 -1000
Neurotrophic factor-mediated Trk receptor signaling 31 3723 120 -0.24 0.12 1000 -1000 -0.042 -1000
ErbB2/ErbB3 signaling events 29 1911 65 -0.35 0.046 1000 -1000 -0.063 -1000
Syndecan-1-mediated signaling events 29 1011 34 -0.041 0.11 1000 -1000 -0.013 -1000
FOXA2 and FOXA3 transcription factor networks 28 1291 46 -0.75 0.051 1000 -1000 -0.001 -1000
Signaling events regulated by Ret tyrosine kinase 28 2323 82 -0.1 0.11 1000 -1000 -0.053 -1000
RXR and RAR heterodimerization with other nuclear receptor 28 1503 52 -0.38 0.1 1000 -1000 -0.019 -1000
TCGA08_p53 28 197 7 -0.009 0.028 1000 -1000 -0.004 -1000
TCGA08_rtk_signaling 28 745 26 -0.27 0.042 1000 -1000 -0.019 -1000
TCR signaling in naïve CD8+ T cells 27 2585 93 -0.039 0.082 1000 -1000 -0.041 -1000
Canonical Wnt signaling pathway 27 1388 51 -0.38 0.16 1000 -1000 -0.032 -1000
mTOR signaling pathway 26 1417 53 -0.051 0.044 1000 -1000 -0.031 -1000
S1P3 pathway 26 1116 42 -0.17 0.062 1000 -1000 -0.013 -1000
Regulation of nuclear SMAD2/3 signaling 25 3434 136 -0.37 0.075 1000 -1000 -0.042 -1000
Syndecan-2-mediated signaling events 25 1787 69 -0.32 0.13 1000 -1000 -0.021 -1000
amb2 Integrin signaling 25 2086 82 -0.52 0.13 1000 -1000 -0.021 -1000
ErbB4 signaling events 24 1656 69 -0.36 0.14 1000 -1000 -0.028 -1000
HIF-2-alpha transcription factor network 24 1067 43 -0.22 0.26 1000 -1000 -0.092 -1000
Syndecan-3-mediated signaling events 24 845 35 -0.36 0.074 1000 -1000 -0.019 -1000
IL12-mediated signaling events 23 2053 87 -0.83 0.087 1000 -1000 -0.044 -1000
Thromboxane A2 receptor signaling 23 2450 105 -0.27 0.066 1000 -1000 -0.034 -1000
Ceramide signaling pathway 23 1774 76 -0.25 0.083 1000 -1000 -0.021 -1000
Angiopoietin receptor Tie2-mediated signaling 23 2106 88 -0.39 0.13 1000 -1000 -0.06 -1000
IL1-mediated signaling events 22 1402 62 -0.05 0.067 1000 -1000 -0.021 -1000
Coregulation of Androgen receptor activity 21 1668 76 -0.22 0.053 1000 -1000 -0.013 -1000
Osteopontin-mediated events 21 823 38 -0.36 0.14 1000 -1000 -0.015 -1000
Reelin signaling pathway 21 1227 56 -0.055 0.083 1000 -1000 -0.019 -1000
Regulation of p38-alpha and p38-beta 20 1100 54 -0.31 0.071 1000 -1000 -0.042 -1000
Regulation of Telomerase 20 2130 102 -0.36 0.085 1000 -1000 -0.02 -1000
Syndecan-4-mediated signaling events 20 1373 67 -0.39 0.15 1000 -1000 -0.025 -1000
Regulation of Androgen receptor activity 20 1413 70 -0.43 0.078 1000 -1000 -0.033 -1000
Hedgehog signaling events mediated by Gli proteins 18 1177 65 -0.17 0.077 1000 -1000 -0.025 -1000
IL2 signaling events mediated by PI3K 18 1061 58 -0.12 0.048 1000 -1000 -0.03 -1000
Signaling mediated by p38-gamma and p38-delta 17 269 15 -0.006 0.034 1000 -1000 -0.028 -1000
E-cadherin signaling in the nascent adherens junction 16 1236 76 -0.039 0.059 1000 -1000 -0.049 -1000
Noncanonical Wnt signaling pathway 15 403 26 -0.015 0.04 1000 -1000 -0.025 -1000
Signaling events mediated by PRL 15 521 34 -0.31 0.051 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 14 563 39 -0.063 0.038 1000 -1000 -0.017 -1000
E-cadherin signaling events 14 74 5 0.006 0.035 1000 -1000 0.021 -1000
Caspase cascade in apoptosis 13 1022 74 -0.15 0.049 1000 -1000 -0.03 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 13 593 45 -0.006 0.06 1000 -1000 -0.025 -1000
JNK signaling in the CD4+ TCR pathway 12 207 17 -0.039 0.089 1000 -1000 -0.017 -1000
IFN-gamma pathway 12 852 68 -0.019 0.098 1000 -1000 -0.036 -1000
Wnt signaling 12 88 7 -0.015 0.04 1000 -1000 -0.014 -1000
BCR signaling pathway 12 1282 99 -0.15 0.092 1000 -1000 -0.045 -1000
VEGFR1 specific signals 12 695 56 -0.38 0.075 1000 -1000 -0.027 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 11 600 54 -0.041 0.08 1000 -1000 -0.015 -1000
Class I PI3K signaling events mediated by Akt 11 773 68 -0.15 0.061 1000 -1000 -0.02 -1000
ceramide signaling pathway 11 575 49 -0.074 0.053 1000 -1000 -0.024 -1000
FoxO family signaling 11 743 64 0.001 0.15 1000 -1000 -0.015 -1000
Signaling events mediated by VEGFR1 and VEGFR2 11 1415 125 -0.38 0.075 1000 -1000 -0.032 -1000
Sphingosine 1-phosphate (S1P) pathway 10 282 28 -0.17 0.053 1000 -1000 -0.01 -1000
PLK2 and PLK4 events 10 31 3 0.017 0.055 1000 -1000 0.003 -1000
Arf6 downstream pathway 9 398 43 -0.09 0.092 1000 -1000 -0.037 -1000
EPO signaling pathway 9 522 55 -0.093 0.067 1000 -1000 -0.015 -1000
TRAIL signaling pathway 8 405 48 -0.002 0.047 1000 -1000 -0.024 -1000
Canonical NF-kappaB pathway 7 308 39 0 0.074 1000 -1000 -0.008 -1000
Signaling events mediated by HDAC Class II 7 556 75 -0.06 0.066 1000 -1000 -0.029 -1000
Circadian rhythm pathway 7 168 22 -0.02 0.1 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class III 7 316 40 -0.061 0.062 1000 -1000 -0.034 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 7 584 83 -0.074 0.065 1000 -1000 -0.004 -1000
Arf6 trafficking events 7 510 71 -0.26 0.056 1000 -1000 -0.025 -1000
Paxillin-independent events mediated by a4b1 and a4b7 6 242 37 -0.019 0.084 1000 -1000 -0.018 -1000
Retinoic acid receptors-mediated signaling 6 365 58 -0.053 0.08 1000 -1000 -0.016 -1000
Paxillin-dependent events mediated by a4b1 6 225 36 -0.07 0.075 1000 -1000 -0.028 -1000
PDGFR-beta signaling pathway 6 586 97 -0.034 0.08 1000 -1000 -0.04 -1000
p38 MAPK signaling pathway 6 290 44 -0.015 0.066 1000 -1000 -0.014 -1000
Visual signal transduction: Cones 5 201 38 0 0.068 1000 -1000 0 -1000
Insulin-mediated glucose transport 5 161 32 -0.099 0.053 1000 -1000 -0.011 -1000
Class I PI3K signaling events 5 381 73 -0.008 0.059 1000 -1000 -0.025 -1000
Nephrin/Neph1 signaling in the kidney podocyte 4 168 34 -0.047 0.083 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class I 4 485 104 -0.21 0.081 1000 -1000 -0.033 -1000
Atypical NF-kappaB pathway 4 135 31 -0.019 0.048 1000 -1000 -0.008 -1000
IL2 signaling events mediated by STAT5 4 98 22 -0.018 0.08 1000 -1000 -0.011 -1000
Aurora A signaling 3 197 60 0 0.12 1000 -1000 -0.011 -1000
Aurora C signaling 3 22 7 0 0.078 1000 -1000 -0.012 -1000
Effects of Botulinum toxin 3 90 26 0 0.069 1000 -1000 0 -1000
LPA4-mediated signaling events 1 20 12 -0.01 0.035 1000 -1000 -0.022 -1000
Ephrin A reverse signaling 1 7 7 0 0.043 1000 -1000 0 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 1 49 33 0 0.076 1000 -1000 -0.034 -1000
Rapid glucocorticoid signaling 1 25 20 0 0.043 1000 -1000 -0.002 -1000
Arf1 pathway 1 58 54 -0.001 0.062 1000 -1000 -0.012 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 21 23 -0.007 0.064 1000 -1000 -0.016 -1000
BARD1 signaling events 0 45 57 -0.075 0.12 1000 -1000 -0.041 -1000
a4b1 and a4b7 Integrin signaling 0 0 5 0.033 0.053 1000 -1000 0.017 -1000
Glypican 2 network 0 0 4 0 0.032 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 25 27 0 0.077 1000 -1000 -0.03 -1000
Alternative NF-kappaB pathway 0 2 13 0 0.094 1000 -1000 0 -1000
Total 4334 262490 7203 -30 -990 131000 -131000 -3.2 -131000
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.6 0.54 0.39 4 -1 300 304
MKNK1 0.033 0.006 -10000 0 -10000 0 0
MAPK14 -0.2 0.2 -10000 0 -0.36 299 299
ATF2/c-Jun -0.26 0.32 -10000 0 -0.69 139 139
MAPK11 -0.18 0.2 -10000 0 -0.36 281 281
MITF -0.24 0.24 -10000 0 -0.42 301 301
MAPKAPK5 -0.23 0.22 -10000 0 -0.41 302 302
KRT8 -0.22 0.22 -10000 0 -0.41 271 271
MAPKAPK3 0.033 0.012 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.015 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.31 0.32 -10000 0 -0.55 303 303
CEBPB -0.21 0.23 0.3 1 -0.41 276 277
SLC9A1 -0.23 0.23 -10000 0 -0.42 298 298
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.24 0.24 -10000 0 -0.42 296 296
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 -0.39 280 280
RAB5/GDP/GDI1 -0.17 0.18 -10000 0 -0.31 293 293
NOS2 -0.24 0.22 -10000 0 -0.41 302 302
DDIT3 -0.23 0.22 -10000 0 -0.41 297 297
RAB5A 0.034 0.005 -10000 0 -10000 0 0
HSPB1 -0.18 0.18 -10000 0 -0.34 267 267
p38alpha-beta/HBP1 -0.24 0.28 -10000 0 -0.46 298 298
CREB1 -0.25 0.24 -10000 0 -0.43 299 299
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.23 0.24 -10000 0 -0.42 288 288
RPS6KA4 -0.23 0.23 -10000 0 -0.42 298 298
PLA2G4A -0.36 0.27 -10000 0 -0.52 350 350
GDI1 -0.23 0.22 -10000 0 -0.41 297 297
TP53 -0.3 0.3 -10000 0 -0.54 292 292
RPS6KA5 -0.24 0.23 -10000 0 -0.42 309 309
ESR1 -0.29 0.27 0.31 1 -0.46 309 310
HBP1 0.034 0.005 -10000 0 -10000 0 0
MEF2C -0.26 0.26 -10000 0 -0.44 306 306
MEF2A -0.23 0.23 0.3 1 -0.41 297 298
EIF4EBP1 -0.25 0.25 -10000 0 -0.44 294 294
KRT19 -0.21 0.23 -10000 0 -0.42 256 256
ELK4 -0.21 0.21 -10000 0 -0.4 281 281
ATF6 -0.22 0.21 -10000 0 -0.39 289 289
ATF1 -0.25 0.24 -10000 0 -0.43 299 299
p38alpha-beta/MAPKAPK2 -0.22 0.24 -10000 0 -0.42 279 279
p38alpha-beta/MAPKAPK3 -0.25 0.28 -10000 0 -0.46 298 298
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 -0.38 372 372
CRKL -0.32 0.17 -10000 0 -0.4 385 385
HRAS -0.23 0.15 -10000 0 -0.34 217 217
mol:PIP3 -0.27 0.18 -10000 0 -0.38 304 304
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 -0.38 265 265
AKT1 -0.29 0.18 -10000 0 -0.39 346 346
BAD -0.28 0.16 -10000 0 -0.38 281 281
megakaryocyte differentiation -0.32 0.18 -10000 0 -0.41 395 395
GSK3B -0.27 0.16 -10000 0 -0.38 272 272
RAF1 -0.19 0.13 -10000 0 -0.32 49 49
SHC1 0.027 0.014 -10000 0 -10000 0 0
STAT3 -0.33 0.18 -10000 0 -0.42 390 390
STAT1 -0.81 0.43 -10000 0 -1 400 400
HRAS/SPRED1 -0.19 0.14 -10000 0 -0.32 53 53
cell proliferation -0.33 0.17 -10000 0 -0.41 397 397
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
TEC 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.32 0.18 -10000 0 -0.4 392 392
HRAS/SPRED2 -0.19 0.14 -10000 0 -0.32 51 51
LYN/TEC/p62DOK -0.29 0.18 -10000 0 -0.4 331 331
MAPK3 -0.13 0.098 -10000 0 -0.3 9 9
STAP1 -0.32 0.18 -10000 0 -0.41 395 395
GRAP2 0.034 0.019 -10000 0 -10000 0 0
JAK2 -0.68 0.37 -10000 0 -0.85 401 401
STAT1 (dimer) -0.79 0.42 -10000 0 -0.98 402 402
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.28 0.19 -10000 0 -0.4 323 323
actin filament polymerization -0.32 0.17 -10000 0 -0.41 398 398
LYN 0.03 0.015 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.46 0.26 -10000 0 -0.58 403 403
PIK3R1 -0.019 0.16 -10000 0 -0.55 45 45
CBL/CRKL/GRB2 -0.28 0.17 -10000 0 -0.38 341 341
PI3K -0.32 0.2 -10000 0 -0.42 360 360
PTEN 0.026 0.068 -10000 0 -0.54 7 7
SCF/KIT/EPO/EPOR -0.94 0.51 -10000 0 -1.2 397 397
MAPK8 -0.33 0.18 -10000 0 -0.42 397 397
STAT3 (dimer) -0.32 0.17 -10000 0 -0.41 390 390
positive regulation of transcription -0.11 0.083 -10000 0 -0.26 6 6
mol:GDP -0.24 0.16 -10000 0 -0.36 219 219
PIK3C2B -0.3 0.18 -10000 0 -0.42 322 322
CBL/CRKL -0.3 0.16 -10000 0 -0.38 383 383
FER -0.33 0.18 -10000 0 -0.42 394 394
SH2B3 -0.33 0.18 -10000 0 -0.42 395 395
PDPK1 -0.24 0.17 -10000 0 -0.36 273 273
SNAI2 -0.34 0.2 -10000 0 -0.45 357 357
positive regulation of cell proliferation -0.58 0.31 -10000 0 -0.73 402 402
KITLG -0.011 0.069 -10000 0 -0.56 2 2
cell motility -0.58 0.31 -10000 0 -0.73 402 402
PTPN6 0.05 0.021 -10000 0 -10000 0 0
EPOR -0.23 0.19 -10000 0 -1.1 12 12
STAT5A (dimer) -0.48 0.26 -10000 0 -0.6 403 403
SOCS1 0.032 0.012 -10000 0 -10000 0 0
cell migration 0.32 0.17 0.41 393 -10000 0 393
SOS1 0.034 0.004 -10000 0 -10000 0 0
EPO 0.009 0.063 -10000 0 -10000 0 0
VAV1 0.038 0.025 -10000 0 -10000 0 0
GRB10 -0.34 0.18 -10000 0 -0.42 395 395
PTPN11 0.047 0.009 -10000 0 -10000 0 0
SCF/KIT -0.35 0.19 -10000 0 -0.44 398 398
GO:0007205 0.018 0.009 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.28 16 16
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 -0.3 11 11
SHC/Grb2/SOS1 -0.27 0.18 -10000 0 -0.4 278 278
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 -0.42 395 395
SH2B2 -0.33 0.18 -10000 0 -0.42 398 398
DOK1 0.036 0.016 -10000 0 -10000 0 0
MATK -0.33 0.18 -10000 0 -0.42 393 393
CREBBP -0.082 0.075 -10000 0 -0.55 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 -0.35 137 137
PTK2B 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.29 -10000 0 -0.64 103 103
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 0.077 -10000 0 -0.54 1 1
HRAS/GDP -0.25 0.23 -10000 0 -0.45 231 231
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.12 0.18 -10000 0 -0.35 145 145
ADCY4 -0.08 0.15 0.34 2 -0.3 136 138
ADCY5 -0.077 0.15 0.35 1 -0.3 133 134
ADCY6 -0.078 0.15 0.34 2 -0.3 137 139
ADCY7 -0.074 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 -0.3 135 136
ADCY8 -0.065 0.13 0.35 1 -0.3 99 100
ADCY9 -0.072 0.14 -10000 0 -0.3 118 118
arachidonic acid secretion -0.52 0.34 -10000 0 -0.69 374 374
ETB receptor/Endothelin-1/Gq/GTP -0.21 0.21 -10000 0 -0.36 287 287
GNAO1 0.03 0.012 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.089 0.16 -10000 0 -0.32 139 139
ETA receptor/Endothelin-1/Gs/GTP -0.085 0.15 -10000 0 -0.31 139 139
mol:GTP -0.007 0.008 -10000 0 -10000 0 0
COL3A1 -0.096 0.17 -10000 0 -0.35 129 129
EDNRB -0.21 0.29 -10000 0 -0.54 222 222
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.095 0.16 -10000 0 -0.34 134 134
CYSLTR1 -0.097 0.17 0.38 2 -0.35 136 138
SLC9A1 -0.065 0.11 -10000 0 -0.41 14 14
mol:GDP -0.27 0.25 -10000 0 -0.47 244 244
SLC9A3 -0.39 0.39 -10000 0 -0.71 257 257
RAF1 -0.35 0.27 -10000 0 -0.51 328 328
JUN -0.25 0.43 -10000 0 -1 108 108
JAK2 -0.097 0.16 -10000 0 -0.35 136 136
mol:IP3 -0.21 0.21 -10000 0 -0.42 197 197
ETA receptor/Endothelin-1 -0.12 0.19 -10000 0 -0.4 141 141
PLCB1 -0.048 0.2 -10000 0 -0.55 69 69
PLCB2 0.023 0.014 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.29 0.19 -10000 0 -0.4 370 370
FOS -0.69 0.43 -10000 0 -0.96 362 362
Gai/GDP -0.2 0.36 -10000 0 -0.94 83 83
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.26 0.26 -10000 0 -0.53 197 197
BCAR1 0.029 0.013 -10000 0 -10000 0 0
PRKCB1 -0.21 0.21 -10000 0 -0.41 207 207
GNAQ -0.008 0.009 -10000 0 -10000 0 0
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
GNAL 0.03 0.045 -10000 0 -0.54 3 3
Gs family/GDP -0.24 0.22 -10000 0 -0.44 225 225
ETA receptor/Endothelin-1/Gq/GTP -0.094 0.15 -10000 0 -0.3 130 130
MAPK14 -0.22 0.22 -10000 0 -0.41 236 236
TRPC6 -0.18 0.31 -10000 0 -0.7 100 100
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.23 -10000 0 -0.41 267 267
ETB receptor/Endothelin-2 -0.11 0.22 -10000 0 -0.33 237 237
ETB receptor/Endothelin-3 -0.42 0.27 -10000 0 -0.53 410 410
ETB receptor/Endothelin-1 -0.26 0.28 -10000 0 -0.48 292 292
MAPK3 -0.61 0.39 -10000 0 -0.84 366 366
MAPK1 -0.62 0.41 -10000 0 -0.86 366 366
Rac1/GDP -0.25 0.23 -10000 0 -0.45 230 230
cAMP biosynthetic process -0.028 0.15 0.48 3 -0.4 15 18
MAPK8 -0.18 0.3 -10000 0 -0.63 123 123
SRC 0.032 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.28 0.29 -10000 0 -0.53 242 242
p130Cas/CRK/Src/PYK2 -0.27 0.29 -10000 0 -0.56 201 201
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.25 0.23 -10000 0 -0.45 237 237
COL1A2 -0.22 0.27 0.42 1 -0.54 148 149
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 0.22 -10000 0 -0.42 197 197
MAP2K2 -0.47 0.32 -10000 0 -0.64 368 368
MAP2K1 -0.47 0.32 0.36 1 -0.64 368 369
EDNRA 0.007 0.057 -10000 0 -0.44 3 3
positive regulation of muscle contraction -0.088 0.14 -10000 0 -0.31 134 134
Gq family/GDP -0.21 0.21 -10000 0 -0.43 186 186
HRAS/GTP -0.26 0.24 -10000 0 -0.44 259 259
PRKCH -0.21 0.21 -10000 0 -0.43 185 185
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA -0.19 0.21 -10000 0 -0.43 173 173
PRKCB -0.21 0.21 -10000 0 -0.41 207 207
PRKCE -0.21 0.21 -10000 0 -0.44 177 177
PRKCD -0.21 0.21 -10000 0 -0.43 183 183
PRKCG -0.21 0.21 0.3 1 -0.43 189 190
regulation of vascular smooth muscle contraction -0.81 0.5 -10000 0 -1.1 362 362
PRKCQ -0.2 0.21 -10000 0 -0.43 185 185
PLA2G4A -0.59 0.4 -10000 0 -0.78 375 375
GNA14 0.026 0.072 -10000 0 -0.55 4 4
GNA15 0.021 0.03 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.024 -10000 0 -10000 0 0
Rac1/GTP -0.089 0.16 -10000 0 -0.32 138 138
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 0.47 4 -0.55 56 60
NFATC3 -0.15 0.17 0.31 1 -0.32 226 227
CD40LG -0.68 0.53 0.78 4 -1 330 334
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 0.78 6 -0.74 56 62
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.079 0.17 -10000 0 -0.3 190 190
T cell anergy -0.13 0.21 -10000 0 -0.4 180 180
TLE4 -0.067 0.2 -10000 0 -0.53 50 50
Jun/NFAT1-c-4/p21SNFT -0.58 0.55 0.69 3 -0.96 311 314
AP-1/NFAT1-c-4 -0.8 0.68 0.92 5 -1.2 329 334
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 -0.51 291 296
CALM1 -0.037 0.11 -10000 0 -0.31 1 1
EGR2 -0.8 0.77 0.72 3 -1.5 258 261
EGR3 -0.88 0.76 0.68 4 -1.4 338 342
NFAT1/FOXP3 -0.033 0.18 0.46 8 -0.43 38 46
EGR1 -0.43 0.23 -10000 0 -0.54 409 409
JUN -0.064 0.22 0.26 1 -0.54 86 87
EGR4 0.001 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.056 0.09 -10000 0 -0.17 186 186
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 -0.92 310 313
DGKA -0.053 0.16 0.46 1 -0.43 37 38
CREM 0.033 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.76 0.56 -10000 0 -1.1 344 344
CTLA4 -0.025 0.16 0.42 14 -0.49 11 25
NFAT1-c-4 (dimer)/EGR1 -0.78 0.57 -10000 0 -1.1 349 349
NFAT1-c-4 (dimer)/EGR4 -0.56 0.53 0.67 1 -0.93 315 316
FOS -0.35 0.27 0.25 1 -0.54 342 343
IFNG -0.098 0.3 0.58 6 -0.81 43 49
T cell activation -0.39 0.34 0.68 3 -0.7 211 214
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 0.74 305 -0.62 4 309
TNF -0.67 0.48 -10000 0 -0.97 345 345
FASLG -0.89 0.79 0.85 3 -1.4 324 327
TBX21 0.028 0.15 0.28 12 -0.54 30 42
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.043 0.036 0.22 10 -10000 0 10
PTPN1 -0.049 0.16 0.42 1 -0.43 35 36
NFAT1-c-4/ICER1 -0.56 0.53 0.6 1 -0.94 308 309
GATA3 0.031 0.17 -10000 0 -0.54 34 34
T-helper 1 cell differentiation -0.096 0.3 0.58 6 -0.79 43 49
IL2RA -0.26 0.31 0.73 6 -0.7 69 75
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.052 0.16 -10000 0 -0.44 32 32
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 -0.43 36 36
IRF4 0.038 0.027 -10000 0 -10000 0 0
PTGS2 -0.77 0.57 0.73 4 -1.1 346 350
CSF2 -0.68 0.53 0.78 4 -1 327 331
JunB/Fra1/NFAT1-c-4 -0.53 0.52 0.6 2 -0.9 310 312
IL4 -0.13 0.3 -10000 0 -0.82 46 46
IL5 -0.68 0.52 0.73 4 -1 332 336
IL2 -0.39 0.35 0.68 3 -0.72 207 210
IL3 -0.089 0.15 -10000 0 -0.91 13 13
RNF128 -0.21 0.33 -10000 0 -0.63 191 191
NFATC1 -0.45 0.42 0.62 4 -0.74 305 309
CDK4 0.28 0.28 0.56 141 -0.64 2 143
PTPRK -0.09 0.24 -10000 0 -0.71 51 51
IL8 -0.67 0.53 0.73 5 -1 325 330
POU2F1 0.033 0.015 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.013 -9999 0 -10000 0 0
EGFR -0.27 0.29 -9999 0 -0.54 264 264
EGF/EGFR -0.29 0.26 -9999 0 -0.43 360 360
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.19 0.21 -9999 0 -0.36 258 258
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.032 0.038 -9999 0 -0.54 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.15 0.27 -9999 0 -0.54 162 162
EGF/EGFR dimer/SHC -0.23 0.23 -9999 0 -0.41 281 281
mol:GDP -0.19 0.21 -9999 0 -0.36 258 258
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.13 0.26 -9999 0 -0.54 147 147
GRB2/SOS1 0.047 0.018 -9999 0 -10000 0 0
HRAS/GTP -0.18 0.19 -9999 0 -0.34 255 255
SHC1 0.027 0.014 -9999 0 -10000 0 0
HRAS/GDP -0.18 0.2 -9999 0 -0.35 255 255
FRAP1 -0.2 0.17 -9999 0 -0.35 258 258
EGF/EGFR dimer -0.31 0.26 -9999 0 -0.46 352 352
SOS1 0.034 0.004 -9999 0 -10000 0 0
GRB2 0.033 0.017 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.084 0.2 -9999 0 -0.39 154 154
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 0.54 125 -10000 0 125
PI3K Class IB/PDE3B -0.11 0.25 -10000 0 -0.54 125 125
PDE3B -0.11 0.25 -10000 0 -0.54 125 125
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.034 0.007 -10000 0 -10000 0 0
PTK2 0.027 0.014 -10000 0 -10000 0 0
CRKL -0.17 0.2 -10000 0 -0.34 254 254
GRB2/SOS1/SHC 0.051 0.033 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
IRS1/Crk -0.16 0.21 -10000 0 -0.34 257 257
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.21 -10000 0 -0.36 220 220
AKT1 -0.16 0.19 0.23 1 -0.35 216 217
BAD -0.16 0.18 0.22 1 -0.44 95 96
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.17 0.2 -10000 0 -0.34 257 257
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.21 -10000 0 -0.34 256 256
RAF1 -0.12 0.18 -10000 0 -0.46 71 71
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.22 -10000 0 -0.34 222 222
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.17 0.23 -10000 0 -0.37 258 258
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.18 0.23 1 -0.45 93 94
GNB2L1 0.033 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.1 0.15 0.3 2 -0.39 63 65
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 -0.3 157 157
IGF-1R heterotetramer -0.049 0.14 -10000 0 -0.64 21 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.34 255 255
Crk/p130 Cas/Paxillin -0.13 0.21 -10000 0 -0.33 236 236
IGF1R -0.049 0.14 -10000 0 -0.64 21 21
IGF1 -0.27 0.3 -10000 0 -0.57 251 251
IRS2/Crk -0.22 0.26 -10000 0 -0.42 273 273
PI3K -0.15 0.24 -10000 0 -0.37 242 242
apoptosis 0.11 0.15 0.39 65 -0.28 2 67
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
PRKCD -0.18 0.23 -10000 0 -0.39 236 236
RAF1/14-3-3 E -0.096 0.17 0.34 1 -0.4 66 67
BAD/14-3-3 -0.12 0.16 0.29 2 -0.42 65 67
PRKCZ -0.16 0.19 0.22 1 -0.34 223 224
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.17 -10000 0 -0.41 72 72
PTPN1 0.036 0.028 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.19 0.23 -10000 0 -0.41 244 244
BCAR1 0.029 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.095 0.19 -10000 0 -0.33 179 179
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 -0.34 256 256
IRS1 -0.18 0.22 -10000 0 -0.37 257 257
IRS2 -0.23 0.26 -10000 0 -0.43 278 278
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 -0.47 242 242
SHC1 0.027 0.014 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.56 0.46 1.1 127 -1 2 129
PLK1 0.22 0.2 0.65 37 -10000 0 37
BIRC5 0.36 0.25 0.67 135 -0.66 3 138
HSPA1B 0.56 0.46 1.1 144 -0.95 3 147
MAP2K1 0.17 0.13 0.34 127 -10000 0 127
BRCA2 0.59 0.49 1.2 143 -1.1 2 145
FOXM1 0.6 0.61 1.3 155 -1.2 3 158
XRCC1 0.56 0.47 1.1 128 -1.1 2 130
FOXM1B/p19 0.074 0.29 0.94 7 -1.1 3 10
Cyclin D1/CDK4 0.48 0.46 0.99 125 -0.88 10 135
CDC2 0.61 0.52 1.2 153 -1 3 156
TGFA 0.44 0.52 1 133 -0.94 20 153
SKP2 0.57 0.47 1.1 132 -1.1 2 134
CCNE1 0.085 0.062 0.23 26 -10000 0 26
CKS1B 0.61 0.5 1.2 148 -1.1 2 150
RB1 0.27 0.35 0.72 132 -0.77 8 140
FOXM1C/SP1 0.5 0.45 0.99 116 -1 7 123
AURKB 0.2 0.31 0.65 64 -0.81 22 86
CENPF 0.68 0.53 1.2 185 -1.3 1 186
CDK4 0.091 0.06 0.24 17 -10000 0 17
MYC 0.31 0.44 0.94 92 -0.87 10 102
CHEK2 0.16 0.13 0.34 130 -10000 0 130
ONECUT1 0.49 0.48 1 145 -0.9 6 151
CDKN2A -0.016 0.077 -10000 0 -0.22 21 21
LAMA4 0.55 0.48 1.1 128 -1.1 4 132
FOXM1B/HNF6 0.49 0.5 1.1 125 -1.1 6 131
FOS -0.13 0.65 1.1 50 -1 74 124
SP1 0.031 0.033 -10000 0 -0.21 5 5
CDC25B 0.57 0.47 1.1 126 -1.3 1 127
response to radiation 0.11 0.093 0.25 116 -10000 0 116
CENPB 0.56 0.46 1.1 135 -0.95 3 138
CENPA 0.63 0.51 1.2 159 -1.1 2 161
NEK2 0.69 0.52 1.2 186 -1.2 1 187
HIST1H2BA 0.56 0.46 1.1 131 -1.1 2 133
CCNA2 0.11 0.075 0.23 46 -10000 0 46
EP300 0.032 0.008 -10000 0 -10000 0 0
CCNB1/CDK1 0.59 0.52 1.2 132 -1.1 3 135
CCNB2 0.62 0.51 1.2 154 -1.1 2 156
CCNB1 0.63 0.54 1.2 149 -1 3 152
ETV5 0.53 0.52 1.1 124 -1.2 10 134
ESR1 0.37 0.61 1.1 118 -0.97 16 134
CCND1 0.5 0.51 1.1 150 -0.9 10 160
GSK3A 0.14 0.1 0.3 80 -10000 0 80
Cyclin A-E1/CDK1-2 0.2 0.13 0.38 130 -10000 0 130
CDK2 0.07 0.036 0.23 6 -10000 0 6
G2/M transition of mitotic cell cycle 0.14 0.12 0.28 155 -10000 0 155
FOXM1B/Cbp/p300 0.3 0.38 0.84 34 -1 3 37
GAS1 0.27 0.71 1.1 108 -1 59 167
MMP2 0.55 0.48 1.1 119 -1.2 6 125
RB1/FOXM1C 0.45 0.46 0.97 136 -0.97 7 143
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.018 0.018 -10000 0 -0.34 1 1
ARNO/beta Arrestin1-2 -0.11 0.14 -10000 0 -0.26 245 245
EGFR -0.27 0.29 -10000 0 -0.54 264 264
EPHA2 0.026 0.063 -10000 0 -0.54 6 6
USP6 0.032 0.018 -10000 0 -10000 0 0
IQSEC1 0.033 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.31 0.26 -10000 0 -0.46 352 352
ARRB2 0.015 0.029 -10000 0 -0.33 3 3
mol:GTP 0.013 0.029 0.12 26 -10000 0 26
ARRB1 0.03 0.028 -10000 0 -0.54 1 1
FBXO8 0.033 0.007 -10000 0 -10000 0 0
TSHR 0.029 0.045 -10000 0 -0.54 3 3
EGF -0.15 0.27 -10000 0 -0.54 162 162
somatostatin receptor activity 0 0 -10000 0 -0.001 242 242
ARAP2 0 0 -10000 0 0 253 253
mol:GDP -0.14 0.14 -10000 0 -0.27 216 216
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 242 242
ITGA2B 0.034 0.013 -10000 0 -10000 0 0
ARF6 0.033 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.058 -10000 0 -0.32 6 6
ADAP1 0 0 -10000 0 0 150 150
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 -0.25 233 233
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.26 0.24 -10000 0 -0.41 344 344
ADRB2 -0.26 0.29 -10000 0 -0.54 259 259
receptor agonist activity 0 0 -10000 0 0 219 219
actin filament binding 0 0 -10000 0 0 261 261
SRC 0.032 0.008 -10000 0 -10000 0 0
ITGB3 0.035 0.018 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -0.001 164 164
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 162 162
ARF6/GDP -0.03 0.084 0.18 1 -0.26 30 31
ARF6/GDP/GULP/ACAP1 -0.16 0.18 -10000 0 -0.34 209 209
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.031 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 0 1 1
ACAP2 0 0 -10000 0 0 250 250
LHCGR/beta Arrestin2 0.022 0.048 -10000 0 -0.47 3 3
EFNA1 0.028 0.015 -10000 0 -10000 0 0
HGF 0.034 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 218 218
CYTH2 -0.002 0.002 -10000 0 -0.004 259 259
NCK1 0.034 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 153 153
endosomal lumen acidification 0 0 0.001 5 0 151 156
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.069 0.22 -10000 0 -0.54 91 91
GNAQ/ARNO -0.003 0.003 -10000 0 -0.007 147 147
mol:Phosphatidic acid 0 0 -10000 0 0 250 250
PIP3-E 0 0 -10000 0 0 339 339
MET -0.023 0.17 -10000 0 -0.54 50 50
GNA14 0.042 0.067 -10000 0 -0.54 4 4
GNA15 0.035 0.019 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -0.001 201 201
GNA11 0.033 0.006 -10000 0 -10000 0 0
LHCGR 0.031 0.046 -10000 0 -0.54 3 3
AGTR1 -0.19 0.3 -10000 0 -0.54 206 206
desensitization of G-protein coupled receptor protein signaling pathway 0.022 0.048 -10000 0 -0.46 3 3
IPCEF1/ARNO -0.21 0.18 -10000 0 -0.32 350 350
alphaIIb/beta3 Integrin 0.05 0.019 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.01 0.13 -10000 0 -0.32 66 66
regulation of S phase of mitotic cell cycle -0.045 0.13 -10000 0 -0.3 90 90
GNAO1 0.029 0.012 -10000 0 -10000 0 0
HRAS 0.032 0.013 -10000 0 -10000 0 0
SHBG/T-DHT 0.021 0.007 -10000 0 -10000 0 0
PELP1 0.029 0.01 -10000 0 -10000 0 0
AKT1 0.011 0.014 0.14 6 -10000 0 6
MAP2K1 -0.11 0.11 -10000 0 -0.38 52 52
T-DHT/AR -0.033 0.14 -10000 0 -0.4 67 67
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.003 -10000 0 -0.007 360 360
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.033 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
mol:GDP -0.079 0.17 -10000 0 -0.43 79 79
cell proliferation -0.3 0.21 -10000 0 -0.44 306 306
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
FOS -0.57 0.37 -10000 0 -0.8 362 362
mol:Ca2+ -0.038 0.037 -10000 0 -0.075 229 229
MAPK3 -0.21 0.16 -10000 0 -0.46 74 74
MAPK1 -0.16 0.16 -10000 0 -0.59 33 33
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 -0.003 0.002 -10000 0 -0.004 340 340
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 -0.004 340 340
HRAS/GTP -0.059 0.12 -10000 0 -0.33 64 64
actin cytoskeleton reorganization 0.016 0.094 -10000 0 -0.28 42 42
SRC 0.03 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.003 0.002 -10000 0 -0.004 340 340
PI3K 0.008 0.11 -10000 0 -0.34 42 42
apoptosis 0.3 0.22 0.43 347 -10000 0 347
T-DHT/AR/PELP1 -0.015 0.13 -10000 0 -0.35 66 66
HRAS/GDP -0.069 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 0.034 0.011 -10000 0 -10000 0 0
RAF1 -0.086 0.11 -10000 0 -0.34 61 61
RAC1-CDC42/GDP -0.033 0.17 -10000 0 -0.44 66 66
T-DHT/AR/PELP1/Src -0.005 0.13 -10000 0 -0.33 65 65
MAP2K2 -0.12 0.11 -10000 0 -0.38 52 52
T-DHT/AR/PELP1/Src/PI3K -0.045 0.13 -10000 0 -0.3 90 90
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
SHBG 0.03 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.11 0.19 -10000 0 -0.48 76 76
mol:T-DHT -0.001 0.002 -10000 0 -0.004 90 90
RAC1 0.034 0.005 -10000 0 -10000 0 0
GNRH1 -0.001 0.057 -10000 0 -0.4 10 10
Gi family/GTP -0.11 0.14 -10000 0 -0.26 187 187
CDC42 0.033 0.007 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.11 0.11 0.52 5 -10000 0 5
SMARCC2 0.034 0.004 -10000 0 -10000 0 0
SMARCC1 0.035 0.019 -10000 0 -10000 0 0
TBX21 -0.12 0.22 0.4 1 -0.82 32 33
SUMO2 0.001 0.025 -10000 0 -10000 0 0
STAT1 (dimer) 0.071 0.067 0.28 25 -10000 0 25
FKBP4 0.036 0.024 -10000 0 -10000 0 0
FKBP5 0.024 0.082 -10000 0 -0.54 10 10
GR alpha/HSP90/FKBP51/HSP90 0.13 0.14 0.31 71 -0.34 5 76
PRL -0.06 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.51 182 -10000 0 182
RELA -0.095 0.12 0.32 1 -0.27 26 27
FGG 0.23 0.23 0.45 220 -10000 0 220
GR beta/TIF2 0.11 0.14 0.3 112 -0.33 4 116
IFNG -0.39 0.34 -10000 0 -0.72 202 202
apoptosis -0.25 0.18 -10000 0 -0.56 33 33
CREB1 0.057 0.041 -10000 0 -10000 0 0
histone acetylation 0.036 0.14 0.4 36 -0.33 8 44
BGLAP -0.093 0.14 -10000 0 -0.48 8 8
GR/PKAc 0.15 0.14 0.35 43 -0.31 3 46
NF kappa B1 p50/RelA -0.16 0.2 0.47 3 -0.34 141 144
SMARCD1 0.034 0.004 -10000 0 -10000 0 0
MDM2 0.12 0.099 0.21 212 -10000 0 212
GATA3 0.039 0.17 -10000 0 -0.54 34 34
AKT1 0.028 0.024 -10000 0 -10000 0 0
CSF2 -0.007 0.11 -10000 0 -10000 0 0
GSK3B 0.001 0.027 -10000 0 -10000 0 0
NR1I3 -0.19 0.17 -10000 0 -0.58 6 6
CSN2 0.19 0.19 0.38 196 -10000 0 196
BRG1/BAF155/BAF170/BAF60A 0.084 0.026 -10000 0 -10000 0 0
NFATC1 0.037 0.038 -10000 0 -0.54 2 2
POU2F1 0.033 0.015 -10000 0 -10000 0 0
CDKN1A 0.023 0.12 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.011 0.006 -10000 0 -10000 0 0
SFN 0.033 0.04 -10000 0 -0.54 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.14 0.14 0.34 40 -0.33 4 44
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.65 0.33 -10000 0 -0.8 421 421
JUN -0.21 0.24 0.38 2 -0.48 165 167
IL4 -0.12 0.15 -10000 0 -0.52 9 9
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 -0.49 331 331
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.15 0.14 0.34 43 -0.33 4 47
cortisol/GR alpha (monomer) 0.29 0.31 0.57 235 -0.44 1 236
NCOA2 0.028 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.42 0.26 -10000 0 -0.58 358 358
AP-1/NFAT1-c-4 -0.58 0.41 -10000 0 -0.82 341 341
AFP -0.17 0.2 -10000 0 -0.57 30 30
SUV420H1 0.031 0.01 -10000 0 -10000 0 0
IRF1 0.2 0.18 0.46 81 -10000 0 81
TP53 0.046 0.034 -10000 0 -0.51 1 1
PPP5C 0.036 0.016 -10000 0 -10000 0 0
KRT17 -0.89 0.65 -10000 0 -1.4 318 318
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 0.3 278 -0.28 1 279
HDAC1 0.029 0.01 -10000 0 -10000 0 0
HDAC2 0.029 0.021 -10000 0 -10000 0 0
AP-1 -0.58 0.41 -10000 0 -0.83 341 341
MAPK14 0.01 0.023 -10000 0 -10000 0 0
MAPK10 -0.011 0.082 -10000 0 -0.55 10 10
MAPK11 0 0.025 -10000 0 -10000 0 0
KRT5 -0.95 0.63 -10000 0 -1.4 350 350
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 0.068 0.28 25 -10000 0 25
CGA -0.085 0.16 -10000 0 -0.51 7 7
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.19 0.36 122 -0.35 1 123
MAPK3 -0.001 0.024 -10000 0 -10000 0 0
MAPK1 0.009 0.023 -10000 0 -10000 0 0
ICAM1 -0.26 0.25 0.48 5 -0.49 199 204
NFKB1 -0.095 0.11 0.27 3 -0.23 42 45
MAPK8 -0.15 0.19 0.57 1 -0.35 169 170
MAPK9 0.009 0.024 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.19 -10000 0 -0.59 34 34
BAX 0.029 0.074 -10000 0 -10000 0 0
POMC -0.14 0.19 0.57 1 -0.73 12 13
EP300 0.18 0.14 0.3 246 -10000 0 246
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.52 193 -10000 0 193
proteasomal ubiquitin-dependent protein catabolic process 0.091 0.11 0.29 68 -10000 0 68
SGK1 0.23 0.17 0.36 297 -0.43 1 298
IL13 -0.3 0.25 -10000 0 -0.7 57 57
IL6 -0.75 0.48 0.5 2 -1 371 373
PRKACG 0.032 0.026 -10000 0 -0.54 1 1
IL5 -0.25 0.2 -10000 0 -0.69 23 23
IL2 -0.42 0.32 -10000 0 -0.68 262 262
CDK5 0.031 0.022 -10000 0 -10000 0 0
PRKACB 0.035 0.082 -10000 0 -0.54 8 8
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
IL8 -0.24 0.26 0.59 2 -0.55 113 115
CDK5R1/CDK5 0.036 0.021 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.095 0.18 0.42 3 -0.43 24 27
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.5 217 -10000 0 217
SMARCA4 0.035 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.17 0.16 0.34 180 -10000 0 180
NF kappa B1 p50/RelA/Cbp -0.003 0.2 0.49 25 -0.37 4 29
JUN (dimer) -0.21 0.24 0.38 2 -0.48 164 166
YWHAH 0.033 0.014 -10000 0 -10000 0 0
VIPR1 -0.11 0.16 -10000 0 -0.52 29 29
NR3C1 0.19 0.2 0.38 195 -0.42 6 201
NR4A1 0.014 0.12 -10000 0 -0.55 23 23
TIF2/SUV420H1 0.038 0.022 -10000 0 -10000 0 0
MAPKKK cascade -0.25 0.18 -10000 0 -0.56 33 33
cortisol/GR alpha (dimer)/Src-1 0.27 0.26 0.51 227 -10000 0 227
PBX1 0.042 0.041 -10000 0 -10000 0 0
POU1F1 0.038 0.026 -10000 0 -0.54 1 1
SELE -0.26 0.35 0.59 2 -0.84 79 81
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.16 0.34 177 -10000 0 177
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.5 217 -10000 0 217
mol:cortisol 0.18 0.17 0.32 245 -0.24 1 246
MMP1 -0.022 0.34 0.41 5 -0.95 51 56
S1P1 pathway

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
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 -0.49 306 311
GNAO1 0.004 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.25 0.26 0.41 3 -0.45 288 291
PLCG1 -0.26 0.27 0.32 7 -0.46 298 305
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.007 -10000 0 -10000 0 0
GNAI2 0.005 0.029 -10000 0 -10000 0 0
GNAI3 0.005 0.029 -10000 0 -10000 0 0
GNAI1 -0.19 0.27 -10000 0 -0.56 181 181
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.004 0.04 0.14 2 -10000 0 2
S1P1/S1P -0.064 0.13 0.3 5 -0.66 10 15
negative regulation of cAMP metabolic process -0.28 0.28 0.33 5 -0.47 306 311
MAPK3 -0.37 0.35 0.37 7 -0.63 307 314
calcium-dependent phospholipase C activity -0.005 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
KDR 0.028 0.011 -10000 0 -10000 0 0
PLCB2 -0.053 0.12 0.36 4 -0.58 10 14
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.063 0.1 -10000 0 -0.55 10 10
receptor internalization -0.063 0.11 0.24 5 -0.61 10 15
PTGS2 -0.62 0.53 0.45 2 -1 309 311
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 -0.47 306 311
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 -0.67 309 314
S1P1/S1P/PDGFB-D/PDGFRB -0.078 0.14 0.34 8 -0.64 10 18
ABCC1 0.031 0.023 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.033 0.006 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.24 0.21 -10000 0 -0.41 243 243
PTP1B/AKT1 -0.16 0.15 0.25 1 -0.29 213 214
FYN 0.029 0.037 -10000 0 -0.54 2 2
p210 bcr-abl/PTP1B -0.19 0.16 0.25 1 -0.32 243 244
EGFR -0.28 0.28 -10000 0 -0.56 264 264
EGF/EGFR -0.35 0.26 -10000 0 -0.5 354 354
CSF1 0.034 0.008 -10000 0 -10000 0 0
AKT1 0.035 0.016 -10000 0 -10000 0 0
INSR 0.033 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.16 0.17 0.34 1 -0.32 187 188
Insulin Receptor/Insulin -0.11 0.13 -10000 0 -0.35 41 41
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 0.44 1 -0.31 215 216
EGF -0.18 0.26 -10000 0 -0.56 162 162
YES1 0.031 0.027 -10000 0 -0.54 1 1
CAV1 -0.37 0.23 -10000 0 -0.49 358 358
TXN 0.028 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.19 0.18 -10000 0 -0.41 128 128
cell migration 0.19 0.16 0.32 243 -0.25 1 244
STAT3 0.031 0.007 -10000 0 -10000 0 0
PRLR 0.073 0.062 -10000 0 -10000 0 0
ITGA2B 0.032 0.013 -10000 0 -10000 0 0
CSF1R 0.033 0.006 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.081 0.048 -10000 0 -10000 0 0
FGR 0.033 0.007 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.17 0.16 0.24 1 -0.31 218 219
Crk/p130 Cas -0.16 0.16 -10000 0 -0.32 158 158
DOK1 -0.15 0.14 0.27 1 -0.4 56 57
JAK2 -0.081 0.14 -10000 0 -0.53 31 31
Jak2/Leptin Receptor/Leptin -0.25 0.2 -10000 0 -0.44 210 210
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
PTPN1 -0.19 0.16 0.25 1 -0.32 247 248
LYN 0.03 0.015 -10000 0 -10000 0 0
CDH2 0.057 0.054 -10000 0 -10000 0 0
SRC -0.051 0.12 -10000 0 -0.67 15 15
ITGB3 0.033 0.018 -10000 0 -10000 0 0
CAT1/PTP1B -0.14 0.18 0.36 1 -0.44 80 81
CAPN1 0.031 0.013 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -10000 0 0
PI3K -0.12 0.16 -10000 0 -0.42 56 56
mol:H2O2 -0.005 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.22 0.19 -10000 0 -0.4 198 198
negative regulation of transcription -0.08 0.14 -10000 0 -0.52 31 31
FCGR2A 0.03 0.025 -10000 0 -10000 0 0
FER 0.027 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.045 0.018 -10000 0 -10000 0 0
BLK 0.039 0.043 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.051 0.03 -10000 0 -10000 0 0
RHOA 0.029 0.007 -10000 0 -10000 0 0
LEPR -0.33 0.28 -10000 0 -0.54 317 317
BCAR1 0.029 0.012 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.033 0.017 -10000 0 -10000 0 0
mol:NADPH -0.006 0.004 -10000 0 -10000 0 0
TRPV6 -0.005 0.15 0.42 2 -0.4 40 42
PRL 0.037 0.009 -10000 0 -10000 0 0
SOCS3 0.001 0.25 -10000 0 -1.3 16 16
SPRY2 -0.32 0.28 -10000 0 -0.55 298 298
Insulin Receptor/Insulin/IRS1 0.014 0.13 -10000 0 -0.35 59 59
CSF1/CSF1R -0.16 0.16 -10000 0 -0.32 150 150
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 -0.37 84 85
STAT5A -0.14 0.16 0.26 1 -0.37 85 86
GRB2 0.033 0.017 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.18 0.16 -10000 0 -0.31 210 210
CSN2 0.079 0.062 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
LAT -0.035 0.077 -10000 0 -0.64 3 3
YBX1 0.044 0.027 -10000 0 -10000 0 0
LCK 0.048 0.043 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
NOX4 0.051 0.053 -10000 0 -10000 0 0
PDGFR-alpha signaling 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
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 -0.41 64 64
AP1 -0.7 0.45 -10000 0 -0.97 363 363
mol:IP3 -0.085 0.14 -10000 0 -0.45 56 56
PLCG1 -0.085 0.14 -10000 0 -0.45 56 56
PDGF/PDGFRA/alphaV Integrin -0.056 0.14 -10000 0 -0.41 64 64
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.085 0.14 -10000 0 -0.45 56 56
CAV3 0.031 0.037 -10000 0 -0.54 2 2
CAV1 -0.38 0.26 -10000 0 -0.54 360 360
SHC/Grb2/SOS1 0.016 0.12 -10000 0 -0.33 44 44
PDGF/PDGFRA/Shf -0.054 0.14 -10000 0 -0.4 64 64
FOS -0.69 0.44 -10000 0 -0.95 363 363
JUN -0.13 0.15 -10000 0 -0.46 84 84
oligodendrocyte development -0.056 0.14 -10000 0 -0.41 64 64
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 -0.41 60 60
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 -0.4 63 63
ELK1/SRF -0.065 0.12 0.33 1 -0.35 58 59
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 -0.41 60 60
PDGF/PDGFRA/Caveolin-1 -0.34 0.24 -10000 0 -0.46 371 371
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 64 64
JAK-STAT cascade -0.065 0.13 -10000 0 -0.4 63 63
cell proliferation -0.054 0.14 -10000 0 -0.4 64 64
Calcium signaling in the CD4+ TCR 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
NFATC1 0.008 0.058 0.26 9 -0.35 2 11
NFATC2 0.01 0.054 0.26 9 -0.34 1 10
NFATC3 0.012 0.052 0.26 9 -10000 0 9
CD40LG -0.22 0.29 0.68 10 -0.52 179 189
PTGS2 -0.32 0.36 0.67 9 -0.62 256 265
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.032 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.032 -10000 0 -10000 0 0
CALM1 0.033 0.018 -10000 0 -10000 0 0
JUN -0.064 0.22 -10000 0 -0.54 86 86
mol:Ca2+ -0.003 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.012 0.13 1 -10000 0 1
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 53 68
FOS -0.36 0.27 -10000 0 -0.54 342 342
IFNG -0.19 0.31 0.66 16 -0.52 173 189
AP-1/NFAT1-c-4 -0.25 0.34 0.7 11 -0.6 188 199
FASLG -0.19 0.29 0.66 15 -0.5 151 166
NFAT1-c-4/ICER1 0.016 0.098 0.4 9 -0.28 1 10
IL2RA -0.21 0.3 0.73 10 -0.51 174 184
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSF2 -0.22 0.3 0.69 11 -0.51 181 192
JunB/Fra1/NFAT1-c-4 0.039 0.11 0.41 9 -0.33 3 12
IL4 -0.22 0.29 0.65 10 -0.51 181 191
IL2 -0.009 0.15 -10000 0 -0.97 11 11
IL3 -0.009 0.13 -10000 0 -0.77 11 11
FKBP1A 0.033 0.012 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.033 0.015 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

Figure 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 0.43 0.78 2 -0.72 76 78
HDAC7 0.007 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.005 0.37 0.82 4 -0.69 48 52
SMAD4 0.032 0.027 -10000 0 -0.54 1 1
ID2 0.005 0.42 -10000 0 -0.73 74 74
AP1 -0.33 0.27 -10000 0 -0.48 350 350
ABCG2 -0.011 0.44 -10000 0 -0.74 82 82
HIF1A 0.023 0.13 0.32 4 -0.41 7 11
TFF3 -0.047 0.44 0.76 1 -0.73 90 91
GATA2 0.021 0.048 -10000 0 -10000 0 0
AKT1 0.021 0.13 0.31 9 -0.19 29 38
response to hypoxia -0.003 0.11 0.25 13 -0.16 60 73
MCL1 -0.027 0.39 -10000 0 -0.72 73 73
NDRG1 -0.014 0.4 0.88 1 -0.73 68 69
SERPINE1 0.014 0.44 0.82 10 -0.72 75 85
FECH 0.001 0.42 0.76 1 -0.72 76 77
FURIN 0.009 0.43 -10000 0 -0.72 76 76
NCOA2 0.034 0.023 -10000 0 -10000 0 0
EP300 0.035 0.17 0.43 19 -0.29 34 53
HMOX1 0.012 0.44 0.82 8 -0.72 76 84
BHLHE40 -0.051 0.39 0.71 6 -0.72 76 82
BHLHE41 -0.051 0.39 0.71 6 -0.72 76 82
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.043 0.16 -10000 0 -0.44 2 2
ENG 0.046 0.14 0.44 2 -0.41 2 4
JUN -0.072 0.22 -10000 0 -0.55 86 86
RORA -0.004 0.43 -10000 0 -0.73 80 80
ABCB1 -0.29 0.47 -10000 0 -0.94 160 160
TFRC 0.009 0.43 0.84 6 -0.72 75 81
CXCR4 0.013 0.43 0.8 4 -0.72 75 79
TF -0.004 0.44 -10000 0 -0.75 78 78
CITED2 -0.003 0.43 -10000 0 -0.73 77 77
HIF1A/ARNT -0.068 0.44 0.9 3 -0.85 64 67
LDHA -0.011 0.13 -10000 0 -0.72 14 14
ETS1 0.001 0.42 0.78 1 -0.72 76 77
PGK1 0.009 0.43 0.82 4 -0.72 76 80
NOS2 -0.051 0.39 0.71 6 -0.72 76 82
ITGB2 0.009 0.43 0.81 8 -0.72 75 83
ALDOA 0.007 0.42 0.76 1 -0.73 73 74
Cbp/p300/CITED2 -0.008 0.42 0.8 3 -0.8 59 62
FOS -0.36 0.27 -10000 0 -0.55 342 342
HK2 0.006 0.43 -10000 0 -0.72 76 76
SP1 -0.018 0.094 -10000 0 -0.21 57 57
GCK 0.067 0.22 0.67 3 -0.52 2 5
HK1 0.007 0.43 0.76 1 -0.72 76 77
NPM1 0.003 0.42 -10000 0 -0.72 76 76
EGLN1 -0.021 0.4 -10000 0 -0.72 74 74
CREB1 0.04 0.01 -10000 0 -10000 0 0
PGM1 0.003 0.43 -10000 0 -0.72 75 75
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 76 76
VEGFA 0.071 0.36 0.8 20 -0.59 47 67
HIF1A/JAB1 0.041 0.1 0.31 5 -0.41 4 9
CP -0.061 0.51 0.83 6 -0.79 116 122
CXCL12 -0.084 0.48 -10000 0 -0.8 112 112
COPS5 0.033 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4 0.047 0.028 -10000 0 -0.4 1 1
BNIP3 0.002 0.43 0.85 1 -0.73 77 78
EGLN3 0.024 0.44 0.82 13 -0.72 74 87
CA9 0.017 0.44 0.82 9 -0.72 77 86
TERT -0.009 0.42 -10000 0 -0.72 75 75
ENO1 0.006 0.43 0.76 1 -0.72 75 76
PFKL 0.004 0.42 -10000 0 -0.72 75 75
NCOA1 0.035 0.027 -10000 0 -0.54 1 1
ADM -0.1 0.5 -10000 0 -0.76 133 133
ARNT 0.021 0.098 -10000 0 -10000 0 0
HNF4A 0.036 0.009 -10000 0 -10000 0 0
ADFP -0.051 0.39 0.71 6 -0.72 76 82
SLC2A1 0.072 0.36 0.81 16 -0.6 44 60
LEP -0.14 0.48 -10000 0 -0.79 132 132
HIF1A/ARNT/Cbp/p300 -0.017 0.36 0.78 6 -0.71 49 55
EPO 0.071 0.32 0.81 10 -0.66 18 28
CREBBP 0.042 0.16 0.45 15 -0.28 12 27
HIF1A/ARNT/Cbp/p300/HDAC7 -0.01 0.35 0.79 6 -0.69 44 50
PFKFB3 -0.003 0.42 -10000 0 -0.73 74 74
NT5E -0.002 0.44 -10000 0 -0.75 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 -0.3 3 3
SMAD6-7/SMURF1 0.063 0.02 -9999 0 -10000 0 0
NOG 0.031 0.03 -9999 0 -0.54 1 1
SMAD9 -0.088 0.24 -9999 0 -0.68 62 62
SMAD4 0.032 0.027 -9999 0 -0.54 1 1
SMAD5 -0.1 0.19 -9999 0 -0.45 78 78
BMP7/USAG1 -0.23 0.2 -9999 0 -0.36 356 356
SMAD5/SKI -0.094 0.19 -9999 0 -0.44 74 74
SMAD1 0.004 0.09 -9999 0 -0.56 5 5
BMP2 -0.23 0.29 -9999 0 -0.54 227 227
SMAD1/SMAD1/SMAD4 0.029 0.088 -9999 0 -0.54 3 3
BMPR1A 0.03 0.045 -9999 0 -0.54 3 3
BMPR1B 0.086 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 -0.38 257 257
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.18 -9999 0 -0.4 91 91
BMP2-4 (homodimer) -0.21 0.25 -9999 0 -0.43 273 273
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 -0.4 110 110
BMP2-4/USAG1 -0.4 0.27 -9999 0 -0.51 401 401
SMAD6/SMURF1/SMAD5 -0.095 0.19 -9999 0 -0.44 73 73
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 -0.38 258 258
SMAD5/SMAD5/SMAD4 -0.096 0.19 -9999 0 -0.45 71 71
MAPK1 0.032 0.008 -9999 0 -10000 0 0
TAK1/TAB family -0.088 0.17 -9999 0 -0.36 98 98
BMP7 (homodimer) 0.042 0.042 -9999 0 -10000 0 0
NUP214 0.034 0.005 -9999 0 -10000 0 0
BMP6/FETUA -0.098 0.21 -9999 0 -0.4 166 166
SMAD1/SKI 0.015 0.096 -9999 0 -0.48 6 6
SMAD6 0.033 0.007 -9999 0 -10000 0 0
CTDSP2 0.033 0.006 -9999 0 -10000 0 0
BMP2-4/FETUA -0.17 0.23 -9999 0 -0.38 257 257
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 0.048 0.045 -9999 0 -10000 0 0
BMPR2 (homodimer) 0.034 0.005 -9999 0 -10000 0 0
GADD34/PP1CA 0.06 0.037 -9999 0 -0.34 2 2
BMPR1A-1B (homodimer) 0.082 0.063 -9999 0 -0.4 3 3
CHRDL1 -0.31 0.28 -9999 0 -0.54 299 299
ENDOFIN/SMAD1 0.014 0.098 -9999 0 -0.5 6 6
SMAD6-7/SMURF1/SMAD1 0.047 0.1 -9999 0 -0.6 3 3
SMAD6/SMURF1 0.034 0.005 -9999 0 -10000 0 0
BAMBI 0.016 0.16 -9999 0 -0.54 36 36
SMURF2 0.031 0.013 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.36 0.31 -9999 0 -0.54 350 350
BMP2-4/GREM1 -0.16 0.23 -9999 0 -0.37 262 262
SMAD7 0.033 0.007 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.078 0.23 -9999 0 -0.66 60 60
SMAD1/SMAD6 0.014 0.098 -9999 0 -0.5 6 6
TAK1/SMAD6 0.047 0.015 -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 0.19 -9999 0 -0.4 108 108
PPM1A 0.033 0.006 -9999 0 -10000 0 0
SMAD1/SMURF2 0.012 0.093 -9999 0 -0.5 6 6
SMAD7/SMURF1 0.048 0.013 -9999 0 -10000 0 0
CTDSPL 0.031 0.037 -9999 0 -0.54 2 2
PPP1CA 0.034 0.02 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.005 -9999 0 -10000 0 0
PPP1R15A 0.032 0.036 -9999 0 -0.54 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.11 0.18 -9999 0 -0.4 101 101
CHRD 0.036 0.021 -9999 0 -10000 0 0
BMPR2 0.034 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.21 -9999 0 -0.45 112 112
BMP4 -0.038 0.19 -9999 0 -0.54 65 65
FST 0.032 0.04 -9999 0 -0.54 2 2
BMP2-4/NOG -0.16 0.22 -9999 0 -0.38 242 242
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.11 0.074 -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 -0.28 177 177
Ephrin B2/EPHB1-2 -0.075 0.19 -10000 0 -0.31 188 188
neuron projection morphogenesis -0.06 0.16 -10000 0 -0.27 177 177
Ephrin B1/EPHB1-2/Tiam1 -0.059 0.18 -10000 0 -0.3 177 177
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.057 0.18 -10000 0 -0.57 55 55
YES1 -0.068 0.26 -10000 0 -0.79 55 55
Ephrin B1/EPHB1-2/NCK2 -0.059 0.18 -10000 0 -0.3 185 185
PI3K -0.044 0.22 -10000 0 -0.61 55 55
mol:GDP -0.059 0.18 -10000 0 -0.29 180 180
ITGA2B 0.034 0.013 -10000 0 -10000 0 0
endothelial cell proliferation 0.038 0.046 -10000 0 -0.31 7 7
FYN -0.071 0.25 -10000 0 -0.79 55 55
MAP3K7 -0.058 0.19 -10000 0 -0.6 55 55
FGR -0.064 0.25 -10000 0 -0.79 55 55
TIAM1 0.035 0.012 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
RGS3 0.034 0.005 -10000 0 -10000 0 0
cell adhesion -0.045 0.2 -10000 0 -0.56 53 53
LYN -0.065 0.25 -10000 0 -0.78 55 55
Ephrin B1/EPHB1-2/Src Family Kinases -0.07 0.24 -10000 0 -0.73 56 56
Ephrin B1/EPHB1-2 -0.061 0.2 -10000 0 -0.64 55 55
SRC -0.064 0.25 -10000 0 -0.78 56 56
ITGB3 0.035 0.018 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 189 189
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
RAC1 0.034 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.038 0.046 -10000 0 -0.31 7 7
alphaIIb/beta3 Integrin 0.05 0.019 -10000 0 -10000 0 0
BLK -0.076 0.26 -10000 0 -0.8 55 55
HCK -0.064 0.25 -10000 0 -0.78 55 55
regulation of stress fiber formation 0.06 0.18 0.29 185 -10000 0 185
MAPK8 -0.055 0.18 -10000 0 -0.55 55 55
Ephrin B1/EPHB1-2/RGS3 -0.06 0.18 -10000 0 -0.3 186 186
endothelial cell migration -0.05 0.17 0.26 1 -0.51 57 58
NCK2 0.034 0.007 -10000 0 -10000 0 0
PTPN13 -0.027 0.2 -10000 0 -0.65 46 46
regulation of focal adhesion formation 0.06 0.18 0.29 185 -10000 0 185
chemotaxis 0.06 0.18 0.29 186 -10000 0 186
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.054 0.17 -10000 0 -0.28 177 177
angiogenesis -0.06 0.2 -10000 0 -0.64 55 55
LCK -0.06 0.26 -10000 0 -0.78 56 56
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.024 0.3 0.66 3 -0.72 31 34
CRP 0 0.31 0.72 6 -0.73 29 35
cell cycle arrest -0.053 0.34 0.63 8 -0.72 58 66
TIMP1 -0.014 0.28 0.65 10 -0.62 33 43
IL6ST 0.037 0.084 -10000 0 -0.54 9 9
Rac1/GDP -0.089 0.22 0.4 9 -0.41 95 104
AP1 -0.16 0.24 0.47 5 -0.53 88 93
GAB2 0.033 0.015 -10000 0 -10000 0 0
TNFSF11 -0.007 0.32 0.67 10 -0.69 35 45
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 -0.52 63 64
AKT1 0.033 0.09 0.34 1 -0.4 9 10
FOXO1 0.006 0.13 0.32 3 -0.41 21 24
MAP2K6 -0.12 0.2 0.35 3 -0.42 99 102
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.056 0.24 0.44 15 -0.45 79 94
MITF -0.11 0.21 0.34 8 -0.42 99 107
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.034 0.005 -10000 0 -10000 0 0
A2M -0.17 0.49 -10000 0 -1.3 74 74
CEBPB 0.038 0.03 -10000 0 -0.54 1 1
GRB2/SOS1/GAB family/SHP2 0 0.14 0.36 2 -0.47 21 23
STAT3 -0.072 0.36 0.64 8 -0.78 60 68
STAT1 0.034 0.12 -10000 0 -0.85 7 7
CEBPD -0.08 0.43 0.67 4 -1 70 74
PIK3CA 0.034 0.009 -10000 0 -10000 0 0
PI3K 0.008 0.13 -10000 0 -0.4 42 42
JUN -0.064 0.22 -10000 0 -0.54 86 86
PIAS3/MITF -0.1 0.2 0.35 4 -0.4 96 100
MAPK11 -0.12 0.2 0.32 1 -0.52 63 64
STAT3 (dimer)/FOXO1 -0.086 0.33 0.56 13 -0.65 78 91
GRB2/SOS1/GAB family -0.082 0.18 0.37 2 -0.43 47 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.19 0.29 6 -0.32 187 193
GRB2 0.036 0.018 -10000 0 -10000 0 0
JAK2 0.032 0.011 -10000 0 -10000 0 0
LBP 0.009 0.28 0.64 15 -0.59 28 43
PIK3R1 -0.017 0.16 -10000 0 -0.54 45 45
JAK1 0.037 0.013 -10000 0 -10000 0 0
MYC -0.016 0.38 0.7 11 -0.91 48 59
FGG -0.026 0.3 0.7 3 -0.71 34 37
macrophage differentiation -0.053 0.34 0.63 8 -0.72 58 66
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.19 -10000 0 -0.3 272 272
JUNB -0.032 0.3 0.64 3 -0.72 34 37
FOS -0.36 0.27 -10000 0 -0.54 342 342
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.34 15 -0.42 106 121
STAT1/PIAS1 -0.074 0.22 0.4 13 -0.42 84 97
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.094 -10000 0 -0.41 10 10
STAT3 (dimer) -0.069 0.35 0.64 8 -0.77 58 66
PRKCD -0.034 0.26 0.49 19 -0.51 63 82
IL6R 0.03 0.031 -10000 0 -0.55 1 1
SOCS3 -0.15 0.24 -10000 0 -0.75 39 39
gp130 (dimer)/JAK1/JAK1/LMO4 0.072 0.12 0.3 4 -0.32 31 35
Rac1/GTP -0.078 0.23 0.42 11 -0.42 92 103
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 0.65 13 -0.65 35 48
IRF1 -0.024 0.3 0.67 7 -0.71 33 40
mol:GDP -0.1 0.21 0.37 13 -0.41 100 113
SOS1 0.037 0.009 -10000 0 -10000 0 0
VAV1 -0.1 0.22 0.37 13 -0.42 100 113
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.2 -10000 0 -0.55 64 64
PTPN11 0.021 0.094 -10000 0 -0.81 5 5
IL6/IL6RA -0.23 0.2 -10000 0 -0.35 346 346
gp130 (dimer)/TYK2/TYK2/LMO4 0.066 0.11 0.28 1 -0.33 27 28
gp130 (dimer)/JAK2/JAK2/LMO4 0.062 0.11 0.28 1 -0.32 30 31
IL6 -0.37 0.27 0.22 1 -0.54 361 362
PIAS3 0.032 0.008 -10000 0 -10000 0 0
PTPRE 0.004 0.043 -10000 0 -0.52 1 1
PIAS1 0.033 0.007 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.14 0.17 0.29 3 -0.29 213 216
LMO4 0.029 0.12 0.24 3 -0.54 21 24
STAT3 (dimer)/PIAS3 -0.067 0.33 0.59 9 -0.7 63 72
MCL1 0.07 0.12 0.52 2 -0.47 1 3
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.2 0.19 -9999 0 -0.41 86 86
MAP3K8 -0.048 0.19 -9999 0 -0.55 64 64
FOS -0.099 0.12 -9999 0 -0.37 26 26
PRKCA -0.006 0.028 -9999 0 -10000 0 0
PTPN7 -0.002 0.044 -9999 0 -10000 0 0
HRAS 0.032 0.013 -9999 0 -10000 0 0
PRKCB -0.013 0.009 -9999 0 -0.018 361 361
NRAS 0.033 0.016 -9999 0 -10000 0 0
RAS family/GTP 0.029 0.038 -9999 0 -10000 0 0
MAPK3 -0.03 0.075 -9999 0 -0.61 3 3
MAP2K1 -0.055 0.088 -9999 0 -0.27 42 42
ELK1 -0.015 0.037 -9999 0 -10000 0 0
BRAF -0.016 0.038 -9999 0 -0.25 6 6
mol:GTP -0.004 0.003 -9999 0 -0.006 362 362
MAPK1 -0.052 0.12 -9999 0 -0.46 27 27
RAF1 -0.017 0.035 -9999 0 -0.25 5 5
KRAS 0.032 0.017 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

Figure 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
GNB1/GNG2 0.008 0.16 -10000 0 -0.3 104 104
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.46 138 138
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+ -0.032 0.12 0.26 3 -0.31 46 49
IGF1R 0.01 0.12 -10000 0 -0.54 21 21
E2/ER alpha (dimer)/Striatin -0.019 0.17 0.23 1 -0.33 108 109
SHC1 0.027 0.014 -10000 0 -10000 0 0
apoptosis 0.17 0.35 0.74 130 -10000 0 130
RhoA/GTP -0.024 0.12 -10000 0 -0.27 81 81
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.13 0.23 0.31 1 -0.45 136 137
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 -0.33 110 110
KRAS 0.034 0.017 -10000 0 -10000 0 0
G13/GTP -0.019 0.15 -10000 0 -0.3 102 102
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 0.03 0.012 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.25 -10000 0 -0.5 137 137
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 -0.5 137 137
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 -0.036 0.12 0.26 3 -0.32 45 48
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 -0.5 137 137
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 0.009 0.15 -10000 0 -0.83 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.03 0.14 -10000 0 -0.58 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.22 0.31 1 -0.46 106 107
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
E2/ER alpha (dimer) -0.046 0.19 -10000 0 -0.39 110 110
STRN 0.033 0.027 -10000 0 -0.54 1 1
GNAL 0.03 0.045 -10000 0 -0.54 3 3
PELP1 0.031 0.01 -10000 0 -10000 0 0
MAPK11 0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
HBEGF -0.11 0.23 0.38 6 -0.57 55 61
cAMP biosynthetic process -0.021 0.13 -10000 0 -0.28 102 102
SRC -0.14 0.23 0.31 3 -0.6 57 60
PI3K 0.006 0.12 -10000 0 -0.4 42 42
GNB1 0.034 0.011 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.18 -10000 0 -0.37 88 88
SOS1 0.034 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.21 0.21 -10000 0 -0.43 207 207
Gs family/GTP -0.012 0.14 -10000 0 -0.28 102 102
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.06 0.025 -10000 0 -10000 0 0
vasodilation -0.14 0.24 -10000 0 -0.48 138 138
mol:DAG -0.036 0.12 0.26 3 -0.32 45 48
Gs family/GDP/Gbeta gamma -0.04 0.16 -10000 0 -0.36 84 84
MSN -0.019 0.12 0.33 5 -10000 0 5
Gq family/GTP 0.002 0.093 -10000 0 -0.43 10 10
mol:PI-3-4-5-P3 -0.17 0.36 -10000 0 -0.76 130 130
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 -0.027 0.19 0.24 12 -0.37 105 117
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 0.33 1 -0.47 136 137
ruffle organization -0.017 0.12 0.25 19 -10000 0 19
ROCK2 -0.017 0.13 0.35 5 -10000 0 5
GNA14 0.043 0.067 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MMP9 -0.098 0.22 0.42 6 -0.56 52 58
MMP2 -0.14 0.22 0.34 1 -0.57 55 56
FAS signaling pathway (CD95)

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
SPTAN1 0.017 0.09 0.22 69 -10000 0 69
RFC1 0.017 0.086 0.21 71 -10000 0 71
PRKDC 0.038 0.11 0.23 106 -10000 0 106
RIPK1 0.04 0.009 -10000 0 -10000 0 0
CASP7 -0.04 0.11 -10000 0 -0.75 9 9
FASLG/FAS/FADD/FAF1 -0.023 0.09 0.34 3 -0.32 14 17
MAP2K4 -0.18 0.19 -10000 0 -0.47 79 79
mol:ceramide -0.075 0.12 -10000 0 -0.4 24 24
GSN -0.059 0.17 0.22 58 -0.34 104 162
FASLG/FAS/FADD/FAF1/Caspase 8 -0.032 0.096 0.31 3 -0.39 6 9
FAS -0.046 0.14 -10000 0 -0.56 32 32
BID -0.022 0.021 -10000 0 -10000 0 0
MAP3K1 -0.092 0.14 0.28 1 -0.49 21 22
MAP3K7 0.025 0.01 -10000 0 -10000 0 0
RB1 0.018 0.083 0.21 68 -10000 0 68
CFLAR 0.04 0.026 -10000 0 -0.52 1 1
HGF/MET -0.01 0.17 -10000 0 -0.36 89 89
ARHGDIB 0.02 0.094 0.23 71 -10000 0 71
FADD -0.008 0.028 -10000 0 -10000 0 0
actin filament polymerization 0.057 0.17 0.34 105 -0.22 58 163
NFKB1 -0.1 0.12 -10000 0 -0.65 8 8
MAPK8 -0.31 0.25 -10000 0 -0.46 356 356
DFFA 0.016 0.085 0.21 63 -10000 0 63
DNA fragmentation during apoptosis 0.02 0.09 0.21 70 -10000 0 70
FAS/FADD/MET -0.031 0.15 -10000 0 -0.39 64 64
CFLAR/RIP1 0.059 0.027 -10000 0 -0.37 1 1
FAIM3 0.034 0.029 -10000 0 -10000 0 0
FAF1 -0.016 0.032 -10000 0 -10000 0 0
PARP1 0.024 0.1 0.24 73 -10000 0 73
DFFB 0.015 0.086 0.21 70 -10000 0 70
CHUK -0.098 0.12 -10000 0 -0.61 8 8
FASLG 0.001 0.061 -10000 0 -0.55 1 1
FAS/FADD -0.032 0.1 -10000 0 -0.4 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 0.087 0.21 72 -10000 0 72
CASP10 -0.012 0.029 -10000 0 -10000 0 0
CASP3 0.021 0.1 0.26 68 -0.22 9 77
PTPN13 -0.019 0.17 -10000 0 -0.54 46 46
CASP8 -0.027 0.021 -10000 0 -10000 0 0
IL6 -0.88 0.56 -10000 0 -1.2 375 375
MET -0.023 0.17 -10000 0 -0.54 50 50
ICAD/CAD 0.011 0.076 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.077 0.12 -10000 0 -0.4 24 24
activation of caspase activity by cytochrome c -0.022 0.021 -10000 0 -10000 0 0
PAK2 0.017 0.1 0.23 71 -10000 0 71
BCL2 -0.073 0.22 -10000 0 -0.54 94 94
EPHB forward signaling

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
Ephrin A5/EPHB2 0.048 0.033 0.23 2 -0.34 1 3
cell-cell adhesion 0.1 0.12 0.26 174 -10000 0 174
Ephrin B/EPHB2/RasGAP 0.081 0.065 -10000 0 -0.3 6 6
ITSN1 0.034 0.005 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.045 0.021 -10000 0 -0.34 1 1
Ephrin B1/EPHB1 -0.099 0.19 -10000 0 -0.34 190 190
HRAS/GDP -0.081 0.16 -10000 0 -0.36 49 49
Ephrin B/EPHB1/GRB7 -0.055 0.18 -10000 0 -0.31 157 157
Endophilin/SYNJ1 0.018 0.048 0.26 1 -0.28 6 7
KRAS 0.034 0.017 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.055 0.19 -10000 0 -0.31 171 171
endothelial cell migration 0.027 0.11 -10000 0 -0.3 45 45
GRB2 0.033 0.017 -10000 0 -10000 0 0
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.008 0.062 0.3 5 -0.29 4 9
HRAS 0.034 0.013 -10000 0 -10000 0 0
RRAS 0.018 0.048 0.26 1 -0.28 6 7
DNM1 0.034 0.008 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.094 0.16 0.36 2 -0.29 187 189
lamellipodium assembly -0.1 0.12 -10000 0 -0.26 174 174
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.062 0.14 -10000 0 -0.41 35 35
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
EPHB2 0.042 0.036 -10000 0 -10000 0 0
EPHB3 0.035 0.015 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 189 189
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
mol:GDP -0.082 0.14 -10000 0 -0.38 46 46
Ephrin B/EPHB2 0.068 0.056 -10000 0 -0.3 6 6
Ephrin B/EPHB3 0.062 0.052 -10000 0 -0.3 6 6
JNK cascade -0.09 0.16 0.39 4 -0.3 180 184
Ephrin B/EPHB1 -0.07 0.18 -10000 0 -0.3 187 187
RAP1/GDP -0.059 0.14 -10000 0 -0.36 40 40
EFNB2 0.026 0.058 -10000 0 -0.54 5 5
EFNB3 0.03 0.011 -10000 0 -10000 0 0
EFNB1 0.033 0.026 -10000 0 -0.54 1 1
Ephrin B2/EPHB1-2 -0.076 0.19 -10000 0 -0.32 188 188
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.061 0.17 -10000 0 -0.28 175 175
Rap1/GTP -0.074 0.14 -10000 0 -0.27 167 167
axon guidance 0.047 0.032 0.22 2 -0.34 1 3
MAPK3 -0.047 0.14 0.26 1 -0.38 30 31
MAPK1 -0.053 0.14 -10000 0 -0.38 31 31
Rac1/GDP -0.073 0.14 -10000 0 -0.36 45 45
actin cytoskeleton reorganization -0.079 0.11 -10000 0 -0.31 29 29
CDC42/GDP -0.072 0.14 -10000 0 -0.36 45 45
PI3K 0.032 0.11 -10000 0 -0.31 45 45
EFNA5 0.032 0.029 -10000 0 -0.54 1 1
Ephrin B2/EPHB4 0.038 0.046 -10000 0 -0.31 7 7
Ephrin B/EPHB2/Intersectin/N-WASP 0.02 0.065 -10000 0 -0.28 7 7
CDC42 0.033 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.076 0.14 -10000 0 -0.27 133 133
PTK2 0.15 0.27 0.67 102 -10000 0 102
MAP4K4 -0.091 0.16 0.39 4 -0.3 180 184
SRC 0.032 0.008 -10000 0 -10000 0 0
KALRN 0.034 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.048 0.022 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.054 0.13 0.45 5 -0.34 12 17
MAP2K1 -0.059 0.13 -10000 0 -0.39 31 31
WASL 0.033 0.026 -10000 0 -0.54 1 1
Ephrin B1/EPHB1-2/NCK1 -0.061 0.2 -10000 0 -0.31 188 188
cell migration -0.064 0.16 0.32 5 -0.42 35 40
NRAS 0.035 0.016 -10000 0 -10000 0 0
SYNJ1 0.018 0.049 0.26 1 -0.28 6 7
PXN 0.034 0.003 -10000 0 -10000 0 0
TF -0.014 0.068 0.25 1 -0.28 21 22
HRAS/GTP -0.061 0.16 -10000 0 -0.28 175 175
Ephrin B1/EPHB1-2 -0.072 0.19 -10000 0 -0.31 188 188
cell adhesion mediated by integrin -0.009 0.048 0.27 6 -0.2 11 17
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.062 0.18 -10000 0 -0.29 178 178
RAC1-CDC42/GTP -0.087 0.14 -10000 0 -0.27 176 176
RASA1 0.033 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.062 0.14 -10000 0 -0.35 42 42
ruffle organization -0.096 0.14 0.41 3 -0.47 7 10
NCK1 0.034 0.005 -10000 0 -10000 0 0
receptor internalization -0.005 0.049 0.25 1 -0.27 6 7
Ephrin B/EPHB2/KALRN 0.082 0.064 -10000 0 -0.3 6 6
ROCK1 0.024 0.034 -10000 0 -0.31 1 1
RAS family/GDP -0.084 0.094 -10000 0 -0.31 26 26
Rac1/GTP -0.088 0.14 -10000 0 -0.28 174 174
Ephrin B/EPHB1/Src/Paxillin -0.086 0.16 -10000 0 -0.28 174 174
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 -1.2 88 91
STAT6 (cleaved dimer) -0.23 0.54 -10000 0 -1.1 106 106
IGHG1 0.022 0.3 0.62 15 -0.66 8 23
IGHG3 -0.16 0.58 0.78 3 -1.1 106 109
AKT1 -0.028 0.35 0.65 1 -0.72 34 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.026 0.28 0.57 6 -0.85 13 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.028 0.37 0.64 6 -0.76 36 42
THY1 -0.15 0.62 1 5 -1.2 90 95
MYB -0.007 0.16 -10000 0 -0.54 40 40
HMGA1 0.037 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.007 0.4 0.73 12 -0.64 60 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.003 0.34 0.63 6 -0.8 18 24
SP1 0.057 0.044 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.008 0.057 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.17 0.59 0.84 1 -1.1 104 105
SOCS1 -0.064 0.41 0.76 1 -0.72 80 81
SOCS3 -0.017 0.38 0.68 2 -1.1 21 23
FCER2 -0.15 0.52 0.89 4 -0.88 80 84
PARP14 0.042 0.031 -10000 0 -10000 0 0
CCL17 -0.13 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 0.027 0.29 0.59 8 -0.69 14 22
T cell proliferation -0.19 0.62 -10000 0 -1.1 107 107
IL4R/JAK1 -0.16 0.61 -10000 0 -1.2 95 95
EGR2 -0.52 0.86 0.98 4 -1.3 248 252
JAK2 0.029 0.089 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 0.036 0.31 0.7 4 -1.2 9 13
CCL26 -0.14 0.62 1.1 4 -1.2 91 95
IL4R -0.14 0.68 1.1 6 -1.2 94 100
PTPN6 0.015 0.044 0.2 1 -10000 0 1
IL13RA2 -0.16 0.63 0.96 4 -1.1 106 110
IL13RA1 0.031 0.091 -10000 0 -10000 0 0
IRF4 0.061 0.21 0.67 4 -0.67 8 12
ARG1 0.046 0.26 0.73 3 -1.1 4 7
CBL -0.018 0.36 0.65 6 -0.6 60 66
GTF3A 0.1 0.065 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
IL13RA1/JAK2 0.049 0.13 0.37 4 -10000 0 4
IRF4/BCL6 0.027 0.21 0.53 1 -0.68 9 10
CD40LG 0.048 0.032 0.31 2 -10000 0 2
MAPK14 -0.017 0.38 0.67 4 -0.66 52 56
mitosis -0.023 0.34 0.65 1 -0.67 34 35
STAT6 -0.16 0.75 1.2 14 -1.3 104 118
SPI1 0.043 0.033 -10000 0 -0.24 1 1
RPS6KB1 -0.006 0.33 0.64 5 -0.68 27 32
STAT6 (dimer) -0.16 0.76 1.2 14 -1.3 104 118
STAT6 (dimer)/PARP14 -0.18 0.64 -10000 0 -1.2 106 106
mast cell activation -0.005 0.026 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.02 0.36 0.62 7 -0.73 39 46
FRAP1 -0.029 0.35 0.65 1 -0.72 34 35
LTA -0.15 0.62 0.93 3 -1.2 91 94
FES 0.031 0.037 -10000 0 -0.54 2 2
T-helper 1 cell differentiation 0.14 0.73 1.3 104 -1.2 14 118
CCL11 -0.11 0.61 0.9 4 -1.1 93 97
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.007 0.34 0.62 7 -0.89 16 23
IL2RG 0.044 0.041 -10000 0 -10000 0 0
IL10 -0.11 0.63 1 11 -1.1 97 108
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 118 118
IL4 0.041 0.3 0.8 6 -1 14 20
IL5 -0.15 0.62 1 3 -1.2 90 93
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.067 0.54 0.98 13 -0.87 91 104
COL1A1 0.11 0.4 0.75 42 -0.91 25 67
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.17 0.62 -10000 0 -1.2 86 86
IL2R gamma/JAK3 0.063 0.039 -10000 0 -10000 0 0
TFF3 -0.27 0.73 0.93 3 -1.3 141 144
ALOX15 -0.15 0.62 0.93 3 -1.1 102 105
MYBL1 0.048 0.053 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.1 0.54 0.81 7 -0.92 98 105
SHC1 0.027 0.014 -10000 0 -10000 0 0
CEBPB 0.035 0.034 -10000 0 -0.39 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.046 0.36 0.62 5 -0.7 44 49
mol:PI-3-4-5-P3 -0.028 0.35 0.65 1 -0.72 34 35
PI3K -0.035 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 0.036 0.28 0.57 9 -0.68 11 20
ITGB3 -0.14 0.62 0.96 4 -1.2 91 95
PIGR -0.4 0.84 1 11 -1.3 206 217
IGHE -0.041 0.1 0.18 14 -0.27 23 37
MAPKKK cascade 0.037 0.27 0.57 9 -0.67 11 20
BCL6 -0.024 0.17 -10000 0 -0.54 49 49
OPRM1 -0.15 0.62 0.93 3 -1.2 90 93
RETNLB -0.15 0.62 0.93 3 -1.2 93 96
SELP -0.3 0.82 0.97 10 -1.4 160 170
AICDA -0.15 0.59 0.94 1 -1.1 95 96
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 0.4 2 -0.49 6 8
IGF1R 0.01 0.12 -10000 0 -0.54 21 21
PI4KB 0.028 0.014 -10000 0 -10000 0 0
MFGE8 0.007 0.13 -10000 0 -0.54 25 25
SRC 0.032 0.008 -10000 0 -10000 0 0
CDKN1B -0.1 0.13 -10000 0 -0.57 27 27
VEGFA 0.05 0.046 -10000 0 -10000 0 0
ILK -0.087 0.096 -10000 0 -0.47 16 16
ROCK1 0.033 0.006 -10000 0 -10000 0 0
AKT1 -0.082 0.089 -10000 0 -0.45 15 15
PTK2B 0.028 0.051 0.3 6 -0.3 1 7
alphaV/beta3 Integrin/JAM-A -0.16 0.17 -10000 0 -0.3 269 269
CBL 0.03 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.064 0.03 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.25 -10000 0 -0.38 256 256
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.039 0.06 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Syndecan-1 0.088 0.052 -10000 0 -0.34 1 1
PI4KA 0.032 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.31 0.25 -10000 0 -0.5 269 269
PI4 Kinase 0.038 0.022 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.099 0.067 -10000 0 -0.34 4 4
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 -0.56 324 324
GPR124 0.008 0.1 -10000 0 -0.54 17 17
MAPK1 -0.38 0.29 -10000 0 -0.56 337 337
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
alphaV/beta3 Integrin/Tumstatin 0.065 0.029 -10000 0 -0.34 1 1
cell adhesion 0.034 0.092 -10000 0 -0.3 30 30
ANGPTL3 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.072 0.037 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.01 0.12 -10000 0 -0.54 21 21
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
TGFBR2 -0.005 0.14 -10000 0 -0.54 34 34
ITGB3 0.035 0.018 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 250 250
RAC1 0.034 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.039 0.08 -10000 0 -0.34 18 18
apoptosis 0.033 0.027 -10000 0 -0.54 1 1
CD47 0.023 0.076 -10000 0 -0.54 9 9
alphaV/beta3 Integrin/CD47 0.057 0.062 -10000 0 -0.34 10 10
VCL 0.034 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.055 0.096 -10000 0 -0.34 23 23
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 -0.51 1 1
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 -10000 0 -0.54 375 375
F11R -0.23 0.2 -10000 0 -0.4 292 292
alphaV/beta3 Integrin/Lactadherin 0.047 0.09 -10000 0 -0.34 22 22
alphaV/beta3 Integrin/TGFBR2 0.039 0.1 -10000 0 -0.34 33 33
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.069 0.041 -10000 0 -0.32 1 1
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.061 0.028 -10000 0 -0.31 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.066 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.056 0.047 0.29 1 -0.3 1 2
SDC1 0.072 0.063 -10000 0 -10000 0 0
VAV3 0.012 0.071 -10000 0 -0.3 19 19
PTPN11 0.034 0.004 -10000 0 -10000 0 0
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
FAK1/Paxillin -0.032 0.12 0.38 3 -0.38 7 10
cell migration -0.032 0.1 0.36 3 -0.36 6 9
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PI3K -0.16 0.18 -10000 0 -0.31 266 266
SPP1 0.089 0.085 -10000 0 -0.54 3 3
KDR 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.033 0.028 -10000 0 -0.54 1 1
COL4A3 0.033 0.006 -10000 0 -10000 0 0
angiogenesis -0.37 0.28 -10000 0 -0.56 320 320
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 -10000 0 -0.34 33 33
IL23-mediated signaling events

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
CCL2 -0.28 0.52 0.97 6 -1.2 61 67
IL23A -0.24 0.47 1.1 6 -1.1 45 51
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.46 0.76 2 -1 58 60
positive regulation of T cell mediated cytotoxicity -0.27 0.52 1.1 8 -1.1 58 66
ITGA3 -0.23 0.46 0.95 6 -0.99 56 62
IL17F -0.18 0.35 0.68 11 -0.67 64 75
IL12B 0.007 0.082 0.3 8 -10000 0 8
STAT1 (dimer) -0.25 0.5 0.88 6 -1.1 58 64
CD4 -0.24 0.46 0.95 5 -0.99 55 60
IL23 -0.24 0.45 0.95 5 -1 44 49
IL23R -0.019 0.21 0.81 3 -1.1 10 13
IL1B -0.25 0.48 1.1 6 -1.1 47 53
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.46 0.92 8 -0.99 51 59
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 0.004 0.06 0.26 3 -10000 0 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.009 0.074 0.27 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 -1.1 58 66
natural killer cell activation 0.001 0.015 0.08 2 -0.061 6 8
JAK2 0.004 0.076 0.32 4 -10000 0 4
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
NFKB1 0.034 0.009 -10000 0 -10000 0 0
RELA 0.034 0.008 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.23 0.44 0.92 6 -0.97 44 50
ALOX12B -0.24 0.46 0.95 5 -1 53 58
CXCL1 -0.64 0.73 1.1 6 -1.2 289 295
T cell proliferation -0.27 0.52 1.1 8 -1.1 58 66
NFKBIA 0.033 0.01 -10000 0 -10000 0 0
IL17A -0.12 0.3 0.62 16 -0.53 46 62
PI3K -0.28 0.47 0.78 2 -1 71 73
IFNG 0.022 0.074 0.18 59 -0.12 5 64
STAT3 (dimer) -0.26 0.46 0.76 2 -0.98 70 72
IL18R1 0.04 0.03 -10000 0 -0.54 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.33 0.76 11 -0.67 36 47
IL18/IL18R 0.064 0.14 0.3 12 -0.34 42 54
macrophage activation -0.013 0.029 0.075 21 -0.045 8 29
TNF -0.25 0.48 1.1 5 -1.1 47 52
STAT3/STAT4 -0.26 0.47 0.81 2 -1 60 62
STAT4 (dimer) -0.27 0.49 0.86 6 -1.1 62 68
IL18 0.047 0.045 -10000 0 -10000 0 0
IL19 -0.2 0.47 0.92 9 -0.98 51 60
STAT5A (dimer) -0.27 0.49 0.85 5 -1.1 60 65
STAT1 0.058 0.054 -10000 0 -10000 0 0
SOCS3 0.019 0.084 -10000 0 -0.54 11 11
CXCL9 -0.22 0.5 1.1 6 -1.1 51 57
MPO -0.23 0.46 0.99 5 -0.99 53 58
positive regulation of humoral immune response -0.27 0.52 1.1 8 -1.1 58 66
IL23/IL23R/JAK2/TYK2 -0.28 0.54 1.1 8 -1.2 58 66
IL6 -0.79 0.68 0.93 6 -1.2 362 368
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
IL2 0.049 0.039 0.24 1 -0.52 1 2
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.015 0.08 2 -0.061 6 8
CD3E -0.24 0.46 0.98 5 -1 52 57
keratinocyte proliferation -0.27 0.52 1.1 8 -1.1 58 66
NOS2 -0.24 0.46 0.88 8 -0.97 60 68
Visual signal transduction: Rods

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.033 0.006 -10000 0 -10000 0 0
GNAT1/GTP 0.024 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.057 0.04 -10000 0 -0.34 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 -0.089 0.17 -10000 0 -0.29 202 202
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 0.19 -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 0.055 0.059 -10000 0 -0.54 1 1
mol:Ca2+ -0.12 0.15 0.36 6 -0.51 7 13
Na + (4 Units) -0.09 0.16 -10000 0 -0.27 212 212
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 0.057 0.092 -10000 0 -0.27 28 28
GUCY2D 0.031 0.011 -10000 0 -10000 0 0
GNGT1 0.066 0.059 -10000 0 -10000 0 0
GUCY2F 0.033 0.038 -10000 0 -0.54 2 2
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.025 0.052 -10000 0 -0.3 11 11
mol:11-cis-retinal -0.43 0.23 -10000 0 -0.54 409 409
mol:cGMP 0.055 0.073 -10000 0 -0.34 13 13
GNB1 0.034 0.011 -10000 0 -10000 0 0
Rhodopsin -0.31 0.18 -10000 0 -0.4 404 404
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 -10000 0 0
GCAP Family/Ca ++ 0.054 0.064 -10000 0 -0.34 12 12
PDE6A/B 0.038 0.071 -10000 0 -0.4 12 12
mol:Pi 0.048 0.099 -10000 0 -0.32 28 28
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.078 0.042 0.24 1 -10000 0 1
PDE6B 0.02 0.089 -10000 0 -0.54 12 12
PDE6A 0.034 0.008 -10000 0 -10000 0 0
PDE6G 0.033 0.014 -10000 0 -10000 0 0
RHO 0.034 0.005 -10000 0 -10000 0 0
PDE6 0.065 0.11 -10000 0 -0.3 25 25
GUCA1A 0.024 0.077 -10000 0 -0.54 9 9
GC2/GCAP Family 0.073 0.076 -10000 0 -0.36 13 13
GUCA1C 0.031 0.046 -10000 0 -0.54 3 3
GUCA1B 0.033 0.027 -10000 0 -0.54 1 1
Aurora B 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
Condensin I complex 0.049 0.077 0.25 33 -10000 0 33
STMN1 0.054 0.083 0.28 45 -10000 0 45
Aurora B/RasGAP/Survivin 0.11 0.075 0.25 3 -10000 0 3
Chromosomal passenger complex/Cul3 protein complex -0.071 0.13 0.21 24 -0.33 26 50
BIRC5 0.12 0.074 -10000 0 -10000 0 0
DES -0.012 0.13 -10000 0 -0.55 26 26
Aurora C/Aurora B/INCENP 0.075 0.051 -10000 0 -10000 0 0
Aurora B/TACC1 0.025 0.087 -10000 0 -0.32 24 24
Aurora B/PP2A 0.058 0.041 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.02 0.022 0.14 3 -10000 0 3
mitotic metaphase/anaphase transition -0.002 0.004 -10000 0 -10000 0 0
NDC80 0.099 0.1 0.28 84 -10000 0 84
Cul3 protein complex -0.23 0.18 -10000 0 -0.35 358 358
KIF2C 0.13 0.1 0.22 259 -10000 0 259
PEBP1 0.039 0.027 -10000 0 -0.54 1 1
KIF20A 0.12 0.069 0.19 9 -10000 0 9
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.056 0.041 -10000 0 -10000 0 0
SEPT1 0.035 0.023 -10000 0 -10000 0 0
SMC2 0.04 0.03 -10000 0 -10000 0 0
SMC4 0.045 0.04 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.063 0.16 0.32 11 -0.42 31 42
PSMA3 0.033 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.005 -10000 0 -10000 0 0
H3F3B 0.031 0.036 -10000 0 -10000 0 0
AURKB 0.05 0.053 -10000 0 -10000 0 0
AURKC 0.035 0.019 -10000 0 -10000 0 0
CDCA8 0.11 0.073 -10000 0 -10000 0 0
cytokinesis 0.18 0.15 0.35 198 -10000 0 198
Aurora B/Septin1 0.18 0.15 0.37 127 -10000 0 127
AURKA 0.077 0.067 -10000 0 -10000 0 0
INCENP 0.053 0.04 -10000 0 -10000 0 0
KLHL13 -0.38 0.26 -10000 0 -0.54 364 364
BUB1 0.15 0.052 0.2 5 -10000 0 5
hSgo1/Aurora B/Survivin 0.12 0.097 0.31 64 -10000 0 64
EVI5 0.036 0.026 -10000 0 -0.53 1 1
RhoA/GTP 0.21 0.14 0.35 199 -10000 0 199
SGOL1 0.073 0.064 -10000 0 -10000 0 0
CENPA 0.14 0.12 0.28 180 -10000 0 180
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.057 0.041 -10000 0 -10000 0 0
NCAPD2 0.035 0.021 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.058 0.041 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
NCAPH 0.078 0.066 -10000 0 -10000 0 0
NPM1 0.025 0.11 -10000 0 -0.76 4 4
RASA1 0.033 0.011 -10000 0 -10000 0 0
KLHL9 0.032 0.009 -10000 0 -10000 0 0
mitotic prometaphase 0.005 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.041 -10000 0 -10000 0 0
PPP1CC 0.034 0.004 -10000 0 -10000 0 0
Centraspindlin 0.23 0.15 0.37 243 -10000 0 243
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
NSUN2 0.026 0.093 0.26 1 -0.36 10 11
MYLK -0.07 0.17 -10000 0 -0.34 137 137
KIF23 0.12 0.073 0.18 292 -10000 0 292
VIM -0.007 0.13 -10000 0 -0.39 47 47
RACGAP1 0.08 0.065 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.025 0.11 -10000 0 -0.42 14 14
Chromosomal passenger complex 0.16 0.13 0.28 236 -10000 0 236
Chromosomal passenger complex/EVI5 0.14 0.11 0.36 25 -10000 0 25
TACC1 0.001 0.12 -10000 0 -0.54 24 24
PPP2R5D 0.033 0.006 -10000 0 -10000 0 0
CUL3 0.031 0.037 -10000 0 -0.54 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A -0.038 0.19 -10000 0 -0.54 62 62
LAT2 -0.03 0.13 -10000 0 -0.36 46 46
AP1 -0.19 0.23 -10000 0 -0.46 156 156
mol:PIP3 0.004 0.19 0.36 22 -0.47 32 54
IKBKB 0.02 0.14 0.28 47 -0.27 33 80
AKT1 -0.006 0.2 0.34 73 -0.46 28 101
IKBKG 0.003 0.13 0.27 23 -0.27 35 58
MS4A2 -0.058 0.21 -10000 0 -0.53 83 83
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
MAP3K1 0.01 0.15 0.35 12 -0.4 24 36
mol:Ca2+ 0.012 0.16 0.31 31 -0.35 31 62
LYN 0.032 0.018 -10000 0 -10000 0 0
CBLB -0.03 0.13 -10000 0 -0.36 45 45
SHC1 0.027 0.014 -10000 0 -10000 0 0
RasGAP/p62DOK -0.093 0.18 -10000 0 -0.31 205 205
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.012 0.2 0.34 64 -0.34 89 153
PTPN13 -0.039 0.19 -10000 0 -0.56 32 32
PTPN11 0.033 0.022 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.002 0.16 0.36 19 -0.34 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 -0.42 47 47
LAT -0.026 0.12 0.21 2 -0.35 45 47
PAK2 0.008 0.16 0.36 12 -0.43 26 38
NFATC2 -0.012 0.057 -10000 0 -0.69 1 1
HRAS 0.003 0.16 0.3 12 -0.45 28 40
GAB2 0.03 0.012 -10000 0 -10000 0 0
PLA2G1B 0.009 0.11 -10000 0 -0.83 7 7
Fc epsilon R1 -0.037 0.19 -10000 0 -0.41 94 94
Antigen/IgE/Fc epsilon R1 -0.032 0.18 -10000 0 -0.38 94 94
mol:GDP -0.024 0.15 0.28 2 -0.45 29 31
JUN -0.065 0.22 -10000 0 -0.54 86 86
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
FOS -0.36 0.27 -10000 0 -0.54 342 342
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.026 0.13 -10000 0 -0.36 51 51
CHUK 0.002 0.13 0.27 23 -0.27 36 59
KLRG1 -0.024 0.12 -10000 0 -0.36 31 31
VAV1 -0.029 0.13 0.22 1 -0.35 47 48
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.028 0.12 -10000 0 -0.35 47 47
negative regulation of mast cell degranulation -0.028 0.11 -10000 0 -0.35 28 28
BTK -0.024 0.15 -10000 0 -0.49 25 25
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.047 0.17 -10000 0 -0.37 91 91
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 50 50
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 36 36
DUSP1 -0.2 0.28 -10000 0 -0.54 209 209
NF-kappa-B/RelA 0.012 0.081 0.18 11 -0.18 20 31
actin cytoskeleton reorganization -0.015 0.18 -10000 0 -0.57 23 23
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.012 0.17 -10000 0 -0.46 36 36
FER -0.029 0.13 -10000 0 -0.35 46 46
RELA 0.034 0.005 -10000 0 -10000 0 0
ITK -0.003 0.069 -10000 0 -0.34 14 14
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG1 -0.001 0.17 0.31 9 -0.46 27 36
cytokine secretion -0.006 0.047 -10000 0 -10000 0 0
SPHK1 -0.026 0.12 -10000 0 -0.36 42 42
PTK2 -0.017 0.18 -10000 0 -0.61 23 23
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.04 0.16 -10000 0 -0.44 49 49
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.032 0.22 0.35 18 -0.5 52 70
MAP2K2 0.004 0.11 -10000 0 -0.84 7 7
MAP2K1 0.004 0.11 -10000 0 -0.84 7 7
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.013 0.11 0.24 1 -0.37 23 24
MAP2K4 -0.073 0.32 -10000 0 -0.86 69 69
Fc epsilon R1/FcgammaRIIB -0.02 0.19 -10000 0 -0.38 94 94
mol:Choline -0.012 0.2 0.34 64 -0.34 89 153
SHC/Grb2/SOS1 0.009 0.14 -10000 0 -0.41 22 22
FYN 0.029 0.037 -10000 0 -0.54 2 2
DOK1 0.036 0.016 -10000 0 -10000 0 0
PXN -0.016 0.17 -10000 0 -0.56 22 22
HCLS1 -0.028 0.13 0.21 2 -0.35 46 48
PRKCB -0.005 0.16 0.3 25 -0.35 44 69
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
IGHE 0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.028 0.11 -10000 0 -0.36 28 28
LCP2 0.036 0.023 -10000 0 -10000 0 0
PLA2G4A -0.16 0.2 -10000 0 -0.35 213 213
RASA1 0.033 0.011 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.012 0.2 0.34 64 -0.34 89 153
IKK complex 0.021 0.12 0.28 36 -0.22 19 55
WIPF1 0.037 0.022 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.036 0.043 0.13 3 -0.12 25 28
BUB1B 0.093 0.062 0.15 189 -0.14 1 190
PLK1 0.046 0.035 0.11 64 -10000 0 64
PLK1S1 0.023 0.019 0.057 56 -10000 0 56
KIF2A 0.038 0.037 0.27 4 -10000 0 4
regulation of mitotic centrosome separation 0.046 0.035 0.1 65 -10000 0 65
GOLGA2 0.034 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.1 0.061 0.16 197 -10000 0 197
WEE1 0.049 0.077 0.22 2 -0.31 16 18
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 0.051 0.039 0.12 25 -0.16 2 27
PICH/PLK1 0.13 0.094 0.24 172 -10000 0 172
CENPE 0.084 0.066 0.16 170 -10000 0 170
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.039 0.037 0.27 4 -10000 0 4
PPP2CA 0.033 0.006 -10000 0 -10000 0 0
FZR1 0.034 0.009 -10000 0 -10000 0 0
TPX2 0.08 0.037 0.13 68 -10000 0 68
PAK1 0.043 0.043 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
CLSPN 0.043 0.053 0.14 13 -0.2 12 25
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 0.057 56 -10000 0 56
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 0.1 65 -10000 0 65
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 0.13 1 -0.16 44 45
CDC25C 0.082 0.066 0.17 10 -0.22 11 21
CDC25B 0.048 0.04 -10000 0 -10000 0 0
SGOL1 0.036 0.043 0.12 25 -0.13 3 28
RHOA 0.033 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.09 0.066 0.24 27 -0.21 1 28
CDC14B -0.002 0.065 -10000 0 -0.4 13 13
CDC20 0.082 0.068 -10000 0 -10000 0 0
PLK1/PBIP1 0.073 0.054 0.14 173 -10000 0 173
mitosis -0.001 0.003 0.033 2 -10000 0 2
FBXO5 0.038 0.043 0.16 19 -10000 0 19
CDC2 0.005 0.004 0.015 32 -10000 0 32
NDC80 0.11 0.073 -10000 0 -10000 0 0
metaphase plate congression 0.028 0.055 -10000 0 -0.21 22 22
ERCC6L 0.12 0.094 0.24 138 -10000 0 138
NLP/gamma Tubulin 0.025 0.024 0.089 13 -0.094 2 15
microtubule cytoskeleton organization 0.014 0.059 0.13 1 -0.16 44 45
G2/M transition DNA damage checkpoint 0 0.003 0.013 11 -10000 0 11
PPP1R12A 0.035 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.013 11 -10000 0 11
PLK1/PRC1-2 0.17 0.097 0.26 221 -10000 0 221
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 80 -10000 0 80
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 0.17 258 -10000 0 258
Golgi organization 0.046 0.035 0.1 65 -10000 0 65
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 0.034 0.005 -10000 0 -10000 0 0
chromosome segregation 0.073 0.054 0.14 173 -10000 0 173
PRC1 0.1 0.072 -10000 0 -10000 0 0
ECT2 0.072 0.073 0.18 115 -10000 0 115
C13orf34 0.039 0.03 0.091 67 -10000 0 67
NUDC 0.028 0.055 -10000 0 -0.21 22 22
regulation of attachment of spindle microtubules to kinetochore 0.093 0.062 0.15 189 -0.14 1 190
spindle assembly 0.036 0.029 0.1 33 -10000 0 33
spindle stabilization 0.023 0.019 0.057 56 -10000 0 56
APC/C/HCDH1 0.021 0.06 -10000 0 -0.34 13 13
MKLP2/PLK1 0.12 0.065 0.18 258 -10000 0 258
CCNB1 0.086 0.069 -10000 0 -10000 0 0
PPP1CB 0.035 0.004 -10000 0 -10000 0 0
BTRC 0.037 0.021 -10000 0 -10000 0 0
ROCK2 0.04 0.05 0.21 1 -0.31 5 6
TUBG1 0.027 0.039 0.13 1 -0.17 13 14
G2/M transition of mitotic cell cycle 0.061 0.064 0.21 26 -10000 0 26
MLF1IP 0.07 0.065 0.15 2 -10000 0 2
INCENP 0.047 0.039 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.012 -10000 0 -10000 0 0
CDC42/GTP -0.067 0.14 -10000 0 -0.31 62 62
PLCG1 -0.073 0.13 -10000 0 -0.24 169 169
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.045 0.017 -10000 0 -10000 0 0
cell migration -0.067 0.14 -10000 0 -0.31 62 62
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.07 0.13 -10000 0 -0.24 163 163
MAPK1 -0.077 0.13 -10000 0 -0.33 56 56
S1P/S1P5/Gi -0.081 0.14 -10000 0 -0.25 184 184
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
CDC42/GDP 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.033 0.05 0.2 3 -10000 0 3
S1P/S1P4/Gi -0.081 0.14 -10000 0 -0.25 184 184
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
S1P/S1P4/G12/G13 0.039 0.014 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.046 0.24 0.58 2 -0.56 73 75
IHH 0.021 0.075 -10000 0 -0.2 1 1
SHH Np/Cholesterol/GAS1 -0.067 0.15 -10000 0 -0.31 124 124
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.067 0.15 0.31 124 -10000 0 124
SMO/beta Arrestin2 -0.003 0.19 0.41 2 -0.48 29 31
SMO -0.017 0.18 0.44 2 -0.5 30 32
AKT1 -0.02 0.19 0.3 1 -0.59 36 37
ARRB2 0.031 0.01 -10000 0 -10000 0 0
BOC -0.09 0.24 -10000 0 -0.54 108 108
ADRBK1 0.031 0.01 -10000 0 -10000 0 0
heart looping -0.016 0.18 0.44 2 -0.49 31 33
STIL 0.041 0.15 0.34 31 -0.34 7 38
DHH N/PTCH2 0.049 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 0.005 0.16 0.38 2 -0.32 81 83
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 0.66 2 -0.9 94 96
determination of left/right symmetry -0.016 0.18 0.44 2 -0.49 31 33
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
skeletal system development -0.11 0.39 0.66 2 -0.89 94 96
IHH N/Hhip 0.038 0.053 -10000 0 -10000 0 0
DHH N/Hhip 0.05 0.012 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.016 0.18 0.44 2 -0.49 31 33
pancreas development 0.034 0.012 -10000 0 -10000 0 0
HHAT 0.023 0.06 -10000 0 -0.54 5 5
PI3K 0.006 0.12 -10000 0 -0.4 42 42
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.14 0.27 -10000 0 -0.54 155 155
somite specification -0.016 0.18 0.44 2 -0.49 31 33
SHH Np/Cholesterol/PTCH1 -0.01 0.12 -10000 0 -0.34 13 13
SHH Np/Cholesterol/PTCH2 0.024 0.037 -10000 0 -0.31 5 5
SHH Np/Cholesterol/Megalin -0.057 0.14 -10000 0 -0.32 110 110
SHH 0.01 0.043 -10000 0 -0.4 5 5
catabolic process -0.01 0.18 0.46 2 -0.36 86 88
SMO/Vitamin D3 0.009 0.17 0.4 16 -0.45 13 29
SHH Np/Cholesterol/Hhip 0.024 0.038 -10000 0 -0.31 5 5
LRP2 -0.12 0.26 -10000 0 -0.54 136 136
receptor-mediated endocytosis -0.063 0.2 0.35 9 -0.51 38 47
SHH Np/Cholesterol/BOC -0.037 0.13 -10000 0 -0.31 84 84
SHH Np/Cholesterol/CDO 0.018 0.051 -10000 0 -0.35 8 8
mesenchymal cell differentiation -0.024 0.038 0.31 5 -10000 0 5
mol:Vitamin D3 0.027 0.16 0.41 17 -0.37 9 26
IHH N/PTCH2 0.037 0.052 -10000 0 -10000 0 0
CDON 0.026 0.052 -10000 0 -0.54 4 4
IHH N/PTCH1 -0.002 0.18 0.46 2 -0.36 86 88
Megalin/LRPAP1 -0.073 0.2 -10000 0 -0.39 139 139
PTCH2 0.034 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.014 0.034 -10000 0 -0.31 5 5
PTCH1 -0.01 0.18 0.46 2 -0.36 86 88
HHIP 0.034 0.012 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.18 -10000 0 -0.35 322 322
fibroblast growth factor receptor signaling pathway -0.22 0.18 -10000 0 -0.35 322 322
LAMA1 0.033 0.01 -10000 0 -10000 0 0
PRNP 0.018 0.091 -10000 0 -0.54 13 13
GPC1/SLIT2 -0.009 0.15 -10000 0 -0.4 63 63
SMAD2 -0.001 0.085 0.28 1 -0.31 32 33
GPC1/PrPc/Cu2+ 0.034 0.062 -10000 0 -0.34 13 13
GPC1/Laminin alpha1 0.048 0.017 -10000 0 -10000 0 0
TDGF1 0.033 0.01 -10000 0 -10000 0 0
CRIPTO/GPC1 0.048 0.016 -10000 0 -10000 0 0
APP/GPC1 0.046 0.044 -10000 0 -0.4 4 4
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.019 0.019 -10000 0 -0.34 1 1
FLT1 0.032 0.013 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.039 0.1 -10000 0 -0.34 34 34
SERPINC1 0.031 0.024 -10000 0 -10000 0 0
FYN 0.018 0.025 -10000 0 -0.34 2 2
FGR 0.02 0.011 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.025 0.083 0.29 2 -0.37 9 11
SLIT2 -0.039 0.19 -10000 0 -0.54 63 63
GPC1/NRG -0.002 0.13 -10000 0 -0.4 43 43
NRG1 -0.02 0.16 -10000 0 -0.54 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.07 0.038 -10000 0 -10000 0 0
LYN 0.018 0.014 -10000 0 -10000 0 0
mol:Spermine 0.01 0.01 -10000 0 -10000 0 0
cell growth -0.22 0.18 -10000 0 -0.35 322 322
BMP signaling pathway -0.034 0.013 -10000 0 -10000 0 0
SRC 0.019 0.01 -10000 0 -10000 0 0
TGFBR1 0.035 0.016 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.034 0.2 -10000 0 -0.54 66 66
GPC1 0.034 0.013 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.035 0.016 -10000 0 -10000 0 0
VEGFA 0.05 0.046 -10000 0 -10000 0 0
BLK 0.025 0.032 -10000 0 -10000 0 0
HCK 0.022 0.018 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 375 375
FGFR1 0.018 0.077 -10000 0 -0.54 9 9
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
TGFBR2 -0.005 0.14 -10000 0 -0.54 34 34
cell death 0.046 0.044 -10000 0 -0.4 4 4
ATIII/GPC1 0.043 0.026 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.006 0.16 -10000 0 -0.4 66 66
LCK 0.031 0.033 -10000 0 -10000 0 0
neuron differentiation -0.002 0.13 -10000 0 -0.4 43 43
PrPc/Cu2+ 0.013 0.067 -10000 0 -0.4 13 13
APP 0.031 0.055 -10000 0 -0.54 4 4
TGFBR2 (dimer) -0.005 0.14 -10000 0 -0.54 34 34
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 59 -10000 0 59
GNAI2 0.033 0.01 -10000 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.012 -10000 0 -10000 0 0
RhoA/GTP -0.067 0.14 -10000 0 -0.32 59 59
negative regulation of cAMP metabolic process -0.08 0.14 -10000 0 -0.25 184 184
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.081 0.14 -10000 0 -0.25 184 184
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
Insulin Pathway

Figure 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 -0.32 281 281
TC10/GTP -0.13 0.16 -10000 0 -0.28 270 270
Insulin Receptor/Insulin/IRS1/Shp2 0.039 0.14 -10000 0 -0.32 59 59
HRAS 0.034 0.013 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.001 0.19 -10000 0 -0.54 52 52
FOXO3 -0.031 0.16 -10000 0 -0.6 33 33
AKT1 -0.046 0.16 0.33 8 -0.45 22 30
INSR 0.039 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.091 0.072 0.36 22 -10000 0 22
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.029 0.051 -10000 0 -0.54 4 4
SORBS1 -0.28 0.29 -10000 0 -0.54 275 275
CRK 0.031 0.01 -10000 0 -10000 0 0
PTPN1 0.019 0.053 0.28 18 -10000 0 18
CAV1 -0.23 0.18 -10000 0 -0.33 365 365
CBL/APS/CAP/Crk-II/C3G -0.13 0.18 -10000 0 -0.3 274 274
Insulin Receptor/Insulin/IRS1/NCK2 0.04 0.13 -10000 0 -0.32 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.15 -10000 0 -0.3 91 91
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.017 0.097 0.36 1 -0.4 6 7
RPS6KB1 -0.04 0.14 0.31 8 -0.4 21 29
PARD6A 0.031 0.019 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.055 -10000 0 -0.55 4 4
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.013 0.15 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 40 40
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 0.058 0.052 -10000 0 -0.47 4 4
PI3K 0.008 0.15 -10000 0 -0.3 91 91
NCK2 0.034 0.007 -10000 0 -10000 0 0
RHOQ 0.033 0.026 -10000 0 -0.54 1 1
mol:H2O2 0.001 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
AKT2 -0.047 0.16 0.33 7 -0.44 22 29
PRKCZ -0.007 0.079 -10000 0 -0.49 7 7
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.011 0.09 -10000 0 -0.28 45 45
F2RL2 0.046 0.065 -10000 0 -0.54 3 3
TRIP10 0.032 0.026 -10000 0 -0.54 1 1
Insulin Receptor/Insulin/Shc 0.055 0.036 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.043 0.026 -10000 0 -0.34 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.076 0.055 -10000 0 -10000 0 0
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.14 0.18 -10000 0 -0.31 275 275
TC10/GDP 0.024 0.019 -10000 0 -0.4 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.068 0.057 -10000 0 -0.32 4 4
INPP5D -0.037 0.096 -10000 0 -0.3 59 59
SOS1 0.034 0.004 -10000 0 -10000 0 0
SGK1 -0.009 0.013 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
p62DOK/RasGAP 0.058 0.053 -10000 0 -0.47 4 4
INS 0.039 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.037 0.095 -10000 0 -0.29 59 59
GRB2 0.033 0.017 -10000 0 -10000 0 0
EIF4EBP1 -0.044 0.14 0.31 5 -0.4 21 26
PTPRA 0.037 0.013 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.043 0.026 -10000 0 -0.34 2 2
PDPK1 0.031 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.001 0.087 -10000 0 -0.25 41 41
Insulin Receptor/Insulin/IRS1 0.022 0.13 -10000 0 -0.32 59 59
Insulin Receptor/Insulin/IRS3 0.056 0.024 -10000 0 -10000 0 0
Par3/Par6 0.072 0.058 -10000 0 -0.29 5 5
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.024 0.12 0.24 1 -0.33 44 45
adherens junction organization -0.024 0.12 -10000 0 -0.41 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 0.32 3 -0.38 99 102
FMN1 -0.024 0.11 -10000 0 -0.31 47 47
mol:IP3 -0.023 0.098 -10000 0 -0.28 41 41
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.022 0.12 -10000 0 -0.33 47 47
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 38 38
CTNND1 0.033 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.02 0.1 -10000 0 -0.38 21 21
VASP -0.02 0.12 0.24 1 -0.37 23 24
ZYX -0.025 0.11 -10000 0 -0.38 23 23
JUB -0.024 0.11 -10000 0 -0.31 47 47
EGFR(dimer) -0.16 0.19 -10000 0 -0.42 112 112
E-cadherin/beta catenin-gamma catenin 0.036 0.09 -10000 0 -0.32 24 24
mol:PI-3-4-5-P3 -0.006 0.12 -10000 0 -0.3 46 46
PIK3CA 0.032 0.01 -10000 0 -10000 0 0
PI3K -0.006 0.13 -10000 0 -0.3 46 46
FYN -0.024 0.11 0.24 1 -0.39 21 22
mol:Ca2+ -0.023 0.096 -10000 0 -0.28 41 41
JUP 0.034 0.011 -10000 0 -10000 0 0
PIK3R1 -0.017 0.16 -10000 0 -0.54 45 45
mol:DAG -0.023 0.098 -10000 0 -0.28 41 41
CDH1 0.006 0.12 -10000 0 -0.54 22 22
RhoA/GDP -0.14 0.18 0.32 3 -0.38 99 102
establishment of polarity of embryonic epithelium -0.019 0.11 0.24 1 -0.37 23 24
SRC 0.032 0.008 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 264 264
CASR -0.022 0.097 0.24 1 -0.32 12 13
RhoA/GTP -0.005 0.1 -10000 0 -0.3 15 15
AKT2 -0.021 0.11 -10000 0 -0.36 15 15
actin cable formation -0.02 0.11 0.25 3 -0.36 23 26
apoptosis 0.017 0.12 0.31 45 -0.26 4 49
CTNNA1 0.033 0.007 -10000 0 -10000 0 0
mol:GDP -0.16 0.18 -10000 0 -0.4 100 100
PIP5K1A -0.021 0.1 -10000 0 -0.38 21 21
PLCG1 -0.024 0.099 -10000 0 -0.29 41 41
Rac1/GTP -0.14 0.18 -10000 0 -0.39 109 109
homophilic cell adhesion -0.001 0.004 -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 -0.044 0.18 -10000 0 -0.36 117 117
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.003 0.15 -10000 0 -0.31 89 89
NGF (dimer)/p75(NTR)/BEX1 -0.007 0.14 -10000 0 -0.33 75 75
NT-4/5 (dimer)/p75(NTR) -0.041 0.15 -10000 0 -0.38 79 79
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 -0.032 0.16 0.33 3 -0.32 96 99
IKBKG 0.034 0.003 -10000 0 -10000 0 0
BDNF 0.038 0.047 -10000 0 -0.54 2 2
MGDIs/NGR/p75(NTR)/LINGO1 0.013 0.15 0.25 4 -0.33 72 76
FURIN 0.036 0.023 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0 0.15 -10000 0 -0.34 75 75
LINGO1 0.054 0.051 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.033 0.029 -10000 0 -0.28 1 1
proBDNF (dimer) 0.038 0.047 -10000 0 -0.54 2 2
NTRK1 0.03 0.021 -10000 0 -10000 0 0
RTN4R 0.041 0.034 -10000 0 -10000 0 0
neuron apoptosis -0.012 0.16 0.41 4 -0.48 14 18
IRAK1 0.035 0.014 -10000 0 -10000 0 0
SHC1 -0.024 0.11 -10000 0 -0.34 50 50
ARHGDIA 0.032 0.011 -10000 0 -10000 0 0
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
Gamma Secretase 0.074 0.054 -10000 0 -0.3 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.008 0.14 -10000 0 -0.33 82 82
MAGEH1 0.018 0.095 -10000 0 -0.54 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.078 0.2 -10000 0 -0.38 147 147
Mammalian IAPs/DIABLO 0.045 0.078 -10000 0 -0.31 17 17
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.044 0.035 -10000 0 -10000 0 0
APP 0.031 0.055 -10000 0 -0.54 4 4
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.033 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.011 0.12 -10000 0 -0.29 73 73
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.036 0.11 0.21 31 -0.27 74 105
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.016 0.095 -10000 0 -0.25 57 57
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.018 0.14 -10000 0 -0.34 75 75
NCSTN 0.028 0.014 -10000 0 -10000 0 0
mol:GTP -0.018 0.15 -10000 0 -0.35 78 78
PSENEN 0.035 0.015 -10000 0 -10000 0 0
mol:ceramide -0.022 0.13 -10000 0 -0.31 74 74
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.012 0.078 -10000 0 -0.21 56 56
p75(NTR)/beta APP -0.025 0.16 -10000 0 -0.39 82 82
BEX1 0.053 0.048 -10000 0 -10000 0 0
mol:GDP -0.053 0.12 -10000 0 -0.34 75 75
NGF (dimer) 0.004 0.13 -10000 0 -0.31 64 64
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.027 0.15 -10000 0 -0.31 70 70
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
RAC1/GTP -0.014 0.12 -10000 0 -0.29 74 74
MYD88 0.034 0.011 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.018 0.15 -10000 0 -0.36 78 78
RHOB 0.032 0.038 -10000 0 -0.54 2 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.057 0.035 -10000 0 -10000 0 0
NT3 (dimer) -0.11 0.25 -10000 0 -0.54 130 130
TP53 -0.028 0.13 0.37 8 -0.29 71 79
PRDM4 -0.018 0.13 -10000 0 -0.31 74 74
BDNF (dimer) 0.054 0.17 -10000 0 -0.31 69 69
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
SORT1 0.034 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.008 0.15 -10000 0 -0.31 89 89
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0 0.13 -10000 0 -0.31 74 74
RHOC 0.034 0.005 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.029 0.14 0.29 7 -0.33 72 79
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 -0.022 0.13 -10000 0 -0.31 74 74
APH1B 0.032 0.027 -10000 0 -0.54 1 1
APH1A 0.031 0.027 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.018 0.14 -10000 0 -0.33 78 78
PSEN1 0.033 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.048 0.011 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.13 0.23 -10000 0 -0.43 172 172
MAPK8 -0.025 0.14 0.29 9 -0.32 70 79
MAPK9 -0.025 0.13 0.28 8 -0.32 69 77
APAF1 0.034 0.003 -10000 0 -10000 0 0
NTF3 -0.11 0.25 -10000 0 -0.54 130 130
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.099 0.24 -10000 0 -0.54 115 115
RAC1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.008 0.14 -10000 0 -0.3 71 71
p75 CTF/Sortilin/TRAF6/NRIF 0.08 0.026 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.019 0.15 -10000 0 -0.35 78 78
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.026 0.14 -10000 0 -0.3 71 71
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.016 0.14 -10000 0 -0.31 75 75
PRKACB 0.035 0.082 -10000 0 -0.54 8 8
proBDNF (dimer)/p75 ECD 0.051 0.037 -10000 0 -0.4 2 2
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BIRC2 0.03 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.16 -10000 0 -0.4 98 98
BAD -0.025 0.15 0.38 10 -0.33 69 79
RIPK2 0.029 0.021 0.18 6 -10000 0 6
NGFR -0.055 0.2 -10000 0 -0.54 75 75
CYCS -0.009 0.13 0.26 7 -0.3 67 74
ADAM17 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.003 0.12 -10000 0 -0.31 61 61
BCL2L11 -0.025 0.15 0.39 10 -0.33 69 79
BDNF (dimer)/p75(NTR) -0.021 0.16 -10000 0 -0.38 80 80
PI3K -0.029 0.16 -10000 0 -0.34 97 97
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.001 0.13 -10000 0 -0.31 74 74
NDNL2 0.033 0.007 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PRKCI 0.034 0.017 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.041 0.15 -10000 0 -0.38 79 79
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.005 0.13 -10000 0 -0.3 74 74
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.031 0.027 -10000 0 -0.54 1 1
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.028 0.13 -10000 0 -0.33 74 74
SQSTM1 0.034 0.008 -10000 0 -10000 0 0
NGFRAP1 0.009 0.12 -10000 0 -0.54 22 22
CASP3 -0.023 0.14 0.38 10 -0.31 66 76
E2F1 0.049 0.046 -10000 0 -10000 0 0
CASP9 0.033 0.007 -10000 0 -10000 0 0
IKK complex 0.03 0.084 -10000 0 -0.3 1 1
NGF (dimer)/TRKA 0.022 0.015 -10000 0 -10000 0 0
MMP7 -0.041 0.19 -10000 0 -0.54 63 63
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.011 0.13 -10000 0 -0.3 73 73
MMP3 0.092 0.098 -10000 0 -0.54 5 5
APAF-1/Caspase 9 -0.033 0.1 -10000 0 -0.32 13 13
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 0.035 0.032 0.19 11 -10000 0 11
CDKN2C -0.024 0.15 -10000 0 -0.52 42 42
CDKN2A 0.057 0.054 0.2 3 -10000 0 3
CCND2 -0.007 0.06 0.17 28 -0.19 16 44
RB1 0.004 0.072 0.22 14 -0.2 31 45
CDK4 -0.003 0.074 0.21 35 -0.21 13 48
CDK6 -0.004 0.073 0.21 33 -0.22 16 49
G1/S progression 0.003 0.087 0.21 52 -0.23 15 67
Nectin adhesion pathway

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
PDGFRB 0.033 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
PTK2 -0.053 0.17 -10000 0 -0.44 67 67
positive regulation of JNK cascade -0.024 0.15 -10000 0 -0.32 74 74
CDC42/GDP -0.018 0.2 0.46 1 -0.44 76 77
Rac1/GDP -0.018 0.2 -10000 0 -0.43 75 75
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
CDC42/GTP -0.023 0.18 -10000 0 -0.4 72 72
nectin-3/I-afadin -0.024 0.17 -10000 0 -0.39 83 83
RAPGEF1 -0.042 0.2 0.47 1 -0.46 78 79
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.22 -10000 0 -0.52 78 78
PDGFB-D/PDGFRB 0.033 0.006 -10000 0 -10000 0 0
TLN1 -0.039 0.12 0.2 3 -0.48 21 24
Rap1/GTP -0.03 0.14 -10000 0 -0.34 66 66
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.054 0.041 -10000 0 -0.31 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.39 83 83
PVR 0.035 0.015 -10000 0 -10000 0 0
Necl-5(dimer) 0.035 0.015 -10000 0 -10000 0 0
mol:GDP -0.045 0.24 0.47 1 -0.53 77 78
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
PI3K -0.004 0.18 -10000 0 -0.34 102 102
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
positive regulation of lamellipodium assembly -0.02 0.16 -10000 0 -0.34 70 70
PVRL1 0.031 0.014 -10000 0 -10000 0 0
PVRL3 -0.053 0.21 -10000 0 -0.54 76 76
PVRL2 0.038 0.026 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
CDH1 0.006 0.12 -10000 0 -0.54 22 22
CLDN1 -0.004 0.16 -10000 0 -0.54 41 41
JAM-A/CLDN1 -0.007 0.17 -10000 0 -0.36 80 80
SRC -0.074 0.24 -10000 0 -0.57 80 80
ITGB3 0.035 0.018 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
FARP2 -0.044 0.24 0.47 1 -0.54 72 73
RAC1 0.034 0.005 -10000 0 -10000 0 0
CTNNA1 0.033 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.001 0.15 -10000 0 -0.35 78 78
nectin-1/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
nectin-2/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
RAC1/GTP/IQGAP1/filamentous actin 0.044 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.005 0.15 -10000 0 -0.35 78 78
CDC42/GTP/IQGAP1/filamentous actin 0.043 0.013 -10000 0 -10000 0 0
F11R 0.028 0.017 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.024 0.15 -10000 0 -0.32 74 74
alphaV/beta3 Integrin/Talin -0.005 0.13 0.3 1 -0.5 17 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
nectin-2(dimer)/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 9 9
PIP5K1C -0.037 0.12 -10000 0 -0.27 83 83
VAV2 -0.042 0.24 0.46 1 -0.55 67 68
RAP1/GDP -0.014 0.19 -10000 0 -0.4 69 69
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.001 0.15 -10000 0 -0.34 78 78
nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.39 83 83
Rac1/GTP -0.022 0.19 -10000 0 -0.42 70 70
PTPRM -0.035 0.14 -10000 0 -0.29 82 82
E-cadherin/beta catenin/alpha catenin 0.052 0.1 -10000 0 -0.29 25 25
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.036 0.085 -10000 0 -0.41 14 14
HDAC1 0.023 0.027 -10000 0 -10000 0 0
AES 0.033 0.008 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
DTX1 0.031 0.044 -10000 0 -0.54 3 3
LRP6/FZD1 0.046 0.024 -10000 0 -0.4 1 1
TLE1 0.016 0.098 -10000 0 -0.55 15 15
AP1 -0.22 0.19 -10000 0 -0.35 309 309
NCSTN 0.028 0.014 -10000 0 -10000 0 0
ADAM10 0.034 0.013 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.019 0.14 -10000 0 -0.73 9 9
NICD/RBPSUH 0.054 0.093 -10000 0 -0.41 14 14
WIF1 -0.38 0.26 -10000 0 -0.54 363 363
NOTCH1 0.019 0.072 -10000 0 -0.42 12 12
PSENEN 0.035 0.015 -10000 0 -10000 0 0
KREMEN2 0.1 0.074 -10000 0 -10000 0 0
DKK1 0.005 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.01 0.092 -10000 0 -0.43 8 8
APH1B 0.032 0.027 -10000 0 -0.54 1 1
APH1A 0.031 0.027 -10000 0 -10000 0 0
AXIN1 0.016 0.07 -10000 0 -0.6 4 4
CtBP/CBP/TCF1/TLE1/AES 0.002 0.08 0.28 3 -0.39 6 9
PSEN1 0.033 0.007 -10000 0 -10000 0 0
FOS -0.36 0.27 -10000 0 -0.54 342 342
JUN -0.065 0.22 -10000 0 -0.54 86 86
MAP3K7 0.03 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.089 -10000 0 -0.43 9 9
MAPK3 0.032 0.009 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.069 0.25 2 -0.31 3 5
HNF1A 0.034 0.014 -10000 0 -10000 0 0
CTBP1 0.032 0.009 -10000 0 -10000 0 0
MYC -0.053 0.32 -10000 0 -1.3 31 31
NKD1 0.031 0.021 -10000 0 -10000 0 0
FZD1 0.033 0.026 -10000 0 -0.54 1 1
NOTCH1 precursor/Deltex homolog 1 0.055 0.095 -10000 0 -0.41 14 14
apoptosis -0.22 0.19 -10000 0 -0.34 309 309
Delta 1/NOTCHprecursor 0.053 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 0.054 -10000 0 -0.3 1 1
APC 0.005 0.1 -10000 0 -0.51 14 14
DVL1 -0.039 0.094 -10000 0 -0.36 28 28
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 0.25 48 -0.29 42 90
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 0.16 2 -10000 0 2
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 -0.47 14 15
DKK2 0.031 0.054 -10000 0 -0.54 4 4
NOTCH1 precursor/DVL1 -0.014 0.12 -10000 0 -0.57 17 17
GSK3B 0.034 0.008 -10000 0 -10000 0 0
FRAT1 0.033 0.008 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.036 0.088 -10000 0 -0.41 14 14
PPP2R5D -0.003 0.065 -10000 0 -0.39 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 0.033 0.008 -10000 0 -10000 0 0
CREBBP 0.033 0.03 -10000 0 -0.55 1 1
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization -0.01 0.09 -10000 0 -0.25 45 45
epithelial cell differentiation 0.04 0.085 -10000 0 -0.29 25 25
CYFIP2 0.049 0.045 -10000 0 -10000 0 0
ENAH -0.007 0.071 0.28 5 -0.32 1 6
EGFR -0.27 0.29 -10000 0 -0.54 264 264
EPHA2 0.026 0.063 -10000 0 -0.54 6 6
MYO6 0.001 0.073 -10000 0 -0.28 24 24
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
ABI1/Sra1/Nap1 0.073 0.034 -10000 0 -10000 0 0
AQP5 -0.14 0.24 -10000 0 -0.51 126 126
CTNND1 0.033 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.071 -10000 0 -0.28 24 24
regulation of calcium-dependent cell-cell adhesion -0.023 0.1 -10000 0 -0.29 62 62
EGF -0.15 0.27 -10000 0 -0.54 162 162
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
AQP3 -0.052 0.18 -10000 0 -0.49 59 59
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 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.058 -10000 0 -0.32 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.001 0.069 -10000 0 -0.42 1 1
PVRL2 0.038 0.026 -10000 0 -10000 0 0
ZYX -0.002 0.072 -10000 0 -0.28 25 25
ARF6/GTP 0.062 0.061 -10000 0 -0.3 6 6
CDH1 0.006 0.12 -10000 0 -0.54 22 22
EGFR/EGFR/EGF/EGF -0.23 0.2 -10000 0 -0.35 352 352
RhoA/GDP 0.041 0.083 -10000 0 -0.28 24 24
actin cytoskeleton organization -0.021 0.067 -10000 0 -0.28 22 22
IGF-1R heterotetramer 0.01 0.12 -10000 0 -0.54 21 21
GIT1 0.032 0.011 -10000 0 -10000 0 0
IGF1R 0.01 0.12 -10000 0 -0.54 21 21
IGF1 -0.25 0.29 -10000 0 -0.54 250 250
DIAPH1 0.056 0.12 -10000 0 -0.56 7 7
Wnt receptor signaling pathway -0.04 0.085 0.29 25 -10000 0 25
RHOA 0.033 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.029 0.058 -10000 0 -0.27 19 19
CTNNA1 0.033 0.006 -10000 0 -10000 0 0
VCL -0.021 0.068 -10000 0 -0.28 22 22
EFNA1 0.028 0.015 -10000 0 -10000 0 0
LPP -0.023 0.065 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.023 0.082 -10000 0 -0.29 25 25
SEC6/SEC8 -0.007 0.067 -10000 0 -0.27 22 22
MGAT3 -0.024 0.11 -10000 0 -0.29 62 62
HGF/MET 0.004 0.13 -10000 0 -0.29 72 72
HGF 0.034 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.091 -10000 0 -0.26 45 45
actin cable formation 0.054 0.11 0.34 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 0.034 0.005 -10000 0 -10000 0 0
EXOC3 0.032 0.008 -10000 0 -10000 0 0
ACTN1 -0.001 0.071 -10000 0 -0.28 24 24
NCK1/GIT1 0.046 0.016 -10000 0 -10000 0 0
mol:GDP 0.04 0.085 -10000 0 -0.29 25 25
EXOC4 0.034 0.005 -10000 0 -10000 0 0
STX4 -0.002 0.07 -10000 0 -0.28 24 24
PIP5K1C -0.001 0.072 -10000 0 -0.28 24 24
LIMA1 0.012 0.11 -10000 0 -0.54 19 19
ABI1 0.033 0.006 -10000 0 -10000 0 0
ROCK1 0.014 0.1 0.3 13 -0.38 1 14
adherens junction assembly -0.03 0.13 0.3 1 -0.62 12 13
IGF-1R heterotetramer/IGF1 -0.13 0.18 -10000 0 -0.3 247 247
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 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 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.091 -10000 0 -0.26 45 45
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 0.005 0.13 -10000 0 -0.38 52 52
CRKL -0.002 0.11 0.37 1 -0.41 14 15
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 0.03 0.012 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.022 0.12 -10000 0 -0.34 50 50
MAP3K5 -0.012 0.13 0.37 1 -0.41 23 24
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.12 -10000 0 -0.31 51 51
AP1 -0.29 0.24 -10000 0 -0.43 343 343
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
apoptosis -0.54 0.38 -10000 0 -0.77 364 364
STAT3 (dimer) -0.007 0.11 -10000 0 -0.42 16 16
GAB1/CRKL/SHP2/PI3K 0.011 0.14 -10000 0 -0.44 15 15
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.014 0.11 0.36 1 -0.42 10 11
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.032 0.008 -10000 0 -10000 0 0
PTEN 0.025 0.068 -10000 0 -0.54 7 7
ELK1 -0.019 0.085 0.28 10 -0.22 4 14
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.007 0.063 -10000 0 -0.26 5 5
PAK1 0.046 0.099 0.41 15 -10000 0 15
HGF/MET/RANBP10 0.021 0.12 -10000 0 -0.34 50 50
HRAS -0.033 0.2 -10000 0 -0.58 57 57
DOCK1 -0.004 0.11 0.43 2 -0.44 10 12
GAB1 -0.004 0.12 -10000 0 -0.41 17 17
CRK -0.003 0.11 0.37 1 -0.41 14 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.023 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 0.28 10 -0.21 4 14
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 -0.39 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.012 0.097 -10000 0 -0.29 41 41
MET/MUC20 -0.017 0.13 -10000 0 -0.39 52 52
RAP1B 0.002 0.11 0.32 2 -0.4 10 12
RAP1A -0.004 0.1 0.51 1 -0.42 9 10
HGF/MET/RANBP9 0.026 0.12 -10000 0 -0.34 48 48
RAF1 -0.026 0.19 -10000 0 -0.56 56 56
STAT3 -0.007 0.11 -10000 0 -0.42 16 16
cell proliferation 0.025 0.15 0.34 9 -0.39 31 40
RPS6KB1 0.001 0.061 -10000 0 -0.38 7 7
MAPK3 -0.037 0.081 0.55 4 -10000 0 4
MAPK1 -0.004 0.17 0.66 28 -10000 0 28
RANBP9 0.033 0.009 -10000 0 -10000 0 0
MAPK8 -0.004 0.12 0.45 1 -0.38 22 23
SRC -0.007 0.097 -10000 0 -0.36 14 14
PI3K -0.009 0.13 -10000 0 -0.28 83 83
MET/Glomulin -0.013 0.11 -10000 0 -0.35 50 50
SOS1 0.034 0.004 -10000 0 -10000 0 0
MAP2K1 -0.022 0.18 0.48 1 -0.52 54 55
MET -0.023 0.17 -10000 0 -0.54 50 50
MAP4K1 0.002 0.12 0.39 1 -0.42 17 18
PTK2 0.027 0.014 -10000 0 -10000 0 0
MAP2K2 -0.023 0.18 0.48 1 -0.52 55 56
BAD 0.018 0.074 0.35 11 -10000 0 11
MAP2K4 -0.012 0.12 0.35 1 -0.38 23 24
SHP2/GRB2/SOS1/GAB1 0.019 0.14 -10000 0 -0.36 51 51
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
SH3KBP1 0.033 0.027 -10000 0 -0.54 1 1
HGS -0.015 0.077 -10000 0 -0.25 44 44
PLCgamma1/PKC 0.024 0.006 -10000 0 -10000 0 0
HGF 0.034 0.01 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
PTPRJ 0.035 0.016 -10000 0 -10000 0 0
NCK/PLCgamma1 0.025 0.094 -10000 0 -0.24 48 48
PDPK1 0.024 0.087 0.47 8 -10000 0 8
HGF/MET/SHIP 0.007 0.12 -10000 0 -0.34 50 50
LPA receptor mediated events

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
GNB1/GNG2 0.047 0.035 -10000 0 -0.3 3 3
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.061 0.28 3 -0.24 2 5
AP1 -0.21 0.19 -10000 0 -0.33 341 341
mol:PIP3 -0.15 0.16 -10000 0 -0.28 271 271
AKT1 0.005 0.09 -10000 0 -0.33 7 7
PTK2B -0.015 0.08 -10000 0 -0.18 85 85
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 -10000 0 -0.19 5 5
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.014 0.078 0.23 5 -0.28 6 11
NF kappa B1 p50/RelA 0.021 0.04 -10000 0 -0.31 1 1
endothelial cell migration 0.016 0.053 0.27 2 -0.47 5 7
ADCY4 -0.048 0.096 -10000 0 -0.23 44 44
ADCY5 -0.047 0.094 -10000 0 -0.28 14 14
ADCY6 -0.047 0.094 -10000 0 -0.22 44 44
ADCY7 -0.037 0.091 -10000 0 -0.28 17 17
ADCY1 -0.046 0.094 -10000 0 -0.29 13 13
ADCY2 -0.048 0.098 -10000 0 -0.24 47 47
ADCY3 -0.046 0.094 -10000 0 -0.28 13 13
ADCY8 -0.041 0.087 -10000 0 -0.23 30 30
ADCY9 -0.043 0.091 -10000 0 -0.23 34 34
GSK3B -0.014 0.079 0.25 4 -0.22 17 21
arachidonic acid secretion -0.053 0.1 -10000 0 -0.24 59 59
GNG2 0.032 0.026 -10000 0 -0.54 1 1
TRIP6 0.023 0.021 -10000 0 -0.39 1 1
GNAO1 0.019 0.021 -10000 0 -0.26 2 2
HRAS 0.034 0.013 -10000 0 -10000 0 0
NFKBIA 0.026 0.061 0.27 3 -0.25 3 6
GAB1 0.033 0.027 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.051 0.1 -10000 0 -0.86 6 6
JUN -0.065 0.22 -10000 0 -0.54 86 86
LPA/LPA2/NHERF2 0.023 0.016 -10000 0 -10000 0 0
TIAM1 0.033 0.12 -10000 0 -1 6 6
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 0.026 0.056 0.2 44 -10000 0 44
PLCB3 0.036 0.05 0.19 41 -10000 0 41
FOS -0.36 0.27 -10000 0 -0.54 342 342
positive regulation of mitosis -0.053 0.1 -10000 0 -0.24 59 59
LPA/LPA1-2-3 0.007 0.02 -10000 0 -0.18 5 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.029 0.012 -10000 0 -10000 0 0
stress fiber formation 0.016 0.058 -10000 0 -0.27 7 7
GNAZ 0.015 0.045 -10000 0 -0.28 10 10
EGFR/PI3K-beta/Gab1 -0.15 0.17 -10000 0 -0.3 271 271
positive regulation of dendritic cell cytokine production 0.007 0.02 -10000 0 -0.18 5 5
LPA/LPA2/MAGI-3 0.029 0.03 -10000 0 -0.2 3 3
ARHGEF1 0.037 0.054 0.2 12 -0.22 2 14
GNAI2 0.02 0.025 -10000 0 -0.21 5 5
GNAI3 0.02 0.023 -10000 0 -0.22 4 4
GNAI1 -0.11 0.17 -10000 0 -0.34 182 182
LPA/LPA3 0.002 0.01 -10000 0 -0.093 5 5
LPA/LPA2 0.002 0.01 -10000 0 -0.093 5 5
LPA/LPA1 0.007 0.026 -10000 0 -0.25 5 5
HB-EGF/EGFR -0.12 0.2 -10000 0 -0.31 244 244
HBEGF 0.065 0.076 -10000 0 -0.4 4 4
mol:DAG 0.026 0.056 0.2 44 -10000 0 44
cAMP biosynthetic process -0.055 0.1 0.24 1 -0.28 27 28
NFKB1 0.034 0.005 -10000 0 -10000 0 0
SRC 0.032 0.008 -10000 0 -10000 0 0
GNB1 0.033 0.011 -10000 0 -10000 0 0
LYN 0.04 0.069 0.27 19 -0.28 1 20
GNAQ 0.003 0.009 0.057 2 -0.075 5 7
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 0.003 0.016 0.074 2 -0.15 5 7
IL8 -0.19 0.22 0.36 9 -0.39 241 250
PTK2 0.02 0.021 -10000 0 -0.16 4 4
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
CASP3 0.017 0.022 -10000 0 -0.19 5 5
EGFR -0.27 0.29 -10000 0 -0.54 264 264
PLCG1 0.017 0.018 -10000 0 -0.1 3 3
PLD2 0.022 0.025 -10000 0 -0.2 5 5
G12/G13 0.044 0.03 -10000 0 -0.19 5 5
PI3K-beta -0.009 0.088 -10000 0 -0.38 7 7
cell migration 0.028 0.042 -10000 0 -0.25 5 5
SLC9A3R2 0.032 0.015 -10000 0 -10000 0 0
PXN 0.015 0.059 -10000 0 -0.28 7 7
HRAS/GTP -0.054 0.1 -10000 0 -0.25 59 59
RAC1 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.092 0.072 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
PRKCD 0.024 0.058 0.22 8 -0.26 1 9
Gi(beta/gamma) -0.05 0.11 -10000 0 -0.31 27 27
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 59 59
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 0.021 0.039 -10000 0 -0.31 4 4
GNA15 0.016 0.014 -10000 0 -0.087 2 2
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MAPT -0.014 0.079 0.23 5 -0.29 6 11
GNA11 0.015 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.053 0.11 -10000 0 -0.92 6 6
MMP2 0.016 0.053 0.27 2 -0.47 5 7
IL27-mediated 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
TGFB1 0.041 0.009 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response -0.011 0.22 0.7 23 -0.49 10 33
IL27/IL27R/JAK1 0.033 0.28 0.64 17 -1 18 35
TBX21 0.025 0.26 0.54 37 -0.59 38 75
IL12B 0.042 0.027 0.2 11 -10000 0 11
IL12A 0.005 0.062 0.14 6 -0.4 11 17
IL6ST 0.033 0.079 0.24 1 -0.54 8 9
IL27RA/JAK1 0.004 0.23 0.53 3 -1.2 17 20
IL27 -0.021 0.18 0.33 1 -0.54 52 53
TYK2 0.043 0.025 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.19 0.14 -10000 0 -0.78 2 2
T-helper 2 cell differentiation -0.011 0.22 0.7 23 -0.49 10 33
T cell proliferation during immune response -0.011 0.22 0.7 23 -0.49 10 33
MAPKKK cascade 0.011 0.22 0.49 10 -0.7 23 33
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT2 0.034 0.004 -10000 0 -10000 0 0
STAT1 0.06 0.056 0.19 32 -10000 0 32
IL12RB1 0.037 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.05 0.25 0.54 48 -0.63 22 70
IL27/IL27R/JAK2/TYK2 0.01 0.22 0.51 9 -0.72 23 32
positive regulation of T cell mediated cytotoxicity 0.011 0.22 0.49 10 -0.7 23 33
STAT1 (dimer) 0.039 0.32 0.78 25 -1 21 46
JAK2 0.039 0.022 0.23 1 -10000 0 1
JAK1 0.036 0.013 -10000 0 -10000 0 0
STAT2 (dimer) 0.025 0.21 0.46 8 -0.67 23 31
T cell proliferation -0.18 0.25 0.5 5 -0.57 81 86
IL12/IL12R/TYK2/JAK2 0.067 0.19 0.52 2 -0.69 20 22
IL17A -0.19 0.14 -10000 0 -0.78 2 2
mast cell activation -0.011 0.22 0.7 23 -0.49 10 33
IFNG 0.033 0.065 0.14 101 -0.11 9 110
T cell differentiation 0 0.009 0.019 28 -0.024 19 47
STAT3 (dimer) 0.024 0.2 0.46 7 -0.68 22 29
STAT5A (dimer) 0.023 0.21 0.46 7 -0.66 24 31
STAT4 (dimer) 0.021 0.21 0.48 7 -0.67 24 31
STAT4 0.027 0.069 -10000 0 -0.54 7 7
T cell activation -0.005 0.027 0.12 16 -0.12 9 25
IL27R/JAK2/TYK2 0.053 0.24 0.54 3 -1.1 17 20
GATA3 -0.017 0.38 0.62 21 -1.3 34 55
IL18 0.019 0.036 0.14 6 -10000 0 6
positive regulation of mast cell cytokine production 0.024 0.2 0.46 7 -0.66 22 29
IL27/EBI3 0.014 0.14 0.3 5 -0.39 51 56
IL27RA -0.014 0.24 0.52 5 -1.3 17 22
IL6 -0.37 0.26 -10000 0 -0.54 361 361
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
monocyte differentiation 0.002 0.003 -10000 0 -10000 0 0
IL2 -0.009 0.11 0.47 17 -1.2 1 18
IL1B 0.009 0.04 0.14 10 -0.4 4 14
EBI3 0.041 0.026 0.22 2 -10000 0 2
TNF 0.013 0.02 0.14 4 -10000 0 4
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 -0.027 0.094 -10000 0 -0.27 17 17
NT3 (dimer)/TRKC -0.08 0.21 -10000 0 -0.41 138 138
NT3 (dimer)/TRKB -0.24 0.29 -10000 0 -0.48 276 276
SHC/Grb2/SOS1/GAB1/PI3K 0.003 0.073 -10000 0 -10000 0 0
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
BDNF 0.038 0.047 -10000 0 -0.54 2 2
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
DYNLT1 0.032 0.009 -10000 0 -10000 0 0
NTRK1 0.03 0.021 -10000 0 -10000 0 0
NTRK2 -0.23 0.29 -10000 0 -0.54 234 234
NTRK3 0.015 0.1 -10000 0 -0.54 16 16
NT-4/5 (dimer)/TRKB -0.17 0.23 -10000 0 -0.37 260 260
neuron apoptosis 0.12 0.21 0.44 111 -10000 0 111
SHC 2-3/Grb2 -0.13 0.23 -10000 0 -0.49 111 111
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 -0.14 0.24 -10000 0 -0.53 115 115
SHC3 -0.12 0.21 -10000 0 -0.49 91 91
STAT3 (dimer) 0.053 0.076 -10000 0 -0.36 10 10
NT3 (dimer)/TRKA -0.083 0.2 -10000 0 -0.38 132 132
RIN/GDP 0.006 0.11 0.26 3 -0.29 14 17
GIPC1 0.034 0.01 -10000 0 -10000 0 0
KRAS 0.034 0.017 -10000 0 -10000 0 0
DNAJA3 -0.054 0.13 -10000 0 -0.37 57 57
RIN/GTP 0.023 0.019 -10000 0 -0.4 1 1
CCND1 0.014 0.12 -10000 0 -0.78 10 10
MAGED1 0.044 0.035 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.033 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.04 0.026 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.032 0.067 -10000 0 -0.38 10 10
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 0.03 0.012 -10000 0 -10000 0 0
RIT2 0.032 0.027 -10000 0 -0.54 1 1
RIT1 0.028 0.013 -10000 0 -10000 0 0
FRS2 0.032 0.029 -10000 0 -0.54 1 1
DNM1 0.034 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.035 0.15 -10000 0 -0.34 75 75
mol:GDP -0.008 0.15 0.34 4 -0.44 17 21
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.025 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.004 0.096 0.24 1 -0.28 16 17
TIAM1 0.035 0.012 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
BDNF (dimer)/TRKB -0.12 0.2 -10000 0 -0.34 231 231
KIDINS220/CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.039 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2 0.064 0.028 -10000 0 -0.34 1 1
SHC/GRB2/SOS1/GAB1 0.063 0.043 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.01 -10000 0 -10000 0 0
NT3 (dimer) -0.11 0.25 -10000 0 -0.54 130 130
RAP1/GDP 0.002 0.089 -10000 0 -0.24 16 16
KIDINS220/CRKL 0.032 0.008 -10000 0 -10000 0 0
BDNF (dimer) 0.038 0.047 -10000 0 -0.54 2 2
ubiquitin-dependent protein catabolic process 0.029 0.057 -10000 0 -0.34 9 9
Schwann cell development -0.037 0.032 -10000 0 -10000 0 0
EHD4 0.033 0.007 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.075 0.038 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.027 0.066 -10000 0 -0.3 6 6
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.22 -10000 0 -0.35 266 266
ABL1 0.034 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
Rap1/GTP -0.041 0.12 -10000 0 -0.41 26 26
STAT3 0.053 0.076 -10000 0 -0.36 10 10
axon guidance -0.16 0.2 -10000 0 -0.34 266 266
MAPK3 0.048 0.066 0.28 4 -10000 0 4
MAPK1 0.051 0.069 0.28 5 -10000 0 5
CDC42/GDP 0.008 0.11 0.28 6 -0.29 14 20
NTF3 -0.11 0.25 -10000 0 -0.54 130 130
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.038 0.022 -10000 0 -10000 0 0
PI3K 0.006 0.12 -10000 0 -0.4 42 42
FRS3 0.033 0.006 -10000 0 -10000 0 0
FAIM 0.033 0.006 -10000 0 -10000 0 0
GAB1 0.033 0.027 -10000 0 -0.54 1 1
RASGRF1 -0.052 0.14 -10000 0 -0.34 76 76
SOS1 0.034 0.004 -10000 0 -10000 0 0
MCF2L -0.081 0.17 -10000 0 -0.35 136 136
RGS19 0.034 0.021 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.099 0.36 1 -0.43 5 6
Rac1/GDP 0.007 0.11 0.26 5 -0.29 14 19
NGF (dimer)/TRKA/GRIT 0.02 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis -0.027 0.22 0.42 1 -0.75 26 27
NGF (dimer)/TRKA/NEDD4-2 0.029 0.058 -10000 0 -0.34 9 9
MAP2K1 0.064 0.087 0.36 13 -10000 0 13
NGFR -0.055 0.2 -10000 0 -0.54 75 75
NGF (dimer)/TRKA/GIPC/GAIP 0.024 0.025 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0 0.084 -10000 0 -0.26 38 38
FRS2 family/SHP2/GRB2/SOS1 0.087 0.043 -10000 0 -0.3 1 1
NRAS 0.035 0.016 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
PRKCI 0.034 0.017 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.018 0.072 -10000 0 -0.56 4 4
RASA1 0.033 0.011 -10000 0 -10000 0 0
TRKA/c-Abl 0.042 0.023 -10000 0 -10000 0 0
SQSTM1 0.034 0.008 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.099 0.2 -10000 0 -0.31 229 229
NGF (dimer)/TRKA/p62/Atypical PKCs 0.049 0.029 -10000 0 -10000 0 0
MATK 0.038 0.027 -10000 0 -10000 0 0
NEDD4L 0.018 0.095 -10000 0 -0.54 14 14
RAS family/GDP -0.033 0.057 -10000 0 -0.22 17 17
NGF (dimer)/TRKA -0.059 0.14 -10000 0 -0.36 80 80
Rac1/GTP -0.05 0.098 -10000 0 -0.29 38 38
FRS2 family/SHP2/CRK family 0.082 0.046 -10000 0 -0.3 1 1
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.005 0.015 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.1 -10000 0 -0.3 8 8
NFATC4 -0.028 0.081 0.28 3 -0.25 13 16
ERBB2IP 0.034 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.033 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.036 0.087 -10000 0 -0.3 28 28
JUN -0.055 0.071 -10000 0 -10000 0 0
HRAS 0.033 0.013 -10000 0 -10000 0 0
DOCK7 -0.036 0.09 0.26 2 -0.29 28 30
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.019 0.097 -10000 0 -0.31 24 24
AKT1 0.007 0.016 0.13 6 -10000 0 6
BAD -0.005 0.014 -10000 0 -10000 0 0
MAPK10 -0.022 0.071 0.26 4 -0.26 6 10
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.037 0.094 -10000 0 -0.32 28 28
RAF1 -0.038 0.095 -10000 0 -0.34 6 6
ErbB2/ErbB3/neuregulin 2 -0.18 0.17 -10000 0 -0.33 267 267
STAT3 0.01 0.16 -10000 0 -0.84 18 18
cell migration -0.014 0.072 0.29 5 -0.26 3 8
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.26 0.27 -10000 0 -0.67 111 111
FOS -0.34 0.26 -10000 0 -0.49 362 362
NRAS 0.034 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.087 -10000 0 -0.3 28 28
MAPK3 -0.16 0.21 -10000 0 -0.52 83 83
MAPK1 -0.18 0.24 -10000 0 -0.56 97 97
JAK2 -0.033 0.09 0.26 2 -0.29 28 30
NF2 0.004 0.061 -10000 0 -0.67 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.081 -10000 0 -0.28 22 22
NRG1 -0.021 0.16 -10000 0 -0.55 43 43
GRB2/SOS1 0.046 0.018 -10000 0 -10000 0 0
MAPK8 -0.038 0.1 -10000 0 -0.29 32 32
MAPK9 -0.019 0.065 0.26 3 -10000 0 3
ERBB2 -0.022 0.013 -10000 0 -10000 0 0
ERBB3 0.036 0.025 -10000 0 -10000 0 0
SHC1 0.026 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.019 0.026 -10000 0 -0.18 2 2
STAT3 (dimer) 0.011 0.16 -10000 0 -0.82 18 18
RNF41 -0.009 0.014 -10000 0 -10000 0 0
FRAP1 -0.002 0.013 0.11 6 -10000 0 6
RAC1-CDC42/GTP -0.037 0.06 -10000 0 -0.22 28 28
ErbB2/ErbB2/HSP90 (dimer) -0.008 0.023 -10000 0 -10000 0 0
CHRNA1 -0.12 0.16 -10000 0 -0.43 36 36
myelination -0.021 0.089 0.33 6 -10000 0 6
PPP3CB -0.033 0.086 0.25 2 -0.27 27 29
KRAS 0.033 0.017 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.035 0.1 -10000 0 -0.32 2 2
NRG2 -0.35 0.27 -10000 0 -0.54 333 333
mol:GDP 0 0.08 -10000 0 -0.28 22 22
SOS1 0.033 0.004 -10000 0 -10000 0 0
MAP2K2 -0.054 0.1 -10000 0 -0.35 11 11
SRC 0.032 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.033 0.092 0.27 2 -0.29 28 30
MAP2K1 -0.17 0.21 -10000 0 -0.6 50 50
heart morphogenesis -0.036 0.087 -10000 0 -0.3 28 28
RAS family/GDP 0.029 0.11 -10000 0 -0.29 6 6
GRB2 0.032 0.017 -10000 0 -10000 0 0
PRKACA 0.006 0.075 -10000 0 -0.67 6 6
CHRNE -0.006 0.018 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.016 -10000 0 -0.13 6 6
nervous system development -0.036 0.087 -10000 0 -0.3 28 28
CDC42 0.033 0.007 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.27 77 -0.29 14 91
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 17 -0.34 9 26
Syndecan-1/Syntenin 0.072 0.14 0.3 24 -0.34 8 32
MAPK3 0.072 0.13 0.28 29 -0.33 7 36
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 17 -0.34 9 26
Syndecan-1/RANTES 0.076 0.15 0.3 31 -0.38 10 41
Syndecan-1/CD147 0.093 0.15 0.35 13 -0.33 9 22
Syndecan-1/Syntenin/PIP2 0.067 0.13 0.28 24 -0.33 8 32
LAMA5 0.032 0.012 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.065 0.13 0.27 24 -0.33 8 32
MMP7 -0.041 0.19 -10000 0 -0.54 63 63
HGF 0.034 0.01 -10000 0 -10000 0 0
Syndecan-1/CASK 0.058 0.13 0.25 24 -0.29 16 40
Syndecan-1/HGF/MET 0.063 0.18 0.33 11 -0.37 33 44
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 0.27 77 -0.29 14 91
SDC1 0.087 0.13 0.26 91 -0.27 10 101
Syndecan-1/Collagen 0.087 0.14 0.27 77 -0.29 14 91
PPIB 0.033 0.009 -10000 0 -10000 0 0
MET -0.023 0.17 -10000 0 -0.54 50 50
PRKACA 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.092 0.072 -10000 0 -10000 0 0
MAPK1 0.072 0.13 0.29 24 -0.34 6 30
homophilic cell adhesion 0.085 0.14 0.27 77 -0.29 14 91
MMP1 0.11 0.075 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.016 0.18 -10000 0 -0.75 3 3
PCK1 -0.75 0.54 -10000 0 -1 384 384
HNF4A 0.031 0.2 0.71 2 -0.74 3 5
KCNJ11 0.036 0.24 0.79 2 -0.75 3 5
AKT1 0.01 0.15 -10000 0 -0.46 5 5
response to starvation 0.005 0.002 -10000 0 -10000 0 0
DLK1 0.026 0.22 0.87 1 -0.81 3 4
NKX2-1 0.033 0.12 0.64 1 -10000 0 1
ACADM 0.013 0.21 -10000 0 -0.86 8 8
TAT -0.055 0.19 -10000 0 -0.72 13 13
CEBPB 0.034 0.028 -10000 0 -0.54 1 1
CEBPA 0.035 0.045 -10000 0 -0.54 3 3
TTR -0.036 0.26 -10000 0 -0.65 44 44
PKLR 0.033 0.19 -10000 0 -0.79 2 2
APOA1 0.02 0.22 -10000 0 -0.88 3 3
CPT1C 0.026 0.2 0.71 1 -0.75 3 4
ALAS1 0.029 0.14 -10000 0 -0.5 1 1
TFRC -0.018 0.2 0.67 3 -0.55 1 4
FOXF1 0.025 0.021 -10000 0 -10000 0 0
NF1 0.037 0.01 -10000 0 -10000 0 0
HNF1A (dimer) 0.051 0.022 -10000 0 -0.22 1 1
CPT1A 0.023 0.21 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 0.041 0.016 -10000 0 -10000 0 0
GCK 0.021 0.19 -10000 0 -0.75 3 3
CREB1 -0.18 0.14 -10000 0 -0.27 331 331
IGFBP1 0.015 0.14 -10000 0 -0.66 4 4
PDX1 0.041 0.16 -10000 0 -1.1 2 2
UCP2 0.024 0.2 0.65 2 -0.7 3 5
ALDOB 0.021 0.22 -10000 0 -0.81 3 3
AFP -0.053 0.14 0.39 1 -0.37 39 40
BDH1 0.023 0.19 0.67 2 -0.75 3 5
HADH 0.016 0.23 -10000 0 -0.93 5 5
F2 0.036 0.22 -10000 0 -0.82 3 3
HNF1A 0.051 0.022 -10000 0 -0.22 1 1
G6PC -0.098 0.12 -10000 0 -10000 0 0
SLC2A2 0.046 0.16 -10000 0 -0.84 2 2
INS 0.022 0.015 0.25 1 -10000 0 1
FOXA1 -0.006 0.23 0.38 3 -0.53 74 77
FOXA3 -0.11 0.14 0.3 1 -0.26 128 129
FOXA2 0.028 0.27 -10000 0 -0.92 3 3
ABCC8 -0.07 0.43 0.9 1 -0.93 87 88
ALB -0.056 0.15 0.39 1 -0.4 42 43
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.027 0.081 -10000 0 -0.49 7 7
Crk/p130 Cas/Paxillin -0.083 0.14 -10000 0 -0.38 69 69
JUN -0.002 0.15 0.28 3 -0.42 22 25
HRAS 0.034 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.11 0.17 -10000 0 -0.29 61 61
RAP1A 0.034 0.005 -10000 0 -10000 0 0
FRS2 0.032 0.029 -10000 0 -0.54 1 1
RAP1A/GDP 0.025 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.11 0.17 0.35 3 -0.3 58 61
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.053 0.14 -10000 0 -0.31 61 61
RHOA 0.033 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.074 0.15 -10000 0 -0.28 47 47
GRB7 0.029 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.11 0.17 -10000 0 -0.3 59 59
MAPKKK cascade 0.056 0.14 -10000 0 -0.29 42 42
BCAR1 0.029 0.012 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.013 0.2 -10000 0 -0.38 93 93
lamellipodium assembly -0.045 0.16 -10000 0 -0.35 72 72
RET51/GFRalpha1/GDNF/SHC 0.089 0.16 -10000 0 -0.3 45 45
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.042 0.13 -10000 0 -0.31 46 46
RET9/GFRalpha1/GDNF/Shank3 0.047 0.14 -10000 0 -0.31 62 62
MAPK3 0.041 0.13 0.26 9 -0.28 43 52
DOK1 0.036 0.016 -10000 0 -10000 0 0
DOK6 0.031 0.055 -10000 0 -0.54 4 4
PXN 0.034 0.003 -10000 0 -10000 0 0
neurite development 0.042 0.13 0.33 1 -0.37 2 3
DOK5 0.012 0.11 -10000 0 -0.54 18 18
GFRA1 0.025 0.23 -10000 0 -0.54 65 65
MAPK8 0.052 0.12 0.27 4 -0.37 8 12
HRAS/GTP 0.09 0.16 0.3 4 -0.32 44 48
tube development 0.054 0.14 0.31 12 -0.3 58 70
MAPK1 0.043 0.13 0.34 3 -10000 0 3
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.019 0.11 -10000 0 -0.26 59 59
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC 0.032 0.008 -10000 0 -10000 0 0
PDLIM7 0.033 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.11 0.17 0.35 2 -0.31 44 46
SHC1 0.027 0.014 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.088 0.17 -10000 0 -0.3 60 60
RET51/GFRalpha1/GDNF/Dok5 0.084 0.18 -10000 0 -0.3 65 65
PRKCA 0.031 0.013 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
CREB1 0.041 0.12 -10000 0 -0.46 3 3
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.017 0.097 -10000 0 -0.25 41 41
RET51/GFRalpha1/GDNF/Grb7 0.096 0.16 -10000 0 -0.3 45 45
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.071 -10000 0 -10000 0 0
DOK4 0.03 0.012 -10000 0 -10000 0 0
JNK cascade -0.001 0.15 0.28 3 -0.41 22 25
RET9/GFRalpha1/GDNF/FRS2 0.048 0.15 -10000 0 -0.31 63 63
SHANK3 0.032 0.009 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.018 0.099 -10000 0 -0.25 41 41
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.052 0.13 0.26 6 -0.39 5 11
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.059 0.13 0.24 4 -0.27 47 51
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.046 0.11 0.24 5 -0.38 3 8
PI3K -0.042 0.26 0.31 2 -0.55 72 74
SOS1 0.034 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.056 0.14 -10000 0 -0.3 58 58
GRB10 0.029 0.051 -10000 0 -0.54 4 4
activation of MAPKK activity 0.055 0.12 0.26 6 -0.38 2 8
RET51/GFRalpha1/GDNF/FRS2 0.1 0.17 0.35 1 -0.3 61 62
GAB1 0.033 0.027 -10000 0 -0.54 1 1
IRS1 -0.035 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 118 118
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.045 0.11 0.24 5 -0.33 4 9
RET51/GFRalpha1/GDNF/PKC alpha 0.095 0.17 -10000 0 -0.3 57 57
GRB2 0.033 0.017 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GDNF 0.033 0.009 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.068 0.23 -10000 0 -0.38 87 87
Rac1/GTP -0.034 0.2 -10000 0 -0.42 72 72
RET9/GFRalpha1/GDNF 0.036 0.15 -10000 0 -0.34 62 62
GFRalpha1/GDNF 0.037 0.17 -10000 0 -0.4 62 62
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.038 0.11 1 1 -10000 0 1
VDR 0.032 0.037 -10000 0 -0.54 2 2
FAM120B 0.032 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.062 0.077 0.29 14 -10000 0 14
RXRs/LXRs/DNA/Oxysterols 0.089 0.089 -10000 0 -0.37 2 2
MED1 0.029 0.012 -10000 0 -10000 0 0
mol:9cRA 0.01 0.014 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.031 0.13 -10000 0 -0.27 98 98
RXRs/NUR77 0.07 0.092 -10000 0 -0.3 17 17
RXRs/PPAR -0.15 0.14 -10000 0 -0.26 260 260
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RARs/VDR/DNA/Vit D3 0.016 0.13 -10000 0 -0.3 72 72
RARA 0.031 0.012 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
VDR/VDR/DNA 0.032 0.037 -10000 0 -0.54 2 2
RARs/RARs/DNA/9cRA 0.007 0.12 -10000 0 -0.29 72 72
RARG 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 0.061 0.17 0.56 50 -10000 0 50
RARs/THRs/DNA/SMRT -0.03 0.13 -10000 0 -0.27 98 98
THRA -0.002 0.13 -10000 0 -0.54 28 28
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.075 0.069 -10000 0 -0.3 4 4
NR1H4 0.035 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.1 0.088 -10000 0 -0.28 5 5
NR1H2 0.043 0.015 -10000 0 -10000 0 0
NR1H3 0.043 0.031 -10000 0 -0.54 1 1
RXRs/VDR/DNA/Vit D3 0.077 0.062 -10000 0 -0.29 4 4
NR4A1 0.008 0.12 -10000 0 -0.54 23 23
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.057 0.057 -10000 0 -0.2 7 7
RXRG 0.031 0.056 0.18 2 -0.54 4 6
RXR alpha/CCPG 0.052 0.02 -10000 0 -10000 0 0
RXRA 0.042 0.015 -10000 0 -10000 0 0
RXRB 0.044 0.016 -10000 0 -10000 0 0
THRB 0.028 0.057 -10000 0 -0.54 5 5
PPARG -0.38 0.26 -10000 0 -0.54 365 365
PPARD 0.034 0.01 -10000 0 -10000 0 0
TNF 0.082 0.089 -10000 0 -10000 0 0
mol:Oxysterols 0.009 0.013 -10000 0 -10000 0 0
cholesterol transport 0.089 0.089 -10000 0 -0.37 2 2
PPARA 0.031 0.027 -10000 0 -0.54 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.054 0.21 -10000 0 -0.54 77 77
RXRs/NUR77/BCL2 -0.028 0.12 -10000 0 -0.26 83 83
SREBF1 0.083 0.1 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.075 0.07 -10000 0 -0.3 4 4
ABCA1 0.077 0.11 -10000 0 -1 2 2
RARs/THRs 0.006 0.16 -10000 0 -0.32 95 95
RXRs/FXR 0.084 0.065 -10000 0 -0.31 4 4
BCL2 -0.074 0.22 -10000 0 -0.54 94 94
TCGA08_p53

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
CDKN2A 0.027 0.046 0.14 77 -10000 0 77
TP53 0 0.051 -10000 0 -0.19 30 30
Senescence -0.005 0.06 -10000 0 -0.19 36 36
Apoptosis -0.005 0.06 -10000 0 -0.19 36 36
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.009 0.067 0.3 18 -10000 0 18
MDM4 0.028 0.017 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.036 0.19 -10000 0 -0.54 61 61
HRAS 0.034 0.013 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 264 264
AKT -0.018 0.12 0.36 5 -0.29 23 28
FOXO3 0.031 0.01 -10000 0 -10000 0 0
AKT1 0.035 0.016 -10000 0 -10000 0 0
FOXO1 -0.023 0.17 -10000 0 -0.54 47 47
AKT3 0.028 0.019 -10000 0 -10000 0 0
FOXO4 0.034 0.002 -10000 0 -10000 0 0
MET -0.023 0.17 -10000 0 -0.54 50 50
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
PIK3CB 0.033 0.006 -10000 0 -10000 0 0
NRAS 0.035 0.016 -10000 0 -10000 0 0
PIK3CG 0.037 0.021 -10000 0 -10000 0 0
PIK3R3 0.042 0.034 -10000 0 -10000 0 0
PIK3R2 0.035 0.016 -10000 0 -10000 0 0
NF1 0.032 0.009 -10000 0 -10000 0 0
RAS -0.076 0.14 0.23 1 -0.33 86 87
ERBB2 0.028 0.029 -10000 0 -0.54 1 1
proliferation/survival/translation -0.016 0.096 0.3 22 -0.28 2 24
PI3K -0.068 0.16 0.29 11 -0.31 100 111
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
KRAS 0.034 0.017 -10000 0 -10000 0 0
FOXO 0.034 0.081 0.29 10 -0.17 10 20
AKT2 0.033 0.006 -10000 0 -10000 0 0
PTEN 0.025 0.068 -10000 0 -0.54 7 7
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 69 -0.39 12 81
FYN 0.062 0.16 0.39 28 -0.4 18 46
LAT/GRAP2/SLP76 0.071 0.16 0.43 26 -0.4 12 38
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 0.059 0.16 0.35 53 -0.31 27 80
B2M 0.036 0.011 -10000 0 -10000 0 0
IKBKG 0.034 0.07 0.19 50 -10000 0 50
MAP3K8 -0.039 0.19 -10000 0 -0.54 64 64
mol:Ca2+ -0.011 0.017 -10000 0 -0.089 12 12
integrin-mediated signaling pathway 0.037 0.022 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.053 0.18 0.49 22 -0.42 27 49
TRPV6 0.013 0.22 1.3 10 -0.54 17 27
CD28 0.027 0.085 -10000 0 -0.54 10 10
SHC1 0.073 0.18 0.34 75 -0.41 21 96
receptor internalization 0.025 0.18 0.35 26 -0.4 62 88
PRF1 0.038 0.16 0.53 10 -0.79 6 16
KRAS 0.034 0.017 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
COT/AKT1 0.036 0.16 0.34 44 -0.31 34 78
LAT 0.055 0.17 0.4 31 -0.41 21 52
EntrezGene:6955 0.002 0.004 -10000 0 -10000 0 0
CD3D 0.04 0.036 0.21 3 -10000 0 3
CD3E 0.034 0.016 -10000 0 -10000 0 0
CD3G 0.038 0.073 -10000 0 -0.54 5 5
RASGRP2 0.009 0.048 0.16 10 -0.16 27 37
RASGRP1 0.065 0.16 0.42 33 -0.33 15 48
HLA-A 0.041 0.025 0.19 10 -10000 0 10
RASSF5 0.029 0.022 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.037 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.067 0.097 0.22 88 -0.13 2 90
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.009 0.047 -10000 0 -0.18 16 16
PRKCA 0.042 0.1 0.32 25 -0.22 6 31
GRAP2 0.034 0.018 -10000 0 -10000 0 0
mol:IP3 0.003 0.09 0.29 10 -0.33 10 20
EntrezGene:6957 0.003 0.006 0.044 1 -10000 0 1
TCR/CD3/MHC I/CD8 0.025 0.13 0.32 20 -0.31 45 65
ORAI1 -0.02 0.17 -10000 0 -1.1 10 10
CSK 0.047 0.16 0.4 20 -0.4 21 41
B7 family/CD28 0.082 0.17 0.47 23 -0.44 13 36
CHUK 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.042 0.17 0.4 22 -0.37 42 64
PTPN6 0.045 0.15 0.37 25 -0.41 18 43
VAV1 0.044 0.16 0.44 19 -0.41 21 40
Monovalent TCR/CD3 0.023 0.1 0.28 21 -0.36 21 42
CBL 0.03 0.011 -10000 0 -10000 0 0
LCK 0.063 0.16 0.39 30 -0.41 14 44
PAG1 0.062 0.16 0.39 30 -0.41 19 49
RAP1A 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.041 0.17 0.37 26 -0.39 33 59
CD80 0.044 0.037 -10000 0 -10000 0 0
CD86 0.036 0.012 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 0.01 0.066 -10000 0 -0.21 16 16
HRAS 0.034 0.013 -10000 0 -10000 0 0
GO:0035030 0.042 0.14 0.38 27 -0.38 14 41
CD8A 0.003 0.006 0.044 4 -10000 0 4
CD8B 0.041 0.025 0.21 3 -10000 0 3
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDK1/PKC theta 0.071 0.18 0.42 55 -0.38 18 73
CSK/PAG1 0.065 0.16 0.38 31 -0.44 13 44
SOS1 0.034 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.056 0.024 -10000 0 -10000 0 0
GRAP2/SLP76 0.066 0.17 0.46 19 -0.42 16 35
STIM1 0.004 0.1 1.2 3 -10000 0 3
RAS family/GTP 0.076 0.11 0.28 53 -0.18 10 63
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.023 0.19 0.35 27 -0.41 62 89
mol:DAG -0.015 0.067 0.13 2 -0.28 13 15
RAP1A/GDP 0.035 0.048 0.13 51 -10000 0 51
PLCG1 0.032 0.008 -10000 0 -10000 0 0
CD247 0.022 0.11 0.2 8 -0.55 15 23
cytotoxic T cell degranulation 0.038 0.16 0.53 10 -0.71 7 17
RAP1A/GTP 0.002 0.016 -10000 0 -0.059 27 27
mol:PI-3-4-5-P3 0.055 0.17 0.44 26 -0.36 27 53
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.025 0.12 0.33 9 -0.41 10 19
NRAS 0.035 0.016 -10000 0 -10000 0 0
ZAP70 0.038 0.024 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.018 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.046 0.13 0.3 12 -0.4 11 23
MALT1 0.033 0.009 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
CD8 heterodimer 0.033 0.022 0.18 5 -10000 0 5
CARD11 0.038 0.026 -10000 0 -10000 0 0
PRKCB -0.012 0.05 0.16 4 -0.2 13 17
PRKCE 0.046 0.11 0.32 29 -0.22 8 37
PRKCQ 0.06 0.18 0.47 28 -0.4 23 51
LCP2 0.036 0.023 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.06 0.15 0.34 53 -0.27 27 80
IKK complex 0.056 0.092 0.23 71 -10000 0 71
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 0.029 0.13 0.28 49 -0.26 27 76
PDPK1 0.064 0.16 0.38 53 -0.3 24 77
TCR/CD3/MHC I/CD8/Fyn 0.015 0.17 0.4 13 -0.54 18 31
Canonical Wnt signaling pathway

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
HDAC1 0.027 0.042 0.26 5 -10000 0 5
AES 0.026 0.035 0.22 4 -10000 0 4
FBXW11 0.033 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.048 0.024 -10000 0 -0.4 1 1
SMAD4 0.032 0.027 -10000 0 -0.54 1 1
DKK2 0.031 0.054 -10000 0 -0.54 4 4
TLE1 0.01 0.1 0.23 5 -0.55 15 20
MACF1 0.034 0.006 -10000 0 -10000 0 0
CTNNB1 0.15 0.11 0.34 33 -0.41 3 36
WIF1 -0.38 0.26 -10000 0 -0.54 363 363
beta catenin/RanBP3 0.042 0.15 0.5 41 -0.4 3 44
KREMEN2 0.1 0.074 -10000 0 -10000 0 0
DKK1 0.005 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.16 0.1 0.34 31 -0.38 3 34
FZD1 0.033 0.026 -10000 0 -0.54 1 1
AXIN2 0.027 0.28 0.64 46 -1.1 15 61
AXIN1 0.032 0.01 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.069 0.087 -10000 0 -0.54 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.091 0.15 0.41 4 -0.63 11 15
Axin1/APC/GSK3 0.065 0.059 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.06 0.076 0.37 1 -0.54 1 2
HNF1A 0.028 0.041 0.25 6 -10000 0 6
CTBP1 0.025 0.038 0.24 4 -10000 0 4
MYC 0.093 0.44 0.62 128 -1.3 29 157
RANBP3 0.033 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.099 0.069 0.25 2 -0.31 3 5
NKD1 0.031 0.021 -10000 0 -10000 0 0
TCF4 0.019 0.076 0.24 5 -0.54 7 12
TCF3 0.028 0.042 0.26 5 -10000 0 5
WNT1/LRP6/FZD1/Axin1 0.076 0.039 -10000 0 -0.32 1 1
Ran/GTP 0.025 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.003 0.21 0.55 33 -0.54 13 46
LEF1 0.054 0.067 0.26 8 -10000 0 8
DVL1 0.078 0.058 0.25 3 -10000 0 3
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.097 0.17 0.34 3 -0.6 14 17
DKK1/LRP6/Kremen 2 0.079 0.13 0.25 46 -0.29 42 88
LRP6 0.033 0.008 -10000 0 -10000 0 0
CSNK1A1 0.028 0.042 0.25 7 -10000 0 7
NLK 0.035 0.031 0.18 15 -10000 0 15
CCND1 0.11 0.38 0.74 95 -1.2 14 109
WNT1 0.035 0.005 -10000 0 -10000 0 0
GSK3A 0.035 0.005 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -10000 0 -10000 0 0
FRAT1 0.034 0.008 -10000 0 -10000 0 0
PPP2R5D 0.055 0.058 -10000 0 -0.39 3 3
APC 0.038 0.062 0.38 4 -0.3 1 5
WNT1/LRP6/FZD1 0.16 0.1 0.24 248 -0.29 1 249
CREBBP 0.023 0.044 0.25 3 -0.55 1 4
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.033 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.047 0.13 0.24 4 -0.3 93 97
FRAP1 -0.013 0.1 0.34 1 -0.48 17 18
AKT1 -0.04 0.12 0.25 5 -0.28 69 74
INSR 0.034 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.044 0.011 -10000 0 -10000 0 0
mol:GTP -0.003 0.11 0.27 3 -0.24 61 64
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.056 -10000 0 -0.22 8 8
TSC2 0.031 0.01 -10000 0 -10000 0 0
RHEB/GDP -0.012 0.092 -10000 0 -0.26 31 31
TSC1 0.034 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.019 0.13 -10000 0 -0.33 71 71
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.005 0.07 -10000 0 -0.25 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.033 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.008 0.1 0.3 4 -0.35 14 18
MAP3K5 -0.018 0.096 0.2 5 -0.29 49 54
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
apoptosis -0.018 0.096 0.2 5 -0.29 49 54
mol:LY294002 0 0.001 0.001 2 -0.002 61 63
EIF4B -0.008 0.094 0.28 4 -0.32 13 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.016 0.096 0.25 2 -0.29 13 15
eIF4E/eIF4G1/eIF4A1 -0.002 0.067 -10000 0 -0.29 17 17
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.025 0.15 -10000 0 -0.31 102 102
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.076 0.24 13 -0.2 11 24
FKBP1A 0.033 0.012 -10000 0 -10000 0 0
RHEB/GTP 0.005 0.1 0.25 3 -0.25 30 33
mol:Amino Acids 0 0.001 0.001 2 -0.002 61 63
FKBP12/Rapamycin 0.025 0.009 -10000 0 -10000 0 0
PDPK1 -0.051 0.12 0.22 7 -0.29 86 93
EIF4E 0.034 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.038 0.2 -10000 0 -0.57 59 59
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.049 -10000 0 -10000 0 0
TSC1/TSC2 -0.002 0.12 0.29 3 -0.26 61 64
tumor necrosis factor receptor activity 0 0.001 0.002 61 -0.001 2 63
RPS6 0.032 0.027 -10000 0 -0.54 1 1
PPP5C 0.036 0.016 -10000 0 -10000 0 0
EIF4G1 0.033 0.006 -10000 0 -10000 0 0
IRS1 -0.041 0.13 -10000 0 -0.35 72 72
INS 0.033 0.007 -10000 0 -10000 0 0
PTEN 0.025 0.067 -10000 0 -0.54 7 7
PDK2 -0.045 0.12 0.22 9 -0.29 76 85
EIF4EBP1 -0.034 0.25 -10000 0 -1 29 29
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PPP2R5D -0.011 0.098 0.35 3 -0.43 17 20
peptide biosynthetic process 0.019 0.016 -10000 0 -10000 0 0
RHEB 0.034 0.008 -10000 0 -10000 0 0
EIF4A1 0.03 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.005 15 -0.003 5 20
EEF2 0.02 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.017 0.24 -10000 0 -0.97 29 29
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.006 -10000 0 -10000 0 0
mol:S1P 0.001 0.003 0.03 6 -10000 0 6
S1P1/S1P/Gi -0.091 0.16 -10000 0 -0.28 185 185
GNAO1 0.031 0.013 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.041 0.016 -10000 0 -10000 0 0
AKT1 -0.01 0.1 -10000 0 -0.5 16 16
AKT3 -0.014 0.12 0.43 1 -0.53 7 8
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.033 0.006 -10000 0 -10000 0 0
GNAI2 0.035 0.011 -10000 0 -10000 0 0
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.002 0.004 0.035 6 -10000 0 6
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.07 0.14 0.24 2 -0.34 58 60
MAPK3 -0.062 0.13 0.23 1 -0.33 49 50
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 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC -0.065 0.13 0.31 2 -0.33 54 56
S1P/S1P3/Gi -0.07 0.15 0.24 2 -0.34 58 60
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.058 0.14 -10000 0 -0.31 58 58
VEGFA 0.052 0.046 0.22 1 -10000 0 1
S1P/S1P2/Gi -0.074 0.14 -10000 0 -0.25 184 184
VEGFR1 homodimer/VEGFA homodimer 0.062 0.039 0.26 1 -10000 0 1
RHOA 0.033 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.025 0.037 -10000 0 -0.27 5 5
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.063 -10000 0 -0.54 6 6
G12/G13 0.045 0.017 -10000 0 -10000 0 0
GNA14 0.043 0.067 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.033 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.059 0.14 -10000 0 -0.31 58 58
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.035 0.016 -10000 0 -10000 0 0
HSPA8 0.029 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.075 0.19 0.33 1 -0.4 107 108
AKT1 0.038 0.02 -10000 0 -10000 0 0
GSC -0.096 0.4 -10000 0 -1.3 46 46
NKX2-5 0.045 0.049 -10000 0 -10000 0 0
muscle cell differentiation 0.001 0.13 0.48 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 -0.3 15 15
CBFB 0.03 0.014 -10000 0 -10000 0 0
SAP18 0.031 0.009 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.16 0.2 -10000 0 -0.34 273 273
SMAD3/SMAD4/VDR 0.052 0.095 -10000 0 -0.35 6 6
MYC -0.007 0.12 -10000 0 -0.55 25 25
CDKN2B -0.049 0.2 -10000 0 -0.74 20 20
AP1 -0.26 0.29 -10000 0 -0.71 110 110
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.1 -10000 0 -0.38 20 20
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.009 0.11 -10000 0 -0.35 24 24
SP3 0.035 0.008 -10000 0 -10000 0 0
CREB1 0.033 0.006 -10000 0 -10000 0 0
FOXH1 0.018 0.042 -10000 0 -0.18 2 2
SMAD3/SMAD4/GR -0.045 0.14 -10000 0 -0.39 49 49
GATA3 0.034 0.16 -10000 0 -0.53 34 34
SKI/SIN3/HDAC complex/NCoR1 0.017 0.084 -10000 0 -0.38 15 15
MEF2C/TIF2 0.007 0.15 0.34 3 -0.54 25 28
endothelial cell migration -0.058 0.11 0.6 5 -10000 0 5
MAX 0.025 0.024 -10000 0 -10000 0 0
RBBP7 0.037 0.021 -10000 0 -10000 0 0
RBBP4 0.033 0.006 -10000 0 -10000 0 0
RUNX2 0.035 0.018 -10000 0 -10000 0 0
RUNX3 -0.005 0.15 -10000 0 -0.54 35 35
RUNX1 0.017 0.099 -10000 0 -0.54 15 15
CTBP1 0.033 0.008 -10000 0 -10000 0 0
NR3C1 -0.019 0.15 -10000 0 -0.55 39 39
VDR 0.032 0.037 -10000 0 -0.54 2 2
CDKN1A 0.005 0.11 -10000 0 -1.1 3 3
KAT2B 0.001 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.025 0.11 -10000 0 -0.32 32 32
DCP1A 0.033 0.008 -10000 0 -10000 0 0
SKI 0.033 0.007 -10000 0 -10000 0 0
SERPINE1 0.058 0.11 -10000 0 -0.61 5 5
SMAD3/SMAD4/ATF2 0.004 0.092 -10000 0 -0.29 9 9
SMAD3/SMAD4/ATF3 -0.09 0.2 -10000 0 -0.41 130 130
SAP30 0.033 0.009 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.063 0.04 -10000 0 -10000 0 0
JUN -0.26 0.28 -10000 0 -0.71 107 107
SMAD3/SMAD4/IRF7 0.021 0.094 -10000 0 -0.29 8 8
TFE3 0.03 0.045 -10000 0 -0.18 8 8
COL1A2 0.075 0.13 0.41 8 -0.71 5 13
mesenchymal cell differentiation -0.004 0.092 0.27 14 -10000 0 14
DLX1 0.043 0.035 -10000 0 -10000 0 0
TCF3 0.035 0.017 -10000 0 -10000 0 0
FOS -0.37 0.28 -10000 0 -0.56 342 342
SMAD3/SMAD4/Max -0.018 0.089 -10000 0 -0.29 9 9
Cbp/p300/SNIP1 0.061 0.032 -10000 0 -0.32 1 1
ZBTB17 0.027 0.021 -10000 0 -10000 0 0
LAMC1 -0.037 0.14 -10000 0 -0.6 26 26
TGIF2/HDAC complex/SMAD3/SMAD4 0.005 0.091 -10000 0 -0.28 10 10
IRF7 0.039 0.023 0.22 1 -10000 0 1
ESR1 -0.07 0.25 0.22 3 -0.55 106 109
HNF4A 0.032 0.008 -10000 0 -10000 0 0
MEF2C 0.014 0.17 0.42 9 -0.54 29 38
SMAD2-3/SMAD4 0.008 0.11 -10000 0 -0.31 20 20
Cbp/p300/Src-1 0.062 0.039 -10000 0 -0.32 2 2
IGHV3OR16-13 -0.007 0.071 -10000 0 -0.45 10 10
TGIF2/HDAC complex 0.033 0.01 -10000 0 -10000 0 0
CREBBP 0.032 0.028 -10000 0 -0.52 1 1
SKIL 0.044 0.04 -10000 0 -10000 0 0
HDAC1 0.033 0.005 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
SNIP1 0.033 0.006 -10000 0 -10000 0 0
GCN5L2 0.003 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.018 0.13 -10000 0 -0.38 29 29
MSG1/HSC70 -0.21 0.22 -10000 0 -0.4 294 294
SMAD2 0.019 0.053 -10000 0 -0.2 3 3
SMAD3 -0.015 0.063 -10000 0 -0.21 6 6
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.069 -10000 0 -0.31 6 6
SMAD2/SMAD2/SMAD4 0.01 0.053 0.22 6 -0.3 2 8
NCOR1 0.031 0.011 -10000 0 -10000 0 0
NCOA2 0.028 0.014 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
MYOD/E2A 0.048 0.035 -10000 0 -0.4 2 2
SMAD2-3/SMAD4/SP1/MIZ-1 0.074 0.12 -10000 0 -0.33 6 6
IFNB1 -0.012 0.071 0.32 3 -0.3 1 4
SMAD3/SMAD4/MEF2C 0.021 0.18 0.41 1 -0.56 29 30
CITED1 -0.3 0.29 -10000 0 -0.54 293 293
SMAD2-3/SMAD4/ARC105 0.024 0.11 -10000 0 -0.3 14 14
RBL1 0.04 0.031 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.002 0.11 -10000 0 -0.4 18 18
RUNX1-3/PEBPB2 0.021 0.12 -10000 0 -0.35 48 48
SMAD7 -0.18 0.22 -10000 0 -0.52 87 87
MYC/MIZ-1 0.008 0.098 -10000 0 -0.41 25 25
SMAD3/SMAD4 0.032 0.097 0.33 11 -0.38 3 14
IL10 -0.007 0.12 0.36 2 -0.37 30 32
PIASy/HDAC complex 0.026 0.028 -10000 0 -10000 0 0
PIAS3 0.034 0.009 -10000 0 -10000 0 0
CDK2 0.04 0.023 -10000 0 -10000 0 0
IL5 -0.004 0.12 0.4 1 -0.37 28 29
CDK4 0.036 0.011 -10000 0 -10000 0 0
PIAS4 0.026 0.028 -10000 0 -10000 0 0
ATF3 -0.12 0.25 -10000 0 -0.54 126 126
SMAD3/SMAD4/SP1 0.039 0.1 -10000 0 -0.31 8 8
FOXG1 0.042 0.036 -10000 0 -10000 0 0
FOXO3 0.021 0.02 -10000 0 -10000 0 0
FOXO1 -0.018 0.12 -10000 0 -0.39 47 47
FOXO4 0.022 0.019 -10000 0 -10000 0 0
heart looping 0.014 0.17 0.42 9 -0.54 29 38
CEBPB 0.031 0.029 -10000 0 -0.54 1 1
SMAD3/SMAD4/DLX1 0.012 0.093 -10000 0 -0.28 8 8
MYOD1 0.033 0.041 -10000 0 -0.54 2 2
SMAD3/SMAD4/HNF4 0.005 0.091 -10000 0 -0.29 9 9
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 0.006 0.15 -10000 0 -0.36 47 47
SMAD3/SMAD4/SP1-3 0.061 0.11 -10000 0 -0.34 4 4
MED15 0.032 0.008 -10000 0 -10000 0 0
SP1 0.047 0.024 -10000 0 -10000 0 0
SIN3B 0.034 0.014 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.045 0.12 -10000 0 -0.36 26 26
ITGB5 -0.003 0.084 0.33 1 -0.53 2 3
TGIF/SIN3/HDAC complex/CtBP 0.024 0.07 -10000 0 -0.33 12 12
SMAD3/SMAD4/AR -0.045 0.16 -10000 0 -0.39 72 72
AR -0.04 0.2 -10000 0 -0.54 66 66
negative regulation of cell growth -0.023 0.12 -10000 0 -0.38 22 22
SMAD3/SMAD4/MYOD 0.004 0.095 -10000 0 -0.3 11 11
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 -0.38 8 8
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.11 -10000 0 -0.35 24 24
TFDP1 0.033 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.25 0.3 -10000 0 -0.73 107 107
SMAD3/SMAD4/RUNX2 0.005 0.093 -10000 0 -0.27 14 14
TGIF2 0.033 0.01 -10000 0 -10000 0 0
TGIF1 0.031 0.027 -10000 0 -0.54 1 1
ATF2 0.034 0.005 -10000 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin 0.07 0.093 0.23 3 -0.32 16 19
EPHB2 0.042 0.036 -10000 0 -10000 0 0
Syndecan-2/TACI 0.016 0.066 -10000 0 -0.33 16 16
LAMA1 0.033 0.01 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.057 0.17 -10000 0 -0.32 134 134
HRAS 0.034 0.013 -10000 0 -10000 0 0
Syndecan-2/CASK -0.001 0.06 -10000 0 -0.33 16 16
ITGA5 0.034 0.007 -10000 0 -10000 0 0
BAX -0.001 0.064 0.49 2 -10000 0 2
EPB41 0.033 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.015 0.06 -10000 0 -0.3 16 16
LAMA3 -0.15 0.27 -10000 0 -0.54 158 158
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.32 0.28 -10000 0 -0.54 315 315
Syndecan-2/MMP2 0.013 0.073 -10000 0 -0.37 16 16
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.081 -10000 0 -0.4 16 16
dendrite morphogenesis 0.021 0.07 -10000 0 -0.33 16 16
Syndecan-2/GM-CSF 0.02 0.068 -10000 0 -0.33 16 16
determination of left/right symmetry 0 0.071 -10000 0 -0.39 16 16
Syndecan-2/PKC delta 0.017 0.066 -10000 0 -0.33 16 16
GNB2L1 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.041 0.093 0.26 4 -0.3 16 20
MAPK1 0.046 0.096 0.27 3 -0.3 15 18
Syndecan-2/RACK1 0.03 0.062 -10000 0 -0.28 16 16
NF1 0.032 0.009 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0 0.071 -10000 0 -0.39 16 16
ITGA2 0.014 0.1 -10000 0 -0.54 17 17
MAPK8 0.001 0.068 0.34 3 -0.33 17 20
Syndecan-2/alpha2/beta1 Integrin 0.034 0.091 -10000 0 -0.33 23 23
Syndecan-2/Kininogen 0.017 0.066 -10000 0 -0.33 16 16
ITGB1 0.033 0.006 -10000 0 -10000 0 0
SRC 0.041 0.089 0.3 6 -0.28 15 21
Syndecan-2/CASK/Protein 4.1 0.015 0.06 -10000 0 -0.3 16 16
extracellular matrix organization 0.017 0.066 -10000 0 -0.33 16 16
actin cytoskeleton reorganization 0.069 0.093 0.23 3 -0.32 16 19
Syndecan-2/Caveolin-2/Ras -0.15 0.18 -10000 0 -0.32 236 236
Syndecan-2/Laminin alpha3 -0.081 0.16 -10000 0 -0.35 130 130
Syndecan-2/RasGAP 0.042 0.066 -10000 0 -0.27 16 16
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
PRKCD 0.034 0.016 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.071 -10000 0 -0.33 16 16
GO:0007205 0.003 0.005 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.058 -10000 0 -0.27 15 15
RHOA 0.033 0.007 -10000 0 -10000 0 0
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.081 -10000 0 -0.4 16 16
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 0.007 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.016 0.066 -10000 0 -0.33 16 16
TRAPPC4 0.03 0.011 -10000 0 -10000 0 0
CSF2 0.039 0.028 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.017 0.066 -10000 0 -0.33 16 16
Syndecan-2/Syntenin/PI-4-5-P2 0.015 0.06 -10000 0 -0.3 16 16
Syndecan-2/Ezrin 0.015 0.06 -10000 0 -0.3 16 16
PRKACA 0.043 0.096 0.2 97 -0.3 16 113
angiogenesis 0.024 0.074 0.23 1 -0.33 16 17
MMP2 0.028 0.039 -10000 0 -0.54 2 2
IL8 0.047 0.052 -10000 0 -0.54 1 1
calcineurin-NFAT signaling pathway 0.016 0.066 -10000 0 -0.33 16 16
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.021 0.077 -10000 0 -0.4 2 2
alphaM/beta2 Integrin/GPIbA -0.016 0.078 0.29 1 -10000 0 1
alphaM/beta2 Integrin/proMMP-9 0.041 0.097 0.29 2 -10000 0 2
PLAUR 0.067 0.06 -10000 0 -10000 0 0
HMGB1 -0.029 0.045 -10000 0 -0.23 2 2
alphaM/beta2 Integrin/Talin -0.019 0.072 -10000 0 -10000 0 0
AGER -0.035 0.051 -10000 0 -0.38 2 2
RAP1A 0.034 0.005 -10000 0 -10000 0 0
SELPLG 0.034 0.028 -10000 0 -0.54 1 1
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.1 0.14 -10000 0 -0.38 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.092 0.072 -10000 0 -10000 0 0
CYR61 -0.13 0.26 -10000 0 -0.54 143 143
TLN1 0.033 0.006 -10000 0 -10000 0 0
Rap1/GTP 0.061 0.086 -10000 0 -0.34 8 8
RHOA 0.033 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.24 -10000 0 -0.54 118 118
MYH2 0.064 0.093 0.29 5 -0.5 4 9
MST1R 0.042 0.037 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.012 0.067 -10000 0 -10000 0 0
APOB 0.034 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.028 0.039 -10000 0 -0.54 2 2
JAM3 -0.009 0.14 -10000 0 -0.54 34 34
GP1BA 0.036 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.032 0.099 -10000 0 -0.38 19 19
alphaM/beta2 Integrin 0.049 0.082 0.24 3 -0.36 8 11
JAM3 homodimer -0.009 0.14 -10000 0 -0.54 34 34
ICAM2 0.02 0.077 -10000 0 -0.54 9 9
ICAM1 0.039 0.028 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor 0.046 0.086 0.24 3 -0.35 10 13
cell adhesion -0.016 0.078 0.29 1 -10000 0 1
NFKB1 -0.22 0.19 0.4 1 -0.36 297 298
THY1 0.034 0.025 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
Lipoprotein(a) 0.043 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.063 0.13 -10000 0 -0.33 74 74
IL6 -0.52 0.36 0.38 1 -0.74 370 371
ITGB2 -0.022 0.062 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.032 0.11 0.3 9 -10000 0 9
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.2 -10000 0 -0.42 123 123
JAM2 -0.12 0.25 -10000 0 -0.54 133 133
alphaM/beta2 Integrin/ICAM1 0.009 0.092 0.3 1 -10000 0 1
alphaM/beta2 Integrin/uPA/Plg 0.011 0.09 -10000 0 -0.36 1 1
RhoA/GTP 0.044 0.1 -10000 0 -0.41 12 12
positive regulation of phagocytosis 0.037 0.083 0.29 2 -0.35 3 5
Ron/MSP 0.055 0.028 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.034 0.11 0.31 9 -10000 0 9
alphaM/beta2 Integrin/uPAR 0.01 0.095 0.29 1 -10000 0 1
PLAU 0.056 0.052 -10000 0 -10000 0 0
PLAT -0.068 0.21 -10000 0 -0.54 85 85
actin filament polymerization 0.064 0.097 0.3 10 -0.44 5 15
MST1 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.01 0.071 -10000 0 -10000 0 0
TNF -0.21 0.18 0.41 3 -0.6 6 9
RAP1B 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.003 0.085 -10000 0 -10000 0 0
fibrinolysis 0.009 0.088 -10000 0 -0.36 1 1
HCK 0.036 0.022 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation 0.046 0.086 0.24 3 -0.35 10 13
VTN 0.032 0.011 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.11 0.18 -10000 0 -0.38 128 128
LPA 0.032 0.009 -10000 0 -10000 0 0
LRP1 0.034 0.004 -10000 0 -10000 0 0
cell migration 0.029 0.091 0.27 2 -0.36 2 4
FN1 0.13 0.066 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.016 0.075 -10000 0 -10000 0 0
MPO 0.031 0.016 -10000 0 -10000 0 0
KNG1 0.033 0.007 -10000 0 -10000 0 0
RAP1/GDP 0.044 0.011 -10000 0 -10000 0 0
ROCK1 0.063 0.11 0.27 8 -0.42 10 18
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 0.29 2 -10000 0 2
ITGAM -0.028 0.043 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.074 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 -0.11 0.24 -10000 0 -0.54 118 118
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.034 0.11 -10000 0 -0.37 4 4
epithelial cell differentiation 0.086 0.091 -10000 0 -10000 0 0
ITCH 0.046 0.025 -10000 0 -10000 0 0
WWP1 0.049 0.15 0.52 28 -10000 0 28
FYN 0.029 0.037 -10000 0 -0.54 2 2
EGFR -0.27 0.29 -10000 0 -0.54 264 264
PRL 0.033 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis 0.027 0.12 0.37 10 -0.47 1 11
PTPRZ1 -0.36 0.27 -10000 0 -0.54 348 348
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.015 0.1 -10000 0 -0.4 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.012 0.11 -10000 0 -0.4 8 8
ADAM17 0.047 0.025 -10000 0 -10000 0 0
ErbB4/ErbB4 0.03 0.12 0.42 24 -0.4 2 26
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.035 0.11 0.35 1 -0.36 2 3
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 -0.38 8 8
GRIN2B -0.017 0.11 -10000 0 -0.38 6 6
ErbB4/ErbB2/betacellulin 0.027 0.096 -10000 0 -0.38 2 2
STAT1 0.058 0.054 -10000 0 -10000 0 0
HBEGF 0.029 0.051 -10000 0 -0.54 4 4
PRLR 0.07 0.063 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.006 0.14 -10000 0 -0.45 22 22
axon guidance 0.12 0.14 0.47 27 -10000 0 27
NEDD4 0.039 0.06 -10000 0 -0.51 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.073 0.046 -10000 0 -10000 0 0
CBFA2T3 -0.023 0.17 -10000 0 -0.54 47 47
ErbB4/ErbB2/HBEGF 0.036 0.085 -10000 0 -0.33 1 1
MAPK3 0.029 0.12 0.38 6 -0.42 2 8
STAT1 (dimer) 0.053 0.11 0.41 4 -0.36 2 6
MAPK1 0.034 0.12 0.41 8 -0.48 1 9
JAK2 0.032 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.002 0.11 -10000 0 -0.38 7 7
NRG1 -0.015 0.12 -10000 0 -0.4 41 41
NRG3 0.035 0.043 -10000 0 -0.54 2 2
NRG2 -0.35 0.27 -10000 0 -0.54 333 333
NRG4 0.034 0.012 -10000 0 -10000 0 0
heart development 0.12 0.14 0.47 27 -10000 0 27
neural crest cell migration 0.002 0.11 -10000 0 -0.38 7 7
ERBB2 0.021 0.028 0.3 1 -0.37 1 2
WWOX/E4ICDs 0.027 0.1 0.4 2 -0.36 2 4
SHC1 0.027 0.014 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.12 0.16 -10000 0 -0.37 20 20
apoptosis -0.036 0.094 0.33 1 -0.33 9 10
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.18 0.17 -10000 0 -0.43 47 47
ErbB4/ErbB2/epiregulin 0.045 0.093 0.35 4 -0.34 1 5
ErbB4/ErbB4/betacellulin/betacellulin 0.02 0.12 -10000 0 -0.41 8 8
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.086 0.12 0.38 9 -10000 0 9
MDM2 0.028 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 -0.37 6 6
STAT5A 0.11 0.12 0.41 28 -10000 0 28
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) 0.14 0.12 0.44 9 -10000 0 9
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.12 0.12 0.41 24 -10000 0 24
LRIG1 0.015 0.1 -10000 0 -0.54 16 16
EREG 0.044 0.048 -10000 0 -0.54 1 1
BTC 0.011 0.12 -10000 0 -0.54 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.11 0.13 0.47 27 -10000 0 27
ERBB4 0.03 0.12 0.42 24 -0.4 2 26
STAT5B 0.033 0.01 -10000 0 -10000 0 0
YAP1 -0.001 0.12 0.28 1 -0.43 26 27
GRB2 0.033 0.017 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.037 0.081 -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 0.42 10 -0.43 4 14
HIF-2-alpha transcription factor network

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
MMP14 0.036 0.1 0.48 1 -0.67 4 5
oxygen homeostasis 0.025 0.03 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 26 -0.32 5 31
EPO 0.22 0.25 0.68 57 -0.48 2 59
FIH (dimer) 0.056 0.031 0.26 1 -10000 0 1
APEX1 0.057 0.038 0.24 2 -10000 0 2
SERPINE1 0.26 0.24 0.7 48 -0.5 4 52
FLT1 -0.014 0.17 -10000 0 -0.68 20 20
ADORA2A 0.26 0.25 0.66 75 -0.48 4 79
germ cell development 0.25 0.23 0.69 39 -0.49 3 42
SLC11A2 0.26 0.24 0.7 41 -0.5 4 45
BHLHE40 0.18 0.23 0.63 47 -0.49 4 51
HIF1AN 0.056 0.031 0.26 1 -10000 0 1
HIF2A/ARNT/SIRT1 0.17 0.19 0.54 44 -0.36 5 49
ETS1 0.041 0.034 -10000 0 -0.54 1 1
CITED2 0.007 0.14 -10000 0 -0.89 9 9
KDR -0.004 0.15 -10000 0 -0.63 18 18
PGK1 0.26 0.24 0.7 43 -0.49 4 47
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 0.75 26 -0.56 4 30
EPAS1 0.16 0.18 0.47 64 -0.32 10 74
SP1 0.047 0.029 -10000 0 -10000 0 0
ABCG2 0.24 0.26 0.69 39 -0.62 10 49
EFNA1 0.18 0.22 0.65 20 -0.5 4 24
FXN 0.25 0.24 0.65 56 -0.48 3 59
POU5F1 0.25 0.24 0.69 38 -0.51 3 41
neuron apoptosis -0.22 0.26 0.55 4 -0.74 26 30
EP300 0.032 0.008 -10000 0 -10000 0 0
EGLN3 0.081 0.068 0.28 12 -10000 0 12
EGLN2 0.059 0.035 0.23 2 -10000 0 2
EGLN1 0.045 0.034 0.26 1 -10000 0 1
VHL/Elongin B/Elongin C 0.053 0.033 -10000 0 -10000 0 0
VHL 0.035 0.018 -10000 0 -10000 0 0
ARNT 0.044 0.038 0.21 1 -10000 0 1
SLC2A1 0.25 0.24 0.65 65 -0.48 4 69
TWIST1 0.21 0.29 0.64 55 -0.54 31 86
ELK1 0.04 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.14 0.18 0.54 21 -0.4 2 23
VEGFA 0.26 0.25 0.72 46 -0.5 4 50
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.013 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.13 0.17 -9999 0 -0.56 19 19
Syndecan-3/Neurocan 0.043 0.1 -9999 0 -0.47 16 16
POMC 0.035 0.031 -9999 0 -0.54 1 1
EGFR -0.27 0.29 -9999 0 -0.54 264 264
Syndecan-3/EGFR -0.12 0.18 -9999 0 -0.61 19 19
AGRP 0.03 0.015 -9999 0 -10000 0 0
NCSTN 0.028 0.014 -9999 0 -10000 0 0
PSENEN 0.035 0.015 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.032 0.027 -9999 0 -0.54 1 1
APH1A 0.031 0.027 -9999 0 -10000 0 0
NCAN 0.039 0.027 -9999 0 -10000 0 0
long-term memory 0.041 0.096 -9999 0 -0.45 13 13
Syndecan-3/IL8 0.048 0.11 -9999 0 -0.46 16 16
PSEN1 0.033 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.04 0.021 -9999 0 -10000 0 0
FYN 0.029 0.037 -9999 0 -0.54 2 2
limb bud formation -0.002 0.09 -9999 0 -0.48 16 16
MC4R 0.034 0.013 -9999 0 -10000 0 0
SRC 0.032 0.008 -9999 0 -10000 0 0
PTN -0.36 0.27 -9999 0 -0.54 348 348
FGFR/FGF/Syndecan-3 -0.002 0.09 -9999 0 -0.49 16 16
neuron projection morphogenesis -0.12 0.16 -9999 0 -0.56 18 18
Syndecan-3/AgRP 0.034 0.1 -9999 0 -0.47 16 16
Syndecan-3/AgRP/MC4R 0.05 0.1 -9999 0 -0.46 15 15
Fyn/Cortactin 0.038 0.03 -9999 0 -0.4 1 1
SDC3 -0.002 0.091 -9999 0 -0.49 16 16
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.048 0.11 -9999 0 -0.46 16 16
IL8 0.047 0.052 -9999 0 -0.54 1 1
Syndecan-3/Fyn/Cortactin 0.043 0.099 -9999 0 -0.46 13 13
Syndecan-3/CASK -0.003 0.087 -9999 0 -0.47 16 16
alpha-MSH/MC4R 0.049 0.027 -9999 0 -0.4 1 1
Gamma Secretase 0.074 0.054 -9999 0 -0.3 1 1
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.011 0.095 0.34 9 -0.28 12 21
TBX21 -0.13 0.37 0.73 5 -1.2 37 42
B2M 0.038 0.013 -10000 0 -10000 0 0
TYK2 0.017 0.036 -10000 0 -10000 0 0
IL12RB1 0.018 0.036 -10000 0 -10000 0 0
GADD45B -0.07 0.28 0.7 2 -0.8 37 39
IL12RB2 0.029 0.074 0.25 6 -0.55 1 7
GADD45G -0.06 0.26 0.69 3 -0.73 34 37
natural killer cell activation -0.007 0.022 0.16 1 -10000 0 1
RELB 0.036 0.019 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL18 0.045 0.045 0.23 2 -10000 0 2
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 0.59 8 -0.59 46 54
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 60 64
CD4 -0.008 0.031 -10000 0 -10000 0 0
SOCS1 0.032 0.012 -10000 0 -10000 0 0
EntrezGene:6955 -0.014 0.015 -10000 0 -10000 0 0
CD3D 0.003 0.05 -10000 0 -10000 0 0
CD3E -0.001 0.033 -10000 0 -10000 0 0
CD3G 0.004 0.081 -10000 0 -0.56 5 5
IL12Rbeta2/JAK2 0.027 0.074 0.3 7 -0.41 1 8
CCL3 -0.085 0.25 0.78 1 -0.81 18 19
CCL4 -0.085 0.25 0.78 1 -0.81 18 19
HLA-A 0.042 0.026 0.19 13 -10000 0 13
IL18/IL18R 0.058 0.14 0.39 11 -0.36 42 53
NOS2 -0.085 0.25 0.59 9 -0.58 67 76
IL12/IL12R/TYK2/JAK2/SPHK2 0.009 0.098 0.34 9 -0.29 13 22
IL1R1 -0.17 0.43 0.7 2 -1.2 60 62
IL4 0.038 0.03 -10000 0 -10000 0 0
JAK2 0.017 0.037 0.25 1 -10000 0 1
EntrezGene:6957 -0.011 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.002 0.15 0.36 14 -0.46 13 27
RAB7A -0.043 0.24 0.65 3 -0.71 24 27
lysosomal transport -0.04 0.23 0.63 4 -0.67 24 28
FOS -0.83 0.6 0.57 1 -1.2 364 365
STAT4 (dimer) -0.033 0.27 0.62 9 -0.68 40 49
STAT5A (dimer) -0.06 0.26 0.57 8 -0.6 55 63
GZMA -0.091 0.24 0.57 7 -0.59 61 68
GZMB -0.09 0.26 0.7 6 -0.87 18 24
HLX 0.025 0.038 -10000 0 -0.54 2 2
LCK -0.084 0.27 0.69 9 -0.63 60 69
TCR/CD3/MHC II/CD4 -0.12 0.16 0.28 5 -0.44 61 66
IL2/IL2R 0.087 0.056 0.37 4 -0.32 1 5
MAPK14 -0.057 0.28 0.63 7 -0.75 41 48
CCR5 -0.066 0.28 0.73 8 -0.76 36 44
IL1B 0.016 0.066 0.25 1 -0.55 4 5
STAT6 -0.039 0.18 0.38 8 -0.66 27 35
STAT4 0.027 0.069 -10000 0 -0.54 7 7
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT1 0.058 0.054 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
NFKB2 0.035 0.012 -10000 0 -10000 0 0
IL12B 0.01 0.047 0.24 3 -10000 0 3
CD8A 0.005 0.009 -10000 0 -10000 0 0
CD8B 0.042 0.026 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.012 0.094 0.28 12 -0.33 10 22
IL2RB 0.035 0.022 0.18 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.26 0.62 9 -0.63 39 48
IL2RG 0.043 0.034 -10000 0 -10000 0 0
IL12 0.007 0.089 0.28 4 -0.41 11 15
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
CD247 -0.004 0.11 0.2 8 -0.55 15 23
IL2 0.033 0.027 -10000 0 -0.54 1 1
SPHK2 0.034 0.005 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.093 0.24 1 -0.56 11 12
IL12/IL12R/TYK2/JAK2 -0.099 0.27 0.67 8 -0.66 61 69
MAP2K3 -0.069 0.29 0.62 8 -0.75 48 56
RIPK2 0.029 0.021 0.18 6 -10000 0 6
MAP2K6 -0.061 0.27 0.62 8 -0.71 45 53
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.012 0.033 -10000 0 -10000 0 0
IL18RAP -0.01 0.16 -10000 0 -0.55 42 42
IL12Rbeta1/TYK2 0.03 0.046 0.25 1 -10000 0 1
EOMES 0.042 0.1 -10000 0 -0.61 3 3
STAT1 (dimer) -0.013 0.26 0.67 15 -0.6 37 52
T cell proliferation -0.03 0.22 0.53 9 -0.54 40 49
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.037 0.031 0.21 1 -0.55 1 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.02 0.23 0.52 2 -0.62 38 40
ATF2 -0.055 0.26 0.6 7 -0.71 38 45
Thromboxane A2 receptor signaling

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
TGM2 0.046 0.041 -10000 0 -10000 0 0
GNB1/GNG2 -0.019 0.054 -10000 0 -0.18 47 47
AKT1 0.059 0.13 0.4 19 -0.28 9 28
EGF -0.15 0.27 -10000 0 -0.54 162 162
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.029 0.053 0.26 2 -10000 0 2
mol:Ca2+ 0.059 0.16 0.48 16 -0.3 44 60
LYN 0.026 0.051 0.26 3 -10000 0 3
RhoA/GTP 0.025 0.066 0.21 9 -0.14 6 15
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK 0.057 0.17 0.49 18 -0.34 44 62
GNG2 0.032 0.026 -10000 0 -0.54 1 1
ARRB2 0.031 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.014 0.12 -10000 0 -0.6 14 14
G beta5/gamma2 -0.013 0.075 -10000 0 -0.24 44 44
PRKCH 0.052 0.17 0.5 15 -0.36 44 59
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 0.18 8 -0.54 5 13
G12 family/GTP 0.005 0.11 -10000 0 -0.3 42 42
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
ADRBK2 0.03 0.037 -10000 0 -0.54 2 2
RhoA/GTP/ROCK1 0.044 0.012 -10000 0 -10000 0 0
mol:GDP -0.041 0.13 0.38 13 -0.46 9 22
mol:NADP 0.034 0.006 -10000 0 -10000 0 0
RAB11A 0.033 0.006 -10000 0 -10000 0 0
PRKG1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 0.058 0.18 0.61 10 -0.37 44 54
cell morphogenesis 0.044 0.012 -10000 0 -10000 0 0
PLCB2 0.05 0.22 0.7 8 -0.5 45 53
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 0.055 0.18 0.52 15 -0.37 45 60
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.034 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.053 0.22 0.72 8 -0.51 46 54
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 0.052 0.13 0.41 19 -0.24 14 33
TGM2/GTP 0.055 0.2 0.67 9 -0.41 39 48
MAPK11 0.05 0.13 0.41 19 -0.23 32 51
ARHGEF1 0.045 0.11 0.34 17 -0.19 14 31
GNAI2 0.033 0.01 -10000 0 -10000 0 0
JNK cascade 0.059 0.18 0.52 16 -0.38 45 61
RAB11/GDP 0.031 0.01 -10000 0 -10000 0 0
ICAM1 0.057 0.15 0.45 20 -0.28 44 64
cAMP biosynthetic process 0.054 0.17 0.57 10 -0.34 40 50
Gq family/GTP/EBP50 0.033 0.047 0.16 2 -0.22 6 8
actin cytoskeleton reorganization 0.044 0.012 -10000 0 -10000 0 0
SRC 0.027 0.052 0.26 2 -10000 0 2
GNB5 0.032 0.026 -10000 0 -0.54 1 1
GNB1 0.034 0.011 -10000 0 -10000 0 0
EGF/EGFR -0.063 0.11 0.26 3 -0.29 41 44
VCAM1 0.053 0.16 0.46 18 -0.31 47 65
TP beta/Gq family/GDP/G beta5/gamma2 0.014 0.12 -10000 0 -0.6 14 14
platelet activation 0.063 0.16 0.48 19 -0.3 37 56
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 0.057 0.2 0.65 9 -0.42 44 53
EGFR -0.27 0.29 -10000 0 -0.54 264 264
TXA2/TP alpha 0.057 0.21 0.7 8 -0.46 42 50
Gq family/GTP 0.009 0.051 0.22 1 -0.22 17 18
YES1 0.029 0.057 0.26 2 -0.43 1 3
GNAI2/GTP 0.03 0.04 -10000 0 -0.24 4 4
PGD2/DP 0.023 0.044 0.12 8 -0.4 5 13
SLC9A3R1 0.058 0.056 -10000 0 -10000 0 0
FYN 0.026 0.055 0.27 1 -0.29 2 3
mol:NO 0.034 0.006 -10000 0 -10000 0 0
GNA15 0.036 0.019 -10000 0 -10000 0 0
PGK/cGMP 0.045 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.011 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.066 0.056 -10000 0 -0.34 1 1
NOS3 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.063 0.18 0.5 16 -0.35 39 55
PRKCB 0.053 0.17 0.52 13 -0.35 46 59
PRKCE 0.055 0.17 0.57 11 -0.35 44 55
PRKCD 0.053 0.18 0.54 13 -0.38 45 58
PRKCG 0.056 0.18 0.58 11 -0.38 44 55
muscle contraction 0.054 0.21 0.68 9 -0.47 45 54
PRKCZ 0.056 0.17 0.5 16 -0.34 45 61
ARR3 0.034 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.044 0.048 -10000 0 -0.25 5 5
PRKCQ 0.059 0.18 0.47 22 -0.35 45 67
MAPKKK cascade 0.054 0.2 0.65 9 -0.44 45 54
SELE 0.049 0.18 0.46 19 -0.38 48 67
TP beta/GNAI2/GDP/G beta/gamma 0.062 0.048 -10000 0 -0.34 1 1
ROCK1 0.033 0.006 -10000 0 -10000 0 0
GNA14 0.043 0.067 -10000 0 -0.54 4 4
chemotaxis 0.049 0.25 0.75 8 -0.59 48 56
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.033 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.026 0.005 -10000 0 -10000 0 0
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 0.004 0.081 -10000 0 -0.39 6 6
BAG4 0.028 0.015 -10000 0 -10000 0 0
PKC zeta/ceramide -0.012 0.067 0.14 9 -0.28 8 17
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BAX 0.008 0.049 -10000 0 -0.35 5 5
RIPK1 0.033 0.006 -10000 0 -10000 0 0
AKT1 0.009 0.076 0.72 5 -10000 0 5
BAD -0.013 0.07 0.18 2 -0.32 6 8
SMPD1 0.019 0.063 0.24 6 -0.25 10 16
RB1 -0.012 0.067 -10000 0 -0.3 7 7
FADD/Caspase 8 0.032 0.12 0.29 9 -0.42 8 17
MAP2K4 -0.013 0.07 -10000 0 -0.35 6 6
NSMAF 0.028 0.028 -10000 0 -0.54 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.007 0.073 0.26 5 -0.35 4 9
EGF -0.15 0.27 -10000 0 -0.54 162 162
mol:ceramide -0.012 0.074 0.16 34 -0.29 8 42
MADD 0.034 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.023 0.12 -10000 0 -0.41 46 46
ASAH1 0.027 0.042 -10000 0 -0.54 2 2
negative regulation of cell cycle -0.014 0.067 -10000 0 -0.29 7 7
cell proliferation -0.11 0.14 -10000 0 -0.27 172 172
BID -0.015 0.19 -10000 0 -0.68 33 33
MAP3K1 -0.011 0.073 0.2 1 -0.34 6 7
EIF2A -0.004 0.073 0.27 7 -0.26 3 10
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 -0.26 8 10
FADD 0.029 0.1 0.28 2 -0.42 4 6
KSR1 -0.006 0.073 0.21 6 -0.33 5 11
MAPK8 -0.008 0.07 -10000 0 -0.28 9 9
PRKRA -0.012 0.07 0.2 1 -0.34 5 6
PDGFA -0.018 0.16 -10000 0 -0.54 45 45
TRAF2 0.034 0.012 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 250 250
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.012 0.073 0.16 34 -0.29 8 42
CTSD 0.046 0.042 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.049 0.01 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.11 0.15 -10000 0 -0.28 172 172
PRKCD 0.034 0.016 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.023 0.12 -10000 0 -0.41 46 46
RelA/NF kappa B1 0.049 0.01 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.034 0.03 0.18 5 -0.54 1 6
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.008 0.09 -10000 0 -0.32 18 18
TNFR1A/BAG4/TNF-alpha 0.053 0.034 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.021 0.12 -10000 0 -0.4 45 45
MAP2K1 -0.007 0.072 0.29 4 -0.34 4 8
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
CYCS 0.027 0.082 0.23 21 -0.25 6 27
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.023 -10000 0 -10000 0 0
EIF2AK2 -0.007 0.069 0.22 5 -0.3 5 10
TNF-alpha/TNFR1A/FAN 0.057 0.036 -10000 0 -0.33 1 1
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.023 0.092 -10000 0 -0.43 13 13
MAP2K2 -0.007 0.072 0.29 4 -0.33 4 8
SMPD3 -0.001 0.11 0.24 3 -0.3 54 57
TNF 0.038 0.023 -10000 0 -10000 0 0
PKC zeta/PAR4 0.025 0.021 -10000 0 -0.4 1 1
mol:PHOSPHOCHOLINE 0.083 0.12 0.23 189 -0.22 3 192
NF kappa B1/RelA/I kappa B alpha 0.075 0.031 -10000 0 -0.3 1 1
AIFM1 0.026 0.082 0.21 30 -0.24 7 37
BCL2 -0.074 0.22 -10000 0 -0.54 94 94
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.008 0.23 -10000 0 -0.9 24 24
NCK1/PAK1/Dok-R -0.033 0.094 -10000 0 -0.41 24 24
NCK1/Dok-R 0.017 0.24 -10000 0 -1 23 23
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
mol:beta2-estradiol -0.001 0.04 0.23 14 -10000 0 14
RELA 0.034 0.005 -10000 0 -10000 0 0
SHC1 0.028 0.014 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
F2 0.018 0.047 0.27 13 -10000 0 13
TNIP2 0.033 0.013 -10000 0 -10000 0 0
NF kappa B/RelA 0.043 0.23 -10000 0 -0.94 23 23
FN1 0.13 0.066 -10000 0 -10000 0 0
PLD2 -0.004 0.23 -10000 0 -1 23 23
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB14 -0.001 0.19 -10000 0 -0.54 52 52
ELK1 0.005 0.22 -10000 0 -0.94 23 23
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.043 0.045 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.094 0.25 -10000 0 -0.96 23 23
CDKN1A -0.002 0.19 -10000 0 -0.67 20 20
ITGA5 0.034 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.016 0.24 -10000 0 -1 23 23
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:NO 0.017 0.18 -10000 0 -0.65 24 24
PLG -0.005 0.23 -10000 0 -1 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.002 0.21 -10000 0 -0.84 24 24
GRB2 0.033 0.017 -10000 0 -10000 0 0
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
ANGPT2 -0.074 0.23 -10000 0 -0.66 34 34
BMX -0.16 0.28 -10000 0 -1.3 23 23
ANGPT1 -0.013 0.21 -10000 0 -1.2 14 14
tube development -0.012 0.2 -10000 0 -0.73 21 21
ANGPT4 0.032 0.008 -10000 0 -10000 0 0
response to hypoxia -0.001 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.003 0.28 -10000 0 -1.1 23 23
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 375 375
STAT5A (dimer) -0.001 0.23 -10000 0 -0.84 21 21
mol:L-citrulline 0.017 0.18 -10000 0 -0.65 24 24
AGTR1 -0.18 0.3 -10000 0 -0.54 206 206
MAPK14 -0.003 0.26 -10000 0 -1.1 25 25
Tie2/SHP2 0.001 0.21 -10000 0 -1 15 15
TEK -0.004 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 -0.005 0.22 -10000 0 -0.96 23 23
Tie2/Ang1/GRB7 0.005 0.24 -10000 0 -1.1 23 23
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.004 0.24 -10000 0 -1 23 23
PI3K -0.004 0.26 -10000 0 -1 24 24
FES -0.01 0.26 -10000 0 -1.1 25 25
Crk/Dok-R 0.017 0.24 -10000 0 -1 23 23
Tie2/Ang1/ABIN2 0.012 0.25 -10000 0 -1.1 23 23
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.013 0.21 -10000 0 -0.8 24 24
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.033 0.23 -10000 0 -0.82 24 24
Tie2/Ang2 -0.027 0.26 -10000 0 -1 21 21
Tie2/Ang1 0 0.25 -10000 0 -1.1 23 23
FOXO1 0.007 0.22 -10000 0 -0.81 25 25
ELF1 0.035 0.027 -10000 0 -10000 0 0
ELF2 0.001 0.23 -10000 0 -1 23 23
mol:Choline -0.002 0.22 -10000 0 -0.99 23 23
cell migration -0.015 0.053 -10000 0 -0.23 24 24
FYN -0.018 0.22 -10000 0 -0.84 21 21
DOK2 0.025 0.039 -10000 0 -0.54 2 2
negative regulation of cell cycle 0.002 0.17 -10000 0 -0.6 20 20
ETS1 0.031 0.056 -10000 0 -0.29 11 11
PXN 0.038 0.2 -10000 0 -0.68 24 24
ITGB1 0.033 0.006 -10000 0 -10000 0 0
NOS3 0.012 0.2 -10000 0 -0.74 24 24
RAC1 0.034 0.005 -10000 0 -10000 0 0
TNF 0.037 0.054 0.26 1 -0.25 13 14
MAPKKK cascade -0.002 0.22 -10000 0 -0.99 23 23
RASA1 0.033 0.011 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.003 0.24 -10000 0 -1 22 22
NCK1 0.034 0.005 -10000 0 -10000 0 0
vasculogenesis 0.02 0.16 -10000 0 -0.58 24 24
mol:Phosphatidic acid -0.002 0.22 -10000 0 -0.99 23 23
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.017 0.18 -10000 0 -0.65 24 24
Rac1/GTP 0.014 0.21 -10000 0 -0.8 24 24
MMP2 -0.004 0.24 -10000 0 -1 23 23
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.18 3 -10000 0 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.1 -10000 0 -0.38 20 20
IRAK/TOLLIP 0.038 0.014 -10000 0 -10000 0 0
IKBKB 0.029 0.013 -10000 0 -10000 0 0
IKBKG 0.034 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.054 0.044 0.25 2 -0.4 3 5
IL1A 0.036 0.017 -10000 0 -10000 0 0
IL1B -0.017 0.12 -10000 0 -0.42 40 40
IRAK/TRAF6/p62/Atypical PKCs 0.064 0.027 -10000 0 -10000 0 0
IL1R2 0.038 0.055 -10000 0 -0.54 3 3
IL1R1 -0.028 0.18 -10000 0 -0.54 55 55
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.029 0.13 -10000 0 -0.42 31 31
TOLLIP 0.033 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.038 0.067 -10000 0 -0.35 1 1
JUN -0.05 0.1 -10000 0 -0.27 80 80
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.022 0.19 -10000 0 -0.37 108 108
IL1 alpha/IL1R1/IL1RAP/MYD88 0.041 0.13 -10000 0 -0.32 55 55
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.053 0.13 -10000 0 -0.3 55 55
IL1 beta fragment/IL1R1/IL1RAP -0.021 0.16 -10000 0 -0.35 87 87
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.01 0.05 -10000 0 -0.27 11 11
IRAK1 0.019 0.011 -10000 0 -10000 0 0
IL1RN/IL1R1 0.016 0.15 -10000 0 -0.39 55 55
IRAK4 0.034 0.005 -10000 0 -10000 0 0
PRKCI 0.034 0.017 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.006 0.12 -10000 0 -0.4 42 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.021 0.14 -10000 0 -0.42 32 32
CHUK 0.034 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.021 0.16 -10000 0 -0.35 87 87
IL1 beta/IL1R2 0.007 0.12 -10000 0 -0.36 43 43
IRAK/TRAF6/TAK1/TAB1/TAB2 0.045 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.032 0.18 -10000 0 -0.34 107 107
IRAK3 0.035 0.033 -10000 0 -0.54 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.006 0.15 -10000 0 -0.32 85 85
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.002 0.1 -10000 0 -0.38 12 12
IL1 alpha/IL1R1/IL1RAP 0.024 0.13 -10000 0 -0.34 55 55
RELA 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.034 0.008 -10000 0 -10000 0 0
MYD88 0.034 0.011 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.053 0.028 -10000 0 -10000 0 0
IL1RAP 0.033 0.006 -10000 0 -10000 0 0
UBE2N 0.034 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.021 0.12 -10000 0 -0.29 80 80
CASP1 -0.013 0.15 -10000 0 -0.54 38 38
IL1RN/IL1R2 0.067 0.056 0.25 7 -0.4 3 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.004 0.16 -10000 0 -0.34 87 87
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.004 0.13 -10000 0 -0.35 58 58
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
IL1RN 0.054 0.049 -10000 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.045 0.016 -10000 0 -10000 0 0
MAP2K6 0.014 0.053 0.36 1 -0.28 10 11
Coregulation of Androgen receptor activity

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
NRIP1 0.029 0.065 -10000 0 -0.54 6 6
SVIL 0.022 0.084 -10000 0 -0.54 11 11
ZNF318 0.03 0.008 -10000 0 -10000 0 0
JMJD2C 0.007 0.01 0.12 4 -10000 0 4
T-DHT/AR/Ubc9 -0.036 0.14 -10000 0 -0.35 64 64
CARM1 0.035 0.013 -10000 0 -10000 0 0
PRDX1 0.034 0.014 -10000 0 -10000 0 0
PELP1 0.031 0.01 -10000 0 -10000 0 0
CTNNB1 0.031 0.045 -10000 0 -0.54 3 3
AKT1 0.034 0.017 -10000 0 -10000 0 0
PTK2B 0.028 0.014 -10000 0 -10000 0 0
MED1 0.028 0.012 -10000 0 -10000 0 0
MAK 0.037 0.032 -10000 0 -10000 0 0
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.035 0.008 -10000 0 -10000 0 0
GSN -0.11 0.25 -10000 0 -0.54 129 129
NCOA2 0.028 0.014 -10000 0 -10000 0 0
NCOA6 0.034 0.008 -10000 0 -10000 0 0
DNA-PK 0.053 0.03 -10000 0 -10000 0 0
NCOA4 0.033 0.026 -10000 0 -0.54 1 1
PIAS3 0.033 0.008 -10000 0 -10000 0 0
cell proliferation 0 0.066 -10000 0 -0.45 5 5
XRCC5 0.033 0.006 -10000 0 -10000 0 0
UBE3A 0.034 0.009 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.052 0.13 -10000 0 -0.31 85 85
FHL2 -0.1 0.32 -10000 0 -0.96 57 57
RANBP9 0.035 0.009 -10000 0 -10000 0 0
JMJD1A -0.027 0.061 -10000 0 -0.14 119 119
CDK6 0.028 0.064 -10000 0 -0.54 6 6
TGFB1I1 0.029 0.045 -10000 0 -0.54 3 3
T-DHT/AR/CyclinD1 -0.037 0.16 -10000 0 -0.36 76 76
XRCC6 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.056 0.17 -10000 0 -0.36 81 81
CTDSP1 0.034 0.006 -10000 0 -10000 0 0
CTDSP2 0.031 0.008 -10000 0 -10000 0 0
BRCA1 0.037 0.021 -10000 0 -10000 0 0
TCF4 0.023 0.068 -10000 0 -0.54 7 7
CDKN2A 0.051 0.053 -10000 0 -10000 0 0
SRF 0.021 0.057 -10000 0 -0.15 43 43
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 0.033 0.006 -10000 0 -10000 0 0
AOF2 0.001 0.002 -10000 0 -10000 0 0
APPL1 0.015 0.014 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.04 0.14 -10000 0 -0.36 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 0.18 5 -0.54 1 6
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 -0.32 80 80
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 -0.017 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 0.088 -10000 0 -0.54 10 10
PIAS1 0.035 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.035 0.049 1 -0.071 137 138
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.037 0.016 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.043 0.14 -10000 0 -0.32 85 85
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.004 0.053 -10000 0 -10000 0 0
CCND3 0.033 0.006 -10000 0 -10000 0 0
TGIF1 0.03 0.027 -10000 0 -0.54 1 1
FKBP4 0.037 0.024 -10000 0 -10000 0 0
Osteopontin-mediated events

Figure 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
IKK alpha homodimer 0.098 0.076 0.32 5 -0.28 4 9
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.1 0.38 10 -10000 0 10
alphaV/beta3 Integrin/Osteopontin/Src 0.098 0.072 0.26 2 -0.39 4 6
AP1 -0.14 0.22 0.49 1 -0.46 89 90
ILK 0.076 0.073 0.36 2 -0.3 4 6
bone resorption 0.06 0.07 -10000 0 -10000 0 0
PTK2B 0.027 0.014 -10000 0 -10000 0 0
PYK2/p130Cas 0.1 0.089 -10000 0 -0.28 4 4
ITGAV 0.04 0.029 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.048 0.024 -10000 0 -0.4 1 1
alphaV/beta3 Integrin/Osteopontin 0.12 0.077 0.32 3 -0.33 4 7
MAP3K1 0.078 0.078 0.3 10 -0.3 5 15
JUN -0.064 0.22 -10000 0 -0.54 86 86
MAPK3 0.078 0.095 0.34 17 -0.28 3 20
MAPK1 0.077 0.092 0.33 13 -0.28 4 17
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.063 0.077 0.29 9 -0.29 6 15
ITGB3 0.041 0.021 -10000 0 -10000 0 0
NFKBIA 0.076 0.098 0.34 21 -10000 0 21
FOS -0.36 0.27 -10000 0 -0.54 342 342
CD44 0.034 0.011 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
PLAU 0.083 0.15 0.47 15 -0.53 1 16
NF kappa B1 p50/RelA 0.14 0.1 0.41 14 -10000 0 14
BCAR1 0.029 0.012 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.061 0.033 -10000 0 -0.39 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.079 0.074 0.31 8 -0.3 4 12
VAV3 0.062 0.095 0.29 13 -0.29 11 24
MAP3K14 0.086 0.082 0.3 10 -0.3 4 14
ROCK2 0.032 0.026 -10000 0 -0.54 1 1
SPP1 0.094 0.086 -10000 0 -0.54 3 3
RAC1 0.034 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.071 0.087 0.29 5 -0.27 10 15
MMP2 -0.13 0.17 0.47 1 -0.41 72 73
Reelin signaling pathway

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
CDK5R1/CDK5 0.048 0.022 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 64 64
CRKL 0.032 0.008 -10000 0 -10000 0 0
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
FYN 0.029 0.037 -10000 0 -0.54 2 2
ITGA3 0.029 0.029 -10000 0 -0.54 1 1
RELN/VLDLR/Fyn -0.011 0.16 -10000 0 -0.36 81 81
MAPK8IP1/MKK7/MAP3K11/JNK1 0.078 0.046 -10000 0 -10000 0 0
AKT1 -0.055 0.14 -10000 0 -0.51 24 24
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
DAB1 0.033 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.07 0.084 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 0.08 0.11 -10000 0 -0.32 20 20
DAB1/LIS1 0.034 0.15 -10000 0 -0.3 63 63
DAB1/CRLK/C3G 0.019 0.14 -10000 0 -0.3 63 63
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
DAB1/NCK2 0.039 0.15 -10000 0 -0.31 63 63
ARHGEF2 0.03 0.022 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.032 0.012 -10000 0 -10000 0 0
CDK5R1 0.033 0.014 -10000 0 -10000 0 0
RELN 0.012 0.11 -10000 0 -0.54 20 20
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
RELN/LRP8/Fyn 0.065 0.095 0.25 1 -0.32 22 23
GRIN2A/RELN/LRP8/DAB1/Fyn 0.083 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 87 92
RELN/LRP8 0.069 0.091 0.25 1 -0.32 20 21
GRIN2B/RELN/LRP8/DAB1/Fyn 0.079 0.11 -10000 0 -0.31 29 29
PI3K 0.006 0.12 -10000 0 -0.4 42 42
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.043 0.027 -10000 0 -0.4 1 1
RAP1A -0.028 0.12 0.35 3 -0.48 5 8
PAFAH1B1 0.032 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.034 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.047 0.014 -10000 0 -10000 0 0
GRIN2B 0.021 0.085 -10000 0 -0.54 11 11
NCK2 0.034 0.007 -10000 0 -10000 0 0
neuron differentiation 0.049 0.069 0.24 3 -0.54 1 4
neuron adhesion -0.011 0.13 0.38 5 -0.46 4 9
LRP8 0.071 0.063 -10000 0 -10000 0 0
GSK3B -0.05 0.14 -10000 0 -0.5 23 23
RELN/VLDLR/DAB1/Fyn 0.005 0.15 -10000 0 -0.31 81 81
MAP3K11 0.034 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.054 0.16 -10000 0 -0.31 111 111
CDK5 0.037 0.021 -10000 0 -10000 0 0
MAPT 0.014 0.12 0.79 10 -0.49 3 13
neuron migration -0.027 0.15 0.38 4 -0.4 28 32
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.048 0.068 -10000 0 -0.55 1 1
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 79 79
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.04 0.016 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.033 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.02 0.081 -10000 0 -0.54 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.03 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.11 0.12 -10000 0 -0.23 236 236
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.031 0.027 -10000 0 -0.54 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
FYN 0.029 0.037 -10000 0 -0.54 2 2
MAP3K12 0.034 0.004 -10000 0 -10000 0 0
FGR 0.033 0.007 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.039 0.092 -10000 0 -0.31 37 37
PRKG1 0.034 0.005 -10000 0 -10000 0 0
DUSP8 0.033 0.007 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.013 0.12 -10000 0 -0.34 28 28
apoptosis -0.038 0.088 -10000 0 -0.3 37 37
RAL/GTP 0.044 0.01 -10000 0 -10000 0 0
LYN 0.03 0.015 -10000 0 -10000 0 0
DUSP1 -0.2 0.28 -10000 0 -0.54 209 209
PAK1 0.043 0.045 -10000 0 -10000 0 0
SRC 0.032 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.071 0.035 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.034 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.044 0.011 -10000 0 -10000 0 0
MAPK11 0.002 0.13 0.35 3 -0.37 29 32
BLK 0.039 0.043 -10000 0 -10000 0 0
HCK 0.036 0.022 -10000 0 -10000 0 0
MAP2K3 0.031 0.01 -10000 0 -10000 0 0
DUSP16 0.033 0.012 -10000 0 -10000 0 0
DUSP10 0.028 0.032 -10000 0 -0.54 1 1
TRAF6/MEKK3 0.038 0.015 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.13 0.39 2 -0.36 32 34
positive regulation of innate immune response 0.002 0.15 0.47 2 -0.42 34 36
LCK 0.048 0.043 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.015 0.15 0.58 1 -0.41 30 31
p38alpha-beta/MKP5 0.01 0.15 0.58 1 -0.41 29 30
PGK/cGMP 0.025 0.004 -10000 0 -10000 0 0
PAK2 0.033 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.086 0.2 -10000 0 -0.42 71 71
CDC42 0.033 0.007 -10000 0 -10000 0 0
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.034 0.005 -10000 0 -10000 0 0
PAK3 -0.31 0.28 -10000 0 -0.54 305 305
Regulation of Telomerase

Figure 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
Telomerase catalytic core complex -0.001 0.18 -10000 0 -0.85 8 8
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 -0.21 104 104
ER alpha/Oestrogen -0.043 0.19 -10000 0 -0.39 110 110
NFX1/SIN3/HDAC complex 0.034 0.073 -10000 0 -0.33 13 13
EGF -0.15 0.27 -10000 0 -0.54 162 162
SMG5 0.029 0.016 -10000 0 -10000 0 0
SMG6 0.031 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.055 0.024 -10000 0 -10000 0 0
TERT/c-Abl 0.008 0.17 -10000 0 -0.78 8 8
SAP18 0.032 0.01 -10000 0 -10000 0 0
MRN complex 0.049 0.033 -10000 0 -10000 0 0
WT1 0.085 0.068 -10000 0 -10000 0 0
WRN 0.028 0.015 -10000 0 -10000 0 0
SP1 0.041 0.017 -10000 0 -10000 0 0
SP3 0.036 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.012 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.026 0.16 -10000 0 -0.7 8 8
Mad/Max 0.054 0.017 -10000 0 -10000 0 0
TERT -0.008 0.18 -10000 0 -0.89 8 8
CCND1 0.032 0.25 0.57 8 -1 14 22
MAX 0.035 0.01 -10000 0 -10000 0 0
RBBP7 0.038 0.021 -10000 0 -10000 0 0
RBBP4 0.034 0.006 -10000 0 -10000 0 0
TERF2 0.027 0.028 -10000 0 -0.49 1 1
PTGES3 0.033 0.026 -10000 0 -0.54 1 1
SIN3A 0.034 0.006 -10000 0 -10000 0 0
Telomerase/911 0.04 0.057 -10000 0 -0.45 2 2
CDKN1B 0.043 0.11 0.31 1 -0.61 10 11
RAD1 0.034 0.009 -10000 0 -10000 0 0
XRCC5 0.034 0.005 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
SAP30 0.034 0.009 -10000 0 -10000 0 0
TRF2/PARP2 0.042 0.028 -10000 0 -0.39 1 1
UBE3A 0.034 0.009 -10000 0 -10000 0 0
JUN -0.063 0.22 -10000 0 -0.54 86 86
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.028 0.012 -10000 0 -10000 0 0
FOS -0.36 0.27 -10000 0 -0.54 342 342
IFN-gamma/IRF1 0.081 0.083 0.29 3 -0.32 10 13
PARP2 0.033 0.006 -10000 0 -10000 0 0
BLM 0.073 0.065 -10000 0 -10000 0 0
Telomerase 0.005 0.092 -10000 0 -0.72 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 0.033 -10000 0 -0.29 1 1
ubiquitin-dependent protein catabolic process 0.043 0.067 -10000 0 -0.35 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.043 0.068 -10000 0 -0.36 6 6
HDAC1 0.034 0.006 -10000 0 -10000 0 0
HDAC2 0.038 0.021 -10000 0 -10000 0 0
ATM 0.017 0.021 0.21 1 -10000 0 1
SMAD3 0.009 0.016 -10000 0 -10000 0 0
ABL1 0.034 0.005 -10000 0 -10000 0 0
MXD1 0.037 0.009 -10000 0 -10000 0 0
MRE11A 0.03 0.011 -10000 0 -10000 0 0
HUS1 0.034 0.01 -10000 0 -10000 0 0
RPS6KB1 0.03 0.012 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.023 0.18 -10000 0 -0.74 11 11
NR2F2 0.008 0.094 -10000 0 -0.55 13 13
MAPK3 0.019 0.022 -10000 0 -0.4 1 1
MAPK1 0.019 0.022 -10000 0 -0.4 1 1
TGFB1/TGF beta receptor Type II 0.032 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
HNRNPC 0.033 0.006 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.017 0.021 0.21 1 -10000 0 1
NBN 0.028 0.015 0.18 1 -10000 0 1
EGFR -0.27 0.29 -10000 0 -0.54 264 264
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.31 0.26 -10000 0 -0.46 350 350
MYC -0.002 0.12 -10000 0 -0.54 25 25
IL2 0.039 0.031 -10000 0 -0.54 1 1
KU 0.047 0.014 -10000 0 -10000 0 0
RAD50 0.033 0.006 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
TGFB1 0.033 0.009 -10000 0 -10000 0 0
TRF2/BLM 0.065 0.055 -10000 0 -0.39 1 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.021 0.18 -10000 0 -0.78 8 8
SP1/HDAC2 0.06 0.032 -10000 0 -10000 0 0
PINX1 0.027 0.014 -10000 0 -10000 0 0
Telomerase/EST1A 0.021 0.16 -10000 0 -0.7 8 8
Smad3/Myc 0.005 0.082 -10000 0 -0.34 25 25
911 complex 0.061 0.025 -10000 0 -10000 0 0
IFNG 0.065 0.072 -10000 0 -0.54 1 1
Telomerase/PinX1 0.01 0.16 -10000 0 -0.7 8 8
Telomerase/AKT1/mTOR/p70S6K 0.021 0.12 -10000 0 -0.52 13 13
SIN3B 0.036 0.014 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.026 0.15 -10000 0 -0.72 7 7
response to DNA damage stimulus -0.001 0.03 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.061 0.051 -10000 0 -0.31 1 1
TRF2/WRN 0.036 0.03 -10000 0 -0.39 1 1
Telomerase/hnRNP C1/C2 0.026 0.16 -10000 0 -0.73 7 7
E2F1 0.053 0.047 0.2 8 -10000 0 8
ZNFX1 0.033 0.016 -10000 0 -10000 0 0
PIF1 0.038 0.028 -10000 0 -10000 0 0
NCL 0.033 0.006 -10000 0 -10000 0 0
DKC1 0.035 0.011 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.12 0.11 -10000 0 -0.63 4 4
Syndecan-4/Syndesmos 0.13 0.12 0.4 4 -0.72 4 8
positive regulation of JNK cascade 0.063 0.18 0.39 2 -0.7 5 7
Syndecan-4/ADAM12 0.15 0.13 0.4 6 -0.76 4 10
CCL5 0.028 0.06 -10000 0 -0.54 5 5
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DNM2 0.034 0.005 -10000 0 -10000 0 0
ITGA5 0.034 0.007 -10000 0 -10000 0 0
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
PLG 0.013 0.04 -10000 0 -0.54 1 1
ADAM12 0.056 0.06 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.032 0.012 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha 0.008 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.13 0.12 0.4 2 -0.72 4 6
Syndecan-4/CXCL12/CXCR4 0.066 0.19 0.4 2 -0.76 5 7
Syndecan-4/Laminin alpha3 0.055 0.16 0.41 2 -0.75 5 7
MDK 0.043 0.036 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.063 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 -0.54 141 141
Syndecan-4/FGFR1/FGF -0.066 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 0.4 3 -0.72 4 7
positive regulation of MAPKKK cascade 0.063 0.18 0.39 2 -0.7 5 7
Syndecan-4/TACI 0.13 0.12 0.4 3 -0.76 4 7
CXCR4 0.044 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 0.033 0.01 -10000 0 -10000 0 0
LAMA3 -0.15 0.27 -10000 0 -0.54 158 158
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.028 0.22 0.71 47 -10000 0 47
Syndecan-4/alpha-Actinin 0.14 0.12 0.4 2 -0.76 4 6
TFPI -0.19 0.28 -10000 0 -0.54 196 196
F2 0.039 0.02 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.044 0.15 0.41 1 -0.69 5 6
ACTN1 0.033 0.007 -10000 0 -10000 0 0
TNC 0.037 0.036 -10000 0 -0.54 1 1
Syndecan-4/CXCL12 0.056 0.18 0.4 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 -0.14 0.26 -10000 0 -0.54 148 148
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 375 375
FGFR1 0.018 0.077 -10000 0 -0.54 9 9
Syndecan-4/PI-4-5-P2 0.095 0.11 -10000 0 -0.76 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.074 -10000 0 -10000 0 0
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 0.092 0.077 -10000 0 -10000 0 0
Rac1/GTP 0.091 0.071 0.27 48 -10000 0 48
cytoskeleton organization 0.13 0.12 0.39 4 -0.69 4 8
GIPC1 0.034 0.01 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.036 0.19 0.39 3 -0.63 8 11
Regulation of Androgen receptor activity

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.017 0.003 -10000 0 -10000 0 0
SMARCC1 0.017 0.054 -10000 0 -0.68 1 1
REL 0.036 0.022 -10000 0 -10000 0 0
HDAC7 -0.052 0.12 -10000 0 -0.35 33 33
JUN -0.064 0.22 -10000 0 -0.54 86 86
EP300 0.032 0.009 -10000 0 -10000 0 0
KAT2B 0 0 0.003 3 -10000 0 3
KAT5 0 0 -10000 0 -0.003 1 1
MAPK14 -0.003 0.063 -10000 0 -0.41 10 10
FOXO1 -0.023 0.17 -10000 0 -0.54 47 47
T-DHT/AR -0.026 0.14 -10000 0 -0.36 33 33
MAP2K6 0.008 0.084 -10000 0 -0.55 10 10
BRM/BAF57 0.046 0.018 -10000 0 -10000 0 0
MAP2K4 0.018 0.027 -10000 0 -10000 0 0
SMARCA2 0.033 0.009 -10000 0 -10000 0 0
PDE9A -0.059 0.26 -10000 0 -1 30 30
NCOA2 0.028 0.014 -10000 0 -10000 0 0
CEBPA 0.03 0.045 -10000 0 -0.54 3 3
EHMT2 0.034 0.004 -10000 0 -10000 0 0
cell proliferation 0.037 0.15 0.42 14 -0.46 3 17
NR0B1 -0.094 0.25 -10000 0 -0.54 118 118
EGR1 -0.43 0.23 -10000 0 -0.54 409 409
RXRs/9cRA 0.051 0.043 -10000 0 -0.31 4 4
AR/RACK1/Src 0.003 0.1 0.34 5 -0.34 6 11
AR/GR -0.04 0.14 -10000 0 -0.29 90 90
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
PKN1 0.034 0.01 -10000 0 -10000 0 0
RCHY1 0.028 0.051 -10000 0 -0.54 4 4
epidermal growth factor receptor activity 0 0.001 0.009 4 -10000 0 4
MAPK8 0.003 0.033 -10000 0 -0.44 1 1
T-DHT/AR/TIF2/CARM1 0.006 0.095 0.35 1 -0.37 6 7
SRC -0.011 0.072 -10000 0 -0.33 7 7
NR3C1 -0.011 0.15 -10000 0 -0.54 39 39
KLK3 -0.042 0.097 0.45 1 -10000 0 1
APPBP2 0.018 0.026 -10000 0 -10000 0 0
TRIM24 0.035 0.013 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.036 0.072 -10000 0 -0.36 11 11
TMPRSS2 -0.22 0.44 -10000 0 -1 120 120
RXRG 0.024 0.053 0.18 2 -0.54 4 6
mol:9cRA 0 0 0.003 4 -10000 0 4
RXRA 0.034 0.006 -10000 0 -10000 0 0
RXRB 0.034 0.005 -10000 0 -10000 0 0
CARM1 0.035 0.014 -10000 0 -10000 0 0
NR2C2 0.034 0.014 -10000 0 -10000 0 0
KLK2 0.013 0.078 0.34 3 -10000 0 3
AR -0.025 0.11 -10000 0 -0.27 62 62
SENP1 0.034 0.004 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
MDM2 0.032 0.013 -10000 0 -10000 0 0
SRY -0.001 0.002 -10000 0 -0.025 4 4
GATA2 0.041 0.032 -10000 0 -10000 0 0
MYST2 0 0.001 -10000 0 -0.006 4 4
HOXB13 0.078 0.068 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.001 0.1 0.35 6 -0.35 7 13
positive regulation of transcription 0.041 0.032 -10000 0 -10000 0 0
DNAJA1 0.019 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.032 -10000 0 -0.33 4 4
NCOA1 0.041 0.033 -10000 0 -0.57 1 1
SPDEF -0.02 0.17 -10000 0 -0.54 50 50
T-DHT/AR/TIF2 0.017 0.079 0.29 5 -0.32 4 9
T-DHT/AR/Hsp90 -0.011 0.099 0.36 2 -0.36 11 13
GSK3B 0.033 0.01 -10000 0 -10000 0 0
NR2C1 0.033 0.026 -10000 0 -0.54 1 1
mol:T-DHT -0.019 0.072 0.22 15 -0.36 10 25
SIRT1 0.034 0.005 -10000 0 -10000 0 0
ZMIZ2 0.032 0.008 -10000 0 -10000 0 0
POU2F1 0.003 0.065 -10000 0 -0.18 7 7
T-DHT/AR/DAX-1 -0.072 0.16 0.36 2 -0.34 104 106
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
SMARCE1 0.032 0.009 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.033 0.005 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
GNB1/GNG2 0.047 0.088 -10000 0 -0.34 23 23
forebrain development -0.044 0.2 -10000 0 -0.53 56 56
GNAO1 0.03 0.012 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.029 0.093 -10000 0 -0.4 22 22
SMO 0.012 0.12 -10000 0 -0.54 22 22
ARRB2 0.032 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.03 0.11 0.29 1 -0.48 9 10
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.077 0.031 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
XPO1 0.036 0.006 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.19 -10000 0 -0.65 27 27
SAP30 0.033 0.009 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 -10000 0 -0.54 22 22
MIM/GLI2A 0.033 0.029 0.31 1 -10000 0 1
IFT88 0.031 0.027 -10000 0 -0.54 1 1
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GLI2 0.016 0.084 -10000 0 -0.37 14 14
GLI3 0.016 0.11 0.3 1 -0.45 12 13
CSNK1D 0.032 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.008 -10000 0 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.031 0.027 -10000 0 -0.54 1 1
GNG2 0.032 0.026 -10000 0 -0.54 1 1
Gi family/GTP -0.083 0.16 -10000 0 -0.26 194 194
SIN3B 0.034 0.014 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.024 0.11 -10000 0 -0.46 14 14
GLI2/Su(fu) 0.019 0.11 -10000 0 -0.45 13 13
FOXA2 0.016 0.12 -10000 0 -0.72 10 10
neural tube patterning -0.044 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 0.034 0.011 -10000 0 -10000 0 0
CSNK1G2 0.033 0.007 -10000 0 -10000 0 0
CSNK1G3 0.033 0.007 -10000 0 -10000 0 0
MTSS1 0.033 0.029 0.31 1 -10000 0 1
embryonic limb morphogenesis -0.044 0.2 -10000 0 -0.53 56 56
SUFU 0.019 0.05 -10000 0 -0.38 1 1
LGALS3 -0.029 0.18 -10000 0 -0.54 55 55
catabolic process 0.037 0.13 -10000 0 -0.6 12 12
GLI3A/CBP 0.001 0.12 -10000 0 -0.36 49 49
KIF3A 0.033 0.006 -10000 0 -10000 0 0
GLI1 -0.045 0.21 -10000 0 -0.55 56 56
RAB23 0.035 0.014 -10000 0 -10000 0 0
CSNK1A1 0.033 0.006 -10000 0 -10000 0 0
IFT172 0.033 0.026 -10000 0 -0.54 1 1
RBBP7 0.037 0.021 -10000 0 -10000 0 0
Su(fu)/Galectin3 -0.009 0.13 -10000 0 -0.33 58 58
GNAZ 0.026 0.063 -10000 0 -0.54 6 6
RBBP4 0.033 0.006 -10000 0 -10000 0 0
CSNK1G1 0.033 0.007 -10000 0 -10000 0 0
PIAS1 0.033 0.007 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.028 0.088 -10000 0 -0.46 9 9
STK36 0.035 0.026 -10000 0 -0.54 1 1
Gi family/GNB1/GNG2/GDP -0.082 0.17 -10000 0 -0.39 70 70
PTCH1 -0.038 0.18 -10000 0 -0.65 21 21
MIM/GLI1 -0.024 0.18 -10000 0 -0.58 33 33
CREBBP 0.001 0.12 -10000 0 -0.36 49 49
Su(fu)/SIN3/HDAC complex 0.015 0.1 -10000 0 -0.45 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 -0.48 1 1
UGCG 0.028 0.12 -10000 0 -0.65 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT 0 0.18 0.33 1 -0.4 41 42
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.029 0.11 -10000 0 -0.64 11 11
mol:DAG 0.005 0.11 -10000 0 -0.85 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.22 0.35 1 -0.42 73 74
FRAP1 -0.036 0.24 0.38 1 -0.47 84 85
FOXO3 0.005 0.18 0.37 3 -0.51 30 33
AKT1 0.002 0.2 0.38 1 -0.54 32 33
GAB2 0.027 0.014 -10000 0 -10000 0 0
SMPD1 0.008 0.12 -10000 0 -0.66 15 15
SGMS1 0.019 0.083 -10000 0 -0.62 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.027 0.096 -10000 0 -0.34 42 42
CALM1 0.033 0.006 -10000 0 -10000 0 0
cell proliferation 0.048 0.12 0.42 1 -0.44 11 12
EIF3A 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.005 0.12 -10000 0 -0.4 42 42
RPS6KB1 0 0.13 -10000 0 -0.83 8 8
mol:sphingomyelin 0.005 0.11 -10000 0 -0.85 7 7
natural killer cell activation -0.002 0.005 -10000 0 -0.02 3 3
JAK3 0.033 0.009 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
JAK1 0.033 0.01 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MYC 0.022 0.27 0.48 2 -0.92 31 33
MYB -0.049 0.34 -10000 0 -1.2 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.028 0.13 0.32 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 0.13 0.32 1 -0.37 13 14
Rac1/GDP -0.01 0.094 -10000 0 -0.31 42 42
T cell proliferation 0.028 0.12 0.3 1 -0.36 12 13
SHC1 0.025 0.016 -10000 0 -10000 0 0
RAC1 0.033 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.028 0.092 25 -0.068 41 66
PRKCZ 0.027 0.12 0.31 1 -0.36 13 14
NF kappa B1 p50/RelA -0.009 0.23 0.37 1 -0.5 44 45
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.022 0.095 -10000 0 -0.39 8 8
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL2RA 0.039 0.035 -10000 0 -10000 0 0
IL2RB 0.035 0.023 0.18 8 -10000 0 8
TERT 0.032 0.028 -10000 0 -0.54 1 1
E2F1 0.012 0.14 0.33 1 -0.4 46 47
SOS1 0.032 0.009 -10000 0 -10000 0 0
RPS6 0.032 0.027 -10000 0 -0.54 1 1
mol:cAMP -0.002 0.014 0.032 41 -0.05 24 65
PTPN11 0.031 0.011 -10000 0 -10000 0 0
IL2RG 0.042 0.036 -10000 0 -10000 0 0
actin cytoskeleton organization 0.028 0.12 0.3 1 -0.36 12 13
GRB2 0.031 0.018 -10000 0 -10000 0 0
IL2 0.032 0.029 -10000 0 -0.54 1 1
PIK3CA 0.032 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.1 -10000 0 -0.29 42 42
LCK 0.047 0.045 -10000 0 -10000 0 0
BCL2 -0.12 0.38 0.52 1 -0.84 104 105
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.006 0.029 0.35 1 -0.34 1 2
SNTA1 0.032 0.027 -10000 0 -0.54 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.012 0.058 0.33 6 -0.34 1 7
MAPK12 0.008 0.086 0.21 39 -0.28 24 63
CCND1 0.008 0.083 0.21 1 -0.5 10 11
p38 gamma/SNTA1 0.027 0.086 0.39 1 -0.26 22 23
MAP2K3 0.031 0.01 -10000 0 -10000 0 0
PKN1 0.034 0.01 -10000 0 -10000 0 0
G2/M transition checkpoint 0.008 0.086 0.21 39 -0.27 24 63
MAP2K6 0.015 0.098 0.25 44 -0.3 25 69
MAPT 0.013 0.067 0.28 7 -0.3 5 12
MAPK13 0.018 0.027 -10000 0 -0.4 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.063 -10000 0 -0.33 17 17
E-cadherin signaling in the nascent adherens junction

Figure 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
CTTN -0.037 0.15 -10000 0 -0.43 43 43
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 -0.3 24 28
ENAH -0.031 0.14 -10000 0 -0.43 36 36
AP1M1 0.034 0.005 -10000 0 -10000 0 0
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
CDC42/GTP 0.009 0.075 -10000 0 -0.29 2 2
ABI1/Sra1/Nap1 -0.016 0.04 -10000 0 -0.18 12 12
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.094 -10000 0 -0.31 25 25
RAPGEF1 -0.029 0.14 0.33 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 0.033 0.008 -10000 0 -10000 0 0
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.055 0.042 -10000 0 -0.31 3 3
DLG1 -0.039 0.16 -10000 0 -0.43 49 49
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.06 -10000 0 -0.2 6 6
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GTP/NME1/Tiam1 0.058 0.025 -10000 0 -10000 0 0
PI3K -0.021 0.079 -10000 0 -0.26 6 6
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 -0.4 21 21
TIAM1 0.035 0.012 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.046 0.088 -10000 0 -0.29 25 25
AKT1 -0.007 0.056 -10000 0 -0.17 1 1
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 0.25 44 -0.2 10 54
CDC42/GDP 0.001 0.12 0.3 7 -0.3 24 31
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 0.043 0.013 -10000 0 -10000 0 0
JUP 0.033 0.01 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.007 0.12 0.34 3 -0.37 4 7
RAC1/GTP/IQGAP1 0.044 0.012 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.049 0.011 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
CTNNA1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.067 0.2 25 -0.23 11 36
NME1 0.031 0.011 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.036 0.16 -10000 0 -0.44 46 46
regulation of cell-cell adhesion 0 0.061 -10000 0 -0.24 3 3
WASF2 0.019 0.043 0.12 31 -0.12 2 33
Rap1/GTP 0.012 0.086 0.28 1 -0.33 2 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.059 0.092 -10000 0 -0.3 21 21
CCND1 0.016 0.079 0.23 22 -0.28 11 33
VAV2 -0.019 0.19 0.41 1 -0.68 15 16
RAP1/GDP 0.01 0.1 0.31 3 -0.36 3 6
adherens junction assembly -0.034 0.15 -10000 0 -0.42 46 46
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.033 0.006 -10000 0 -10000 0 0
PIP5K1C 0.034 0.009 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.044 0.088 -10000 0 -0.29 23 23
E-cadherin/beta catenin -0.007 0.089 -10000 0 -0.34 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.038 0.16 -10000 0 -0.43 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
Noncanonical Wnt signaling pathway

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
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 0.005 0.13 -10000 0 -0.43 24 24
YES1 -0.002 0.13 0.25 1 -0.49 22 23
FZD3 0.014 0.092 -10000 0 -0.54 13 13
FZD6 0.006 0.11 -10000 0 -0.54 18 18
G protein 0.036 0.15 0.35 4 -0.44 22 26
MAP3K7 -0.005 0.11 0.25 1 -0.37 20 21
mol:Ca2+ 0.006 0.12 -10000 0 -0.4 24 24
mol:IP3 0.006 0.13 -10000 0 -0.41 24 24
NLK 0.004 0.13 -10000 0 -0.81 12 12
GNB1 0.034 0.011 -10000 0 -10000 0 0
CAMK2A 0 0.12 0.26 1 -0.4 21 22
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.015 0.13 -10000 0 -0.49 23 23
CSNK1A1 0.033 0.006 -10000 0 -10000 0 0
GNAS -0.005 0.13 0.25 1 -0.45 23 24
GO:0007205 0 0.12 0.26 1 -0.42 23 24
WNT6 0.033 0.04 -10000 0 -0.54 2 2
WNT4 0.04 0.033 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.017 0.14 -10000 0 -0.46 19 19
GNG2 0.032 0.026 -10000 0 -0.54 1 1
WNT5A 0.012 0.12 -10000 0 -0.54 23 23
WNT11 0.023 0.079 -10000 0 -0.54 9 9
CDC42 -0.003 0.12 -10000 0 -0.47 21 21
Signaling events mediated by PRL

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
CCNE1 0.058 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 -10000 0 -10000 0 0
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 -0.39 408 408
CDK2/Cyclin E1 -0.042 0.11 -10000 0 -0.47 15 15
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 0.02 -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
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.035 0.031 -10000 0 -0.54 1 1
ANTXR2 0.022 0.08 -10000 0 -0.54 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.01 -10000 0 -0.073 11 11
monocyte activation 0.013 0.085 -10000 0 -0.35 24 24
MAP2K2 0.005 0.094 -10000 0 -0.57 13 13
MAP2K1 -0.005 0.01 -10000 0 -10000 0 0
MAP2K7 -0.005 0.01 -10000 0 -10000 0 0
MAP2K6 -0.01 0.042 -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 -0.012 0.048 0.24 1 -0.3 7 8
Channel 0.036 0.053 -10000 0 -0.31 11 11
NLRP1 -0.007 0.028 -10000 0 -0.27 5 5
CALM1 0.033 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.002 0.073 -10000 0 -0.41 15 15
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.01 0.073 11 -10000 0 11
MAPK3 -0.005 0.01 -10000 0 -10000 0 0
MAPK1 -0.005 0.01 -10000 0 -10000 0 0
PGR -0.063 0.14 0.086 112 -0.29 141 253
PA/Cellular Receptors 0.037 0.058 -10000 0 -0.34 11 11
apoptosis -0.002 0.01 -10000 0 -0.073 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.035 0.05 -10000 0 -0.29 11 11
macrophage activation -0.006 0.01 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
VCAM1 0.013 0.085 -10000 0 -0.36 24 24
platelet activation 0.002 0.073 -10000 0 -0.41 15 15
MAPKKK cascade -0.003 0.03 0.12 3 -0.14 6 9
IL18 -0.001 0.04 0.14 1 -0.25 3 4
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.073 11 11
LEF -0.002 0.011 -10000 0 -0.073 11 11
CASP1 -0.006 0.033 -10000 0 -0.11 35 35
mol:cAMP 0.002 0.074 -10000 0 -0.41 15 15
necrosis -0.002 0.01 -10000 0 -0.073 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.035 0.05 -10000 0 -0.29 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.035 0.093 -9999 0 -0.34 24 24
E-cadherin/beta catenin 0.019 0.1 -9999 0 -0.4 25 25
CTNNB1 0.03 0.045 -9999 0 -0.54 3 3
JUP 0.033 0.01 -9999 0 -10000 0 0
CDH1 0.006 0.12 -9999 0 -0.54 22 22
Caspase cascade in apoptosis

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
TOP1 0.035 0.074 0.28 2 -0.34 8 10
ACTA1 0.007 0.083 0.24 3 -0.38 3 6
NUMA1 0.027 0.082 0.28 2 -0.38 8 10
SPTAN1 0.02 0.068 0.3 5 -0.48 1 6
LIMK1 0.033 0.074 0.28 11 -0.48 1 12
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BIRC2 0.03 0.011 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
CASP10 -0.003 0.04 0.24 8 -0.34 1 9
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 -10000 0 -0.001 36 36
PTK2 0.029 0.094 0.28 3 -0.47 9 12
DIABLO 0.034 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes 0.02 0.067 0.3 5 -0.48 1 6
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.034 0.005 -10000 0 -10000 0 0
GSN -0.054 0.13 0.35 1 -0.29 87 88
MADD 0.034 0.005 -10000 0 -10000 0 0
TFAP2A 0.04 0.099 -10000 0 -0.65 8 8
BID 0.013 0.025 0.16 9 -0.2 1 10
MAP3K1 0.01 0.096 -10000 0 -0.39 22 22
TRADD 0.029 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.049 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.025 0.07 0.3 5 -0.48 1 6
CASP9 0.033 0.008 -10000 0 -10000 0 0
DNA repair -0.034 0.059 0.32 3 -0.2 17 20
neuron apoptosis 0.01 0.14 -10000 0 -0.69 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.024 0.074 0.32 1 -0.4 3 4
APAF1 0.034 0.003 -10000 0 -10000 0 0
CASP6 0.022 0.14 -10000 0 -0.85 11 11
TRAF2 0.034 0.012 -10000 0 -10000 0 0
ICAD/CAD 0.017 0.062 0.28 2 -0.47 1 3
CASP7 0.015 0.081 0.26 24 -0.31 4 28
KRT18 0.035 0.095 -10000 0 -0.73 6 6
apoptosis 0.012 0.1 0.31 2 -0.44 9 11
DFFA 0.02 0.065 0.28 3 -0.48 1 4
DFFB 0.02 0.064 0.28 3 -0.48 1 4
PARP1 0.034 0.059 0.2 17 -0.32 3 20
actin filament polymerization 0.017 0.13 0.31 12 -0.3 9 21
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.023 0.045 0.22 6 -0.23 3 9
SATB1 -0.011 0.16 -10000 0 -0.78 13 13
SLK 0.02 0.068 0.29 4 -0.38 2 6
p15 BID/BAX 0.026 0.051 -10000 0 -0.31 3 3
CASP2 0.004 0.083 0.22 5 -0.34 9 14
JNK cascade -0.01 0.095 0.39 22 -10000 0 22
CASP3 0.024 0.07 0.31 3 -0.51 1 4
LMNB2 0.019 0.13 0.35 2 -0.53 19 21
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CASP4 0.024 0.058 -10000 0 -0.54 5 5
Mammalian IAPs/DIABLO 0.045 0.078 -10000 0 -0.31 17 17
negative regulation of DNA binding 0.04 0.097 -10000 0 -0.64 8 8
stress fiber formation 0.019 0.067 0.29 4 -0.37 2 6
GZMB 0.022 0.046 0.29 7 -0.4 2 9
CASP1 -0.016 0.12 -10000 0 -0.4 40 40
LMNB1 0.041 0.13 0.28 8 -0.57 13 21
APP 0.009 0.14 -10000 0 -0.7 18 18
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
response to stress 0 0 0.001 16 -0.001 26 42
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM 0.014 0.11 0.31 2 -0.44 10 12
LMNA 0.022 0.082 0.33 2 -0.38 8 10
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.087 -10000 0 -0.32 17 17
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.027 0.069 0.28 4 -0.41 1 5
APAF-1/Caspase 9 0.018 0.11 -10000 0 -0.6 15 15
nuclear fragmentation during apoptosis 0.027 0.081 0.28 2 -0.37 8 10
CFL2 -0.018 0.13 0.31 8 -0.31 12 20
GAS2 -0.15 0.15 0.3 5 -0.28 241 246
positive regulation of apoptosis 0.035 0.12 0.33 3 -0.48 17 20
PRF1 0.037 0.022 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.028 0.015 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.048 0.14 -10000 0 -0.45 16 16
NEF 0.011 0.022 -10000 0 -10000 0 0
NFKBIA 0.029 0.036 -10000 0 -0.35 1 1
BIRC3 0.008 0.14 0.38 1 -0.5 25 26
CYCS 0.034 0.13 0.28 15 -0.44 14 29
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CD247 0.029 0.11 0.23 17 -0.55 15 32
MAP2K7 0.04 0.18 0.34 3 -0.68 18 21
protein ubiquitination 0.015 0.11 0.37 2 -0.42 12 14
CRADD 0.034 0.005 -10000 0 -10000 0 0
DAXX 0.034 0.008 -10000 0 -10000 0 0
FAS -0.002 0.14 -10000 0 -0.54 32 32
BID 0.032 0.13 0.27 5 -0.45 16 21
NF-kappa-B/RelA/I kappa B alpha 0.06 0.086 -10000 0 -0.3 16 16
TRADD 0.029 0.012 -10000 0 -10000 0 0
MAP3K5 0.004 0.12 -10000 0 -0.54 25 25
CFLAR 0.032 0.026 -10000 0 -0.54 1 1
FADD 0.028 0.015 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.06 0.086 -10000 0 -0.31 16 16
MAPK8 0.039 0.17 0.43 3 -0.63 17 20
APAF1 0.034 0.003 -10000 0 -10000 0 0
TRAF1 0.035 0.015 -10000 0 -10000 0 0
TRAF2 0.034 0.012 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.037 0.14 0.26 8 -0.46 17 25
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.13 -10000 0 -0.5 16 16
CHUK 0.013 0.12 0.37 2 -0.46 12 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.039 0.12 -10000 0 -0.33 39 39
TCRz/NEF 0.023 0.084 -10000 0 -0.41 15 15
TNF 0.038 0.023 -10000 0 -10000 0 0
FASLG 0.036 0.11 0.36 18 -0.37 15 33
NFKB1 0.03 0.034 -10000 0 -0.17 1 1
TNFR1A/BAG4/TNF-alpha 0.053 0.034 -10000 0 -10000 0 0
CASP6 0.053 0.15 -10000 0 -0.56 13 13
CASP7 0.021 0.19 0.39 16 -0.49 35 51
RELA 0.03 0.033 -10000 0 -10000 0 0
CASP2 0.033 0.006 -10000 0 -10000 0 0
CASP3 0.017 0.19 0.4 15 -0.49 36 51
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.023 -10000 0 -10000 0 0
CASP8 0.034 0.005 -10000 0 -10000 0 0
CASP9 0.033 0.007 -10000 0 -10000 0 0
MAP3K14 0.016 0.13 0.36 1 -0.48 14 15
APAF-1/Caspase 9 0.019 0.13 -10000 0 -0.39 23 23
BCL2 -0.006 0.18 0.48 5 -0.54 22 27
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.079 0.054 0.39 6 -10000 0 6
MAP4K1 0.036 0.02 -10000 0 -10000 0 0
MAP3K8 -0.039 0.19 -10000 0 -0.54 64 64
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.035 0.012 -10000 0 -10000 0 0
CRKL 0.032 0.008 -10000 0 -10000 0 0
MAP3K1 0.031 0.058 0.3 3 -0.3 4 7
JUN -0.039 0.13 -10000 0 -0.3 80 80
MAP3K7 0.029 0.052 0.27 3 -0.27 3 6
GRAP2 0.034 0.019 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
MAP2K4 0.002 0.1 0.28 3 -0.35 20 23
LAT 0.035 0.024 -10000 0 -10000 0 0
LCP2 0.036 0.023 -10000 0 -10000 0 0
MAPK8 0.011 0.081 -10000 0 -0.58 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.037 0.06 0.3 3 -0.29 4 7
LAT/GRAP2/SLP76/HPK1/HIP-55 0.089 0.059 0.39 6 -10000 0 6
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.087 0.074 0.31 1 -0.28 5 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.032 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.098 0.11 0.4 35 -10000 0 35
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.063 0.055 -10000 0 -0.34 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.003 0.096 0.16 4 -0.28 35 39
CaM/Ca2+ 0.085 0.071 -10000 0 -0.27 5 5
RAP1A 0.034 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.074 0.088 0.31 24 -0.27 5 29
AKT1 0.019 0.11 0.32 10 -0.3 27 37
MAP2K1 0.026 0.073 0.34 3 -0.27 1 4
MAP3K11 0.043 0.069 0.32 4 -0.27 5 9
IFNGR1 0.03 0.058 -10000 0 -0.54 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.047 0.089 -10000 0 -0.41 9 9
Rap1/GTP 0.018 0.035 -10000 0 -10000 0 0
CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.095 0.075 -10000 0 -0.3 5 5
CEBPB 0.057 0.14 0.42 6 -0.59 5 11
STAT3 0.033 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.092 0.1 -10000 0 -0.7 5 5
STAT1 0.058 0.092 0.3 27 -0.27 5 32
CALM1 0.033 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.061 0.063 -10000 0 -0.55 1 1
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.074 0.089 0.3 26 -0.26 3 29
CEBPB/PTGES2/Cbp/p300 0.039 0.085 0.29 3 -0.37 5 8
mol:Ca2+ 0.082 0.071 0.29 1 -0.28 5 6
MAPK3 0.042 0.12 -10000 0 -0.63 9 9
STAT1 (dimer) 0.021 0.15 0.32 3 -0.39 34 37
MAPK1 0.01 0.2 -10000 0 -0.71 32 32
JAK2 0.035 0.016 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
JAK1 0.036 0.013 -10000 0 -10000 0 0
CAMK2D 0.029 0.052 -10000 0 -0.54 4 4
DAPK1 0.058 0.11 0.41 12 -0.37 2 14
SMAD7 0.022 0.07 0.23 8 -0.19 4 12
CBL/CRKL/C3G 0.069 0.069 0.33 3 -0.26 1 4
PI3K 0.05 0.12 -10000 0 -0.31 31 31
IFNG 0.061 0.063 -10000 0 -0.55 1 1
apoptosis 0.048 0.12 0.38 11 -0.46 9 20
CAMK2G 0.034 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.033 0.007 -10000 0 -10000 0 0
CAMK2A 0.033 0.006 -10000 0 -10000 0 0
CAMK2B 0.039 0.064 -10000 0 -0.54 4 4
FRAP1 0.003 0.1 0.3 10 -0.3 15 25
PRKCD 0.019 0.11 0.32 11 -0.29 26 37
RAP1B 0.033 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.003 0.096 0.16 4 -0.28 35 39
PTPN2 0.033 0.007 -10000 0 -10000 0 0
EP300 0.033 0.009 -10000 0 -10000 0 0
IRF1 0.066 0.11 0.4 35 -10000 0 35
STAT1 (dimer)/PIASy 0.072 0.09 0.3 26 -0.26 4 30
SOCS1 0.018 0.1 -10000 0 -1 5 5
mol:GDP 0.064 0.065 0.31 3 -0.25 2 5
CASP1 0.006 0.11 0.25 11 -0.27 55 66
PTGES2 0.034 0.005 -10000 0 -10000 0 0
IRF9 0.052 0.068 0.27 17 -10000 0 17
mol:PI-3-4-5-P3 0.032 0.1 -10000 0 -0.3 31 31
RAP1/GDP 0.051 0.051 -10000 0 -10000 0 0
CBL 0.04 0.068 0.31 4 -0.27 5 9
MAP3K1 0.045 0.071 0.33 3 -0.27 6 9
PIAS1 0.033 0.007 -10000 0 -10000 0 0
PIAS4 0.034 0.015 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.003 0.096 0.16 4 -0.28 35 39
PTPN11 0.044 0.072 0.3 6 -0.28 5 11
CREBBP 0.031 0.028 -10000 0 -0.54 1 1
RAPGEF1 0.033 0.006 -10000 0 -10000 0 0
Wnt signaling

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

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

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

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.016 0.15 0.32 10 -0.38 17 27
IKBKB 0.05 0.091 0.36 7 -0.35 2 9
AKT1 0.062 0.12 0.32 44 -0.25 2 46
IKBKG 0.056 0.077 0.33 8 -0.3 2 10
CALM1 0.031 0.086 0.28 8 -0.39 6 14
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
MAP3K1 0.067 0.14 0.44 4 -0.49 12 16
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.031 0.091 0.28 8 -0.34 11 19
DOK1 0.036 0.016 -10000 0 -10000 0 0
AP-1 -0.074 0.11 0.27 2 -0.24 65 67
LYN 0.03 0.015 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
BCR complex 0.041 0.07 0.25 3 -0.4 10 13
CD22 0.015 0.089 0.31 3 -0.45 11 14
CAMK2G 0.029 0.084 0.26 10 -0.37 6 16
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.023 0.044 -10000 0 -0.27 6 6
GO:0007205 0.032 0.092 0.28 8 -0.35 11 19
SYK 0.039 0.027 -10000 0 -10000 0 0
ELK1 0.033 0.09 0.28 8 -0.38 7 15
NFATC1 0.063 0.11 0.32 10 -0.41 8 18
B-cell antigen/BCR complex 0.041 0.07 0.25 3 -0.4 10 13
PAG1/CSK 0.043 0.028 0.25 1 -10000 0 1
NFKBIB 0.043 0.052 0.21 9 -0.13 15 24
HRAS 0.044 0.094 0.26 19 -0.34 9 28
NFKBIA 0.043 0.051 0.21 9 -0.12 10 19
NF-kappa-B/RelA/I kappa B beta 0.047 0.048 0.21 9 -10000 0 9
RasGAP/Csk 0.064 0.079 0.34 2 -0.36 7 9
mol:GDP 0.032 0.089 0.27 8 -0.35 9 17
PTEN 0.025 0.068 -10000 0 -0.54 7 7
CD79B 0.02 0.081 -10000 0 -0.54 10 10
NF-kappa-B/RelA/I kappa B alpha 0.047 0.047 0.21 9 -10000 0 9
GRB2 0.033 0.017 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.049 0.15 0.39 8 -0.46 16 24
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 0.03 0.09 0.29 7 -0.36 10 17
CSK 0.034 0.011 -10000 0 -10000 0 0
FOS -0.15 0.14 0.27 1 -0.36 59 60
CHUK 0.053 0.084 0.33 8 -0.31 7 15
IBTK 0.033 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.054 0.09 0.3 4 -0.36 6 10
PTPN6 0.03 0.1 0.28 9 -0.55 6 15
RELA 0.034 0.005 -10000 0 -10000 0 0
BCL2A1 0.042 0.043 0.19 10 -10000 0 10
VAV2 0.044 0.11 0.32 2 -0.57 6 8
ubiquitin-dependent protein catabolic process 0.046 0.052 0.21 9 -0.12 15 24
BTK 0.017 0.091 -10000 0 -0.97 4 4
CD19 0.022 0.093 0.28 5 -0.43 11 16
MAP4K1 0.036 0.02 -10000 0 -10000 0 0
CD72 0.062 0.058 -10000 0 -10000 0 0
PAG1 0.031 0.025 -10000 0 -10000 0 0
MAPK14 0.064 0.13 0.4 8 -0.43 11 19
SH3BP5 0.017 0.095 -10000 0 -0.54 14 14
PIK3AP1 0.029 0.096 0.33 6 -0.4 10 16
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.047 0.095 0.31 4 -0.44 7 11
RAF1 0.042 0.09 0.26 13 -0.34 7 20
RasGAP/p62DOK/SHIP 0.054 0.071 0.3 1 -0.35 7 8
CD79A 0.041 0.033 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.071 0.11 0.32 1 -0.24 58 59
RASA1 0.033 0.011 -10000 0 -10000 0 0
MAPK3 0.048 0.091 0.28 18 -0.34 4 22
MAPK1 0.038 0.083 0.29 7 -0.34 4 11
CD72/SHP1 0.092 0.12 0.37 18 -0.52 6 24
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.064 0.13 0.38 9 -0.42 12 21
actin cytoskeleton organization 0.069 0.11 0.32 16 -0.49 6 22
NF-kappa-B/RelA 0.092 0.087 0.35 9 -0.22 2 11
Calcineurin 0.042 0.091 -10000 0 -0.34 8 8
PI3K -0.001 0.073 -10000 0 -0.4 7 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.032 0.095 0.29 9 -0.42 10 19
SOS1 0.034 0.004 -10000 0 -10000 0 0
Bam32/HPK1 0.064 0.16 -10000 0 -0.64 15 15
DAPP1 0.031 0.16 -10000 0 -0.71 16 16
cytokine secretion 0.062 0.11 0.3 15 -0.38 8 23
mol:DAG 0.03 0.09 0.29 7 -0.36 10 17
PLCG2 0.021 0.074 -10000 0 -0.54 8 8
MAP2K1 0.039 0.087 0.27 9 -0.37 4 13
B-cell antigen/BCR complex/FcgammaRIIB 0.046 0.074 0.34 1 -0.43 7 8
mol:PI-3-4-5-P3 0.031 0.1 0.31 19 -0.3 6 25
ETS1 0.026 0.081 0.28 6 -0.34 7 13
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.075 0.079 0.43 1 -0.3 9 10
B-cell antigen/BCR complex/LYN 0.016 0.084 -10000 0 -0.47 11 11
MALT1 0.033 0.009 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.062 0.11 0.33 14 -0.52 6 20
B-cell antigen/BCR complex/LYN/SYK 0.043 0.098 0.34 3 -0.53 6 9
CARD11 0.033 0.094 0.28 12 -0.34 10 22
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
PPP3CA 0.029 0.052 -10000 0 -0.54 4 4
BCL10 0.033 0.007 -10000 0 -10000 0 0
IKK complex 0.044 0.058 0.18 31 -0.14 1 32
PTPRC 0.035 0.034 -10000 0 -10000 0 0
PDPK1 0.038 0.095 0.28 29 -0.23 2 31
PPP3CB 0.034 0.004 -10000 0 -10000 0 0
PPP3CC 0.024 0.046 -10000 0 -0.54 3 3
POU2F2 0.036 0.038 0.24 5 -10000 0 5
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.037 0.039 -10000 0 -0.34 4 4
VEGFR1 homodimer/NRP1 0.015 0.034 -10000 0 -0.33 4 4
mol:DAG 0.019 0.041 -10000 0 -0.3 4 4
VEGFR1 homodimer/NRP1/VEGFR 121 0.042 0.044 -10000 0 -0.3 3 3
CaM/Ca2+ 0.037 0.04 -10000 0 -0.29 4 4
HIF1A 0.039 0.055 -10000 0 -0.54 4 4
GAB1 0.033 0.027 -10000 0 -0.54 1 1
AKT1 -0.007 0.097 -10000 0 -0.37 3 3
PLCG1 0.019 0.041 -10000 0 -0.31 4 4
NOS3 0.02 0.081 -10000 0 -0.45 5 5
CBL 0.03 0.011 -10000 0 -10000 0 0
mol:NO 0.021 0.088 0.3 1 -0.45 6 7
FLT1 0.021 0.043 -10000 0 -0.39 4 4
PGF 0.034 0.011 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.061 0.05 -10000 0 -0.31 3 3
CALM1 0.033 0.006 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
eNOS/Hsp90 0.037 0.09 -10000 0 -0.44 6 6
endothelial cell proliferation 0.027 0.069 0.38 2 -0.3 1 3
mol:Ca2+ 0.019 0.041 -10000 0 -0.3 4 4
MAPK3 -0.005 0.035 0.25 1 -10000 0 1
MAPK1 -0.006 0.038 0.25 1 -10000 0 1
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
PLGF homodimer 0.034 0.011 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.38 0.26 -10000 0 -0.54 360 360
VEGFA homodimer 0.05 0.046 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.046 0.049 -10000 0 -0.34 3 3
platelet activating factor biosynthetic process 0.019 0.073 0.34 2 -10000 0 2
PI3K 0.038 0.11 -10000 0 -0.3 42 42
PRKCA -0.004 0.04 0.26 1 -0.28 4 5
PRKCB -0.003 0.039 -10000 0 -0.28 4 4
VEGFR1 homodimer/PLGF homodimer 0.038 0.039 -10000 0 -0.34 4 4
VEGFA 0.05 0.046 -10000 0 -10000 0 0
VEGFB 0.033 0.006 -10000 0 -10000 0 0
mol:IP3 0.019 0.041 -10000 0 -0.3 4 4
RASA1 0.02 0.042 -10000 0 -0.31 4 4
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer 0.021 0.043 -10000 0 -0.39 4 4
VEGFB homodimer 0.033 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.16 0.15 -10000 0 -0.4 48 48
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.036 0.11 -10000 0 -0.3 42 42
mol:L-citrulline 0.021 0.088 0.3 1 -0.45 6 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.075 0.058 -10000 0 -0.29 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.061 0.049 -10000 0 -0.31 3 3
CD2AP 0.033 0.009 -10000 0 -10000 0 0
PI3K/GAB1 0.048 0.12 -10000 0 -0.29 32 32
PDPK1 -0.001 0.093 -10000 0 -0.36 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.062 0.049 -10000 0 -0.31 3 3
mol:NADP 0.021 0.088 0.3 1 -0.45 6 7
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.071 0.055 -10000 0 -0.29 3 3
VEGFR1 homodimer/NRP2 0.038 0.04 -10000 0 -0.34 4 4
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.033 0.006 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 64 64
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
NUDC 0.033 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.069 0.091 0.25 1 -0.32 20 21
CaM/Ca2+ 0.025 0.004 -10000 0 -10000 0 0
KATNA1 0.032 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.029 0.079 0.28 3 -0.29 20 23
IQGAP1/CaM 0.047 0.014 -10000 0 -10000 0 0
DAB1 0.033 0.006 -10000 0 -10000 0 0
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
PLA2G7 0.043 0.097 -10000 0 -0.54 10 10
CALM1 0.033 0.006 -10000 0 -10000 0 0
DYNLT1 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.072 0.047 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.034 0.007 -10000 0 -10000 0 0
CDK5R1 0.033 0.014 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.011 0.004 -10000 0 -10000 0 0
CDK5R2 0.034 0.005 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.007 0.16 -10000 0 -0.36 79 79
YWHAE 0.031 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.041 0.079 0.38 2 -0.32 2 4
MAP1B -0.022 0.09 -10000 0 -0.29 49 49
RAC1 0.016 0.007 -10000 0 -10000 0 0
p35/CDK5 0.034 0.074 0.27 3 -0.28 13 16
RELN 0.012 0.11 -10000 0 -0.54 20 20
PAFAH/LIS1 0.039 0.067 -10000 0 -0.34 10 10
LIS1/CLIP170 0.034 0.014 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.032 0.069 -10000 0 -0.27 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.008 0.13 -10000 0 -0.3 54 54
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.025 0.074 0.32 4 -0.33 2 6
LIS1/IQGAP1 0.032 0.014 -10000 0 -10000 0 0
RHOA 0.016 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.015 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.08 0.067 -10000 0 -10000 0 0
PAFAH1B2 0.03 0.011 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.005 0.076 -10000 0 -0.21 45 45
NDEL1/Katanin 60/Dynein heavy chain 0.048 0.087 0.36 3 -0.31 2 5
LRP8 0.071 0.063 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.035 0.082 0.38 2 -0.32 2 4
P39/CDK5 0.035 0.073 0.27 2 -0.28 13 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.013 -10000 0 -10000 0 0
CDK5 0.006 0.076 0.28 2 -0.3 13 15
PPP2R5D 0.033 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.029 0.012 -10000 0 -10000 0 0
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.002 0.14 -10000 0 -0.32 79 79
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 79 79
CDC42 0.016 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.042 0.027 -10000 0 -10000 0 0
CDKN1B 0.019 0.07 0.31 3 -0.36 6 9
CDKN1A 0.021 0.065 0.28 2 -0.35 7 9
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.031 0.019 -10000 0 -10000 0 0
FOXO3 0.024 0.061 0.28 1 -0.38 5 6
AKT1 0.022 0.063 -10000 0 -0.36 8 8
BAD 0.033 0.007 -10000 0 -10000 0 0
AKT3 0.015 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.02 0.061 -10000 0 -0.35 8 8
AKT1/ASK1 0.034 0.093 -10000 0 -0.35 8 8
BAD/YWHAZ 0.051 0.032 -10000 0 -10000 0 0
RICTOR 0.033 0.006 -10000 0 -10000 0 0
RAF1 0.033 0.006 -10000 0 -10000 0 0
JNK cascade -0.033 0.091 0.34 8 -10000 0 8
TSC1 0.021 0.055 -10000 0 -0.37 5 5
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
AKT1/RAF1 0.056 0.076 0.3 2 -0.35 8 10
EP300 0.032 0.008 -10000 0 -10000 0 0
mol:GDP 0.022 0.062 -10000 0 -0.36 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.027 0.079 0.28 21 -0.35 8 29
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.003 0.046 0.25 2 -0.32 9 11
MAP3K5 0.004 0.12 -10000 0 -0.54 25 25
MAPKAP1 0.034 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.042 0.078 0.28 8 -0.28 2 10
YWHAH 0.033 0.014 -10000 0 -10000 0 0
AKT1S1 0.023 0.066 -10000 0 -0.35 8 8
CASP9 0.022 0.047 -10000 0 -0.3 4 4
YWHAB 0.032 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.05 0.083 0.35 2 -0.34 7 9
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
SRC 0.032 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.023 0.061 -10000 0 -0.42 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.054 -10000 0 -0.33 9 9
CHUK 0.021 0.059 -10000 0 -0.35 7 7
BAD/BCL-XL 0.057 0.072 0.31 1 -0.6 1 2
mTORC2 0.042 0.01 -10000 0 -10000 0 0
AKT2 0.017 0.006 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.044 0.11 0.37 4 -0.41 9 13
PDPK1 0.031 0.01 -10000 0 -10000 0 0
MDM2 0.025 0.069 0.28 4 -0.35 8 12
MAPKKK cascade -0.055 0.074 0.34 8 -0.3 2 10
MDM2/Cbp/p300 0.061 0.08 0.36 2 -0.58 1 3
TSC1/TSC2 0.025 0.079 0.28 22 -0.34 8 30
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.077 0.35 2 -0.55 1 3
glucose import -0.15 0.15 0.21 1 -0.31 235 236
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.021 0.054 0.19 1 -0.64 1 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 0.21 1 -0.31 235 236
GSK3A 0.021 0.063 -10000 0 -0.35 8 8
FOXO1 -0.004 0.093 -10000 0 -0.41 8 8
GSK3B 0.021 0.061 0.28 1 -0.35 7 8
SFN 0.033 0.04 -10000 0 -0.54 2 2
G1/S transition of mitotic cell cycle 0.032 0.075 0.39 1 -0.39 4 5
p27Kip1/14-3-3 family 0.031 0.044 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
KPNA1 0.034 0.005 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
RHEB 0.034 0.008 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.004 0.13 0.28 1 -0.48 18 19
BAG4 0.028 0.015 -10000 0 -10000 0 0
BAD 0.007 0.047 0.18 3 -0.18 7 10
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BAX 0.007 0.051 0.3 2 -0.18 8 10
EnzymeConsortium:3.1.4.12 0.003 0.032 0.089 4 -0.099 18 22
IKBKB 0.012 0.12 0.35 1 -0.47 12 13
MAP2K2 0.012 0.059 0.23 10 -0.24 1 11
MAP2K1 0.012 0.06 0.23 11 -0.24 1 12
SMPD1 0.004 0.04 0.2 1 -0.17 10 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.032 0.14 0.36 4 -0.48 14 18
MAP2K4 0.007 0.052 0.21 1 -0.24 5 6
protein ubiquitination 0.002 0.13 0.36 3 -0.45 17 20
EnzymeConsortium:2.7.1.37 0.011 0.062 0.24 9 -0.24 2 11
response to UV 0 0.001 0.003 8 -0.002 1 9
RAF1 0.011 0.06 0.21 18 -0.23 2 20
CRADD 0.034 0.005 -10000 0 -10000 0 0
mol:ceramide 0.008 0.049 0.16 3 -0.15 19 22
I-kappa-B-alpha/RELA/p50/ubiquitin 0.043 0.014 -10000 0 -10000 0 0
MADD 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.008 0.054 0.2 2 -0.26 5 7
TRADD 0.03 0.012 -10000 0 -10000 0 0
RELA/p50 0.034 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.06 0.23 11 -0.24 1 12
MAPK1 0.01 0.068 0.23 11 -0.25 3 14
p50/RELA/I-kappa-B-alpha 0.048 0.016 -10000 0 -10000 0 0
FADD 0.027 0.14 0.31 6 -0.47 16 22
KSR1 0.012 0.057 0.2 14 -0.18 8 22
MAPK8 0.004 0.056 0.28 3 -0.25 4 7
TRAF2 0.034 0.012 -10000 0 -10000 0 0
response to radiation 0 0 0.003 2 -10000 0 2
CHUK -0.006 0.12 -10000 0 -0.48 16 16
TNF R/SODD 0.038 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.025 0.07 0.18 24 -0.18 7 31
IKBKG -0.006 0.12 0.45 1 -0.47 16 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.002 0.14 -10000 0 -0.48 21 21
RELA 0.034 0.005 -10000 0 -10000 0 0
RIPK1 0.033 0.006 -10000 0 -10000 0 0
AIFM1 0.024 0.069 0.18 23 -0.18 9 32
TNF/TNF R/SODD 0.053 0.034 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
response to heat 0 0 0.003 2 -10000 0 2
CASP8 0.019 0.12 -10000 0 -0.66 15 15
NSMAF 0.016 0.13 0.28 3 -0.45 18 21
response to hydrogen peroxide 0 0.001 0.003 8 -0.002 1 9
BCL2 -0.074 0.22 -10000 0 -0.54 94 94
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.004 0.097 -10000 0 -10000 0 0
PLK1 0.13 0.22 0.62 19 -0.86 4 23
CDKN1B 0.099 0.18 0.55 5 -0.45 14 19
FOXO3 0.11 0.23 0.55 21 -0.62 16 37
KAT2B 0.02 0.031 0.084 38 -0.058 10 48
FOXO1/SIRT1 0.006 0.1 -10000 0 -0.33 9 9
CAT 0.054 0.37 0.68 7 -1.1 40 47
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
AKT1 0.052 0.045 0.22 1 -10000 0 1
FOXO1 0.002 0.11 -10000 0 -0.34 10 10
MAPK10 0.024 0.059 0.24 3 -0.29 10 13
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
FOXO4 0.045 0.12 0.43 3 -0.42 5 8
response to oxidative stress 0.023 0.032 0.09 38 -0.063 8 46
FOXO3A/SIRT1 0.084 0.2 0.46 14 -0.6 15 29
XPO1 0.034 0.005 -10000 0 -10000 0 0
EP300 0.035 0.009 -10000 0 -10000 0 0
BCL2L11 0.057 0.082 -10000 0 -0.82 3 3
FOXO1/SKP2 0.016 0.1 -10000 0 -0.31 9 9
mol:GDP 0.023 0.032 0.09 38 -0.063 8 46
RAN 0.034 0.005 -10000 0 -10000 0 0
GADD45A 0.081 0.21 0.5 1 -0.78 16 17
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.036 0.15 -10000 0 -0.54 20 20
MST1 0.047 0.042 -10000 0 -10000 0 0
CSNK1D 0.032 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.026 0.14 -10000 0 -0.46 26 26
YWHAB 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.029 0.041 0.24 3 -0.27 1 4
MAPK9 0.029 0.04 0.24 3 -10000 0 3
YWHAG 0.034 0.008 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
SIRT1 0.022 0.023 -10000 0 -10000 0 0
SOD2 0.096 0.2 0.55 10 -0.52 14 24
RBL2 0.037 0.32 0.57 1 -0.8 41 42
RAL/GDP 0.057 0.035 -10000 0 -10000 0 0
CHUK 0.048 0.042 -10000 0 -10000 0 0
Ran/GTP 0.024 0.014 -10000 0 -10000 0 0
CSNK1G2 0.033 0.007 -10000 0 -10000 0 0
RAL/GTP 0.057 0.041 -10000 0 -10000 0 0
CSNK1G1 0.033 0.007 -10000 0 -10000 0 0
FASLG 0.075 0.12 -10000 0 -1.4 1 1
SKP2 0.035 0.018 -10000 0 -10000 0 0
USP7 0.032 0.01 -10000 0 -10000 0 0
IKBKB 0.041 0.041 -10000 0 -10000 0 0
CCNB1 0.15 0.24 0.6 21 -0.84 4 25
FOXO1-3a-4/beta catenin 0.097 0.22 0.54 11 -0.4 43 54
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.1 -10000 0 -0.31 9 9
CSNK1A1 0.033 0.006 -10000 0 -10000 0 0
SGK1 0.02 0.031 0.084 38 -0.058 10 48
CSNK1G3 0.033 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.02 -10000 0 -10000 0 0
ZFAND5 0.045 0.11 -10000 0 -10000 0 0
SFN 0.033 0.04 -10000 0 -0.54 2 2
CDK2 0.039 0.021 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.055 0.13 -10000 0 -0.48 15 15
CREBBP 0.032 0.028 -10000 0 -0.54 1 1
FBXO32 0.12 0.35 0.66 23 -1.1 25 48
BCL6 0.021 0.4 -10000 0 -1.1 53 53
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.034 0.006 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
AKT1 0.026 0.14 0.37 2 -0.47 13 15
PTK2B 0.015 0.085 0.36 2 -0.43 1 3
VEGFR2 homodimer/Frs2 0.021 0.087 -10000 0 -0.33 27 27
CAV1 -0.38 0.26 -10000 0 -0.54 360 360
CALM1 0.033 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.048 0.092 -10000 0 -0.3 23 23
endothelial cell proliferation 0.051 0.13 0.39 11 -0.44 8 19
mol:Ca2+ 0.02 0.091 0.37 1 -0.5 4 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.068 0.093 -10000 0 -0.3 20 20
RP11-342D11.1 0.002 0.087 0.27 1 -0.43 7 8
CDH5 0.03 0.012 -10000 0 -10000 0 0
VEGFA homodimer 0.069 0.059 -10000 0 -0.28 3 3
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 0.006 0.12 -10000 0 -0.54 24 24
HRAS/GDP 0.03 0.08 -10000 0 -0.41 4 4
SH2D2A 0.043 0.047 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.056 0.12 -10000 0 -0.48 10 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.048 0.095 -10000 0 -0.31 19 19
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.056 0.1 -10000 0 -0.44 4 4
GRB10 0.017 0.11 -10000 0 -0.61 7 7
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
PAK1 0.043 0.045 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.067 0.099 -10000 0 -0.43 1 1
HRAS 0.034 0.013 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.027 0.081 -10000 0 -0.38 7 7
HIF1A 0.031 0.054 -10000 0 -0.54 4 4
FRS2 0.032 0.029 -10000 0 -0.54 1 1
oxygen and reactive oxygen species metabolic process 0.065 0.091 -10000 0 -0.29 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.033 0.006 -10000 0 -10000 0 0
Nck/Pak 0.052 0.037 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.044 0.095 -10000 0 -0.31 26 26
mol:GDP 0.042 0.09 -10000 0 -0.43 4 4
mol:NADP 0.032 0.11 0.58 1 -0.43 12 13
eNOS/Hsp90 0.046 0.11 0.57 1 -0.43 9 10
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 0.02 0.092 0.37 1 -0.5 4 5
HIF1A/ARNT 0.037 0.042 -10000 0 -0.34 4 4
SHB 0.035 0.018 -10000 0 -10000 0 0
VEGFA 0.05 0.047 -10000 0 -10000 0 0
VEGFC 0.02 0.084 -10000 0 -0.54 11 11
FAK1/Vinculin 0.04 0.11 0.37 1 -0.41 4 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.067 0.096 -10000 0 -0.32 5 5
PTPN6 0.033 0.015 -10000 0 -10000 0 0
EPAS1 0.009 0.14 -10000 0 -0.54 29 29
mol:L-citrulline 0.032 0.11 0.58 1 -0.43 12 13
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.062 0.093 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.049 0.11 -10000 0 -0.34 27 27
VEGFR2/3 heterodimer 0.022 0.088 -10000 0 -0.34 28 28
VEGFB 0.033 0.006 -10000 0 -10000 0 0
MAPK11 0.002 0.1 -10000 0 -0.46 8 8
VEGFR2 homodimer 0.003 0.096 -10000 0 -0.39 28 28
FLT1 0.032 0.013 -10000 0 -10000 0 0
NEDD4 0.028 0.058 -10000 0 -0.54 5 5
MAPK3 0.016 0.094 0.37 1 -0.45 4 5
MAPK1 0.012 0.094 0.34 2 -0.45 4 6
VEGFA145/NRP2 0.06 0.037 0.25 1 -10000 0 1
VEGFR1/2 heterodimer 0.021 0.088 -10000 0 -0.34 28 28
KDR 0.003 0.096 -10000 0 -0.39 28 28
VEGFA165/NRP1/VEGFR2 homodimer 0.052 0.1 -10000 0 -0.54 4 4
SRC 0.032 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.018 0.098 0.37 2 -0.46 4 6
PI3K 0.018 0.12 -10000 0 -0.5 8 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.05 0.092 -10000 0 -0.31 24 24
FES 0.017 0.096 -10000 0 -0.55 4 4
GAB1 0.041 0.1 -10000 0 -0.4 6 6
VEGFR2 homodimer/VEGFA homodimer/Src 0.049 0.089 -10000 0 -0.31 21 21
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
SOS1 0.034 0.004 -10000 0 -10000 0 0
ARNT 0.027 0.014 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.13 0.15 -10000 0 -0.44 40 40
VEGFR2 homodimer/VEGFA homodimer/Yes 0.048 0.093 -10000 0 -0.31 24 24
PI3K/GAB1 0.029 0.14 0.39 1 -0.45 13 14
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.075 0.096 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.031 0.1 -10000 0 -0.32 38 38
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
CDC42 0.019 0.098 0.37 1 -0.55 4 5
actin cytoskeleton reorganization 0.048 0.094 -10000 0 -0.31 19 19
PTK2 0.023 0.091 -10000 0 -0.44 3 3
EDG1 0.002 0.087 0.27 1 -0.43 7 8
mol:DAG 0.02 0.092 0.37 1 -0.5 4 5
CaM/Ca2+ 0.033 0.088 -10000 0 -0.47 4 4
MAP2K3 0.003 0.087 -10000 0 -0.53 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.045 0.12 -10000 0 -0.63 7 7
PLCG1 0.02 0.093 0.37 1 -0.51 4 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.066 0.093 -10000 0 -0.44 1 1
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
YES1 0.031 0.027 -10000 0 -0.54 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.051 0.093 -10000 0 -0.31 24 24
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.048 0.092 -10000 0 -0.31 23 23
cell migration 0.044 0.11 0.39 2 -0.47 2 4
mol:PI-3-4-5-P3 0.018 0.11 -10000 0 -0.47 8 8
FYN 0.029 0.037 -10000 0 -0.54 2 2
VEGFB/NRP1 0.022 0.09 -10000 0 -0.52 4 4
mol:NO 0.032 0.11 0.58 1 -0.43 12 13
PXN 0.034 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.013 0.071 -10000 0 -0.41 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.037 0.11 -10000 0 -0.62 7 7
VHL 0.035 0.018 -10000 0 -10000 0 0
ITGB3 0.035 0.018 -10000 0 -10000 0 0
NOS3 0.031 0.12 0.6 1 -0.48 12 13
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.12 -10000 0 -0.32 38 38
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.006 0.08 0.37 1 -0.44 4 5
PRKCB 0.005 0.085 0.36 1 -0.48 4 5
VCL 0.034 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.026 0.094 -10000 0 -0.32 27 27
VEGFR1/2 heterodimer/VEGFA homodimer 0.046 0.093 -10000 0 -0.31 24 24
VEGFA165/NRP2 0.06 0.037 0.25 1 -10000 0 1
MAPKKK cascade 0.062 0.12 0.39 5 -0.56 5 10
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFC homodimer 0.02 0.084 -10000 0 -0.54 11 11
NCK1 0.034 0.005 -10000 0 -10000 0 0
ROCK1 0.033 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.11 0.44 2 -0.41 4 6
MAP3K13 0.017 0.095 -10000 0 -0.55 4 4
PDPK1 0.005 0.098 -10000 0 -0.42 8 8
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.034 0.005 -10000 0 -10000 0 0
SPHK1 0.033 0.059 -10000 0 -0.54 4 4
GNAI2 0.033 0.01 -10000 0 -10000 0 0
mol:S1P 0.02 0.034 0.2 2 -0.26 4 6
GNAO1 0.03 0.012 -10000 0 -10000 0 0
mol:Sphinganine-1-P 0.018 0.045 -10000 0 -0.4 4 4
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.053 0.04 -10000 0 -0.21 3 3
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.045 0.017 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.011 0.031 -10000 0 -0.24 4 4
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 181 181
S1P/S1P5/G12 0.042 0.039 -10000 0 -0.22 4 4
S1P/S1P3/Gq 0.036 0.053 -10000 0 -0.29 6 6
S1P/S1P4/Gi -0.067 0.15 0.27 1 -0.34 59 60
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.063 -10000 0 -0.54 6 6
GNA14 0.043 0.067 -10000 0 -0.54 4 4
GNA15 0.036 0.019 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.033 0.006 -10000 0 -10000 0 0
ABCC1 0.035 0.023 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.017 0.1 -9999 0 -0.54 16 16
PLK4 0.055 0.051 -9999 0 -10000 0 0
regulation of centriole replication 0.024 0.085 -9999 0 -0.39 15 15
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.098 0.13 0.42 7 -10000 0 7
regulation of axonogenesis -0.021 0.05 0.2 13 -10000 0 13
myoblast fusion -0.065 0.073 -10000 0 -0.24 10 10
mol:GTP 0.048 0.044 -10000 0 -0.16 2 2
regulation of calcium-dependent cell-cell adhesion -0.09 0.065 -10000 0 -0.25 7 7
ARF1/GTP 0.052 0.043 -10000 0 -10000 0 0
mol:GM1 0.033 0.04 -10000 0 -10000 0 0
mol:Choline 0.018 0.075 -10000 0 -0.31 19 19
lamellipodium assembly 0.056 0.079 0.25 7 -0.33 1 8
MAPK3 0.071 0.077 0.21 117 -10000 0 117
ARF6/GTP/NME1/Tiam1 0.092 0.067 0.25 7 -10000 0 7
ARF1 0.027 0.014 -10000 0 -10000 0 0
ARF6/GDP 0.065 0.073 0.24 10 -10000 0 10
ARF1/GDP 0.056 0.069 -10000 0 -10000 0 0
ARF6 0.054 0.025 -10000 0 -10000 0 0
RAB11A 0.033 0.006 -10000 0 -10000 0 0
TIAM1 0.039 0.014 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.073 0.079 -10000 0 -10000 0 0
actin filament bundle formation -0.075 0.063 -10000 0 -10000 0 0
KALRN 0.04 0.056 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.045 0.017 -10000 0 -10000 0 0
RhoA/GDP 0.076 0.064 -10000 0 -10000 0 0
NME1 0.035 0.015 -10000 0 -10000 0 0
Rac1/GDP 0.078 0.063 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.048 0.044 -10000 0 -0.16 2 2
cortical actin cytoskeleton organization 0.056 0.079 0.25 7 -0.33 1 8
RAC1 0.034 0.005 -10000 0 -10000 0 0
liver development 0.048 0.044 -10000 0 -0.16 2 2
ARF6/GTP 0.048 0.044 -10000 0 -0.16 2 2
RhoA/GTP 0.062 0.04 -10000 0 -10000 0 0
mol:GDP 0.052 0.076 0.2 100 -0.2 1 101
ARF6/GTP/RAB11FIP3/RAB11A 0.075 0.044 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
PLD1 0.029 0.085 -10000 0 -0.35 19 19
RAB11FIP3 0.031 0.01 -10000 0 -10000 0 0
tube morphogenesis 0.056 0.079 0.25 7 -0.33 1 8
ruffle organization 0.021 0.05 -10000 0 -0.2 13 13
regulation of epithelial cell migration 0.048 0.044 -10000 0 -0.16 2 2
PLD2 0.042 0.045 -10000 0 -0.36 1 1
PIP5K1A 0.021 0.05 -10000 0 -0.2 13 13
mol:Phosphatidic acid 0.018 0.075 -10000 0 -0.31 19 19
Rac1/GTP 0.056 0.079 0.25 7 -0.33 1 8
EPO signaling pathway

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

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

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

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.011 0.11 -10000 0 -0.54 19 19
positive regulation of NF-kappaB transcription factor activity 0.022 0.085 -10000 0 -0.4 19 19
MAP2K4 0.015 0.085 -10000 0 -0.4 12 12
IKBKB 0.029 0.013 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.028 0.018 -10000 0 -10000 0 0
SMPD1 0.004 0.057 -10000 0 -0.27 18 18
IKBKG 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.014 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.022 0.086 -10000 0 -0.37 21 21
TRAIL/TRAILR3 0.023 0.086 -10000 0 -0.4 19 19
TRAIL/TRAILR1 0.023 0.086 -10000 0 -0.39 19 19
TRAIL/TRAILR4 0.023 0.086 -10000 0 -0.4 19 19
TRAIL/TRAILR1/DAP3/GTP 0.031 0.066 -10000 0 -0.31 13 13
IKK complex 0.024 0.074 -10000 0 -0.42 5 5
RIPK1 0.033 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.01 -10000 0 -10000 0 0
MAPK3 0 0.079 -10000 0 -0.4 19 19
MAP3K1 0.016 0.099 -10000 0 -0.47 13 13
TRAILR4 (trimer) 0.027 0.014 -10000 0 -10000 0 0
TRADD 0.029 0.012 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.028 0.018 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.081 -10000 0 -0.4 12 12
CFLAR 0.032 0.026 -10000 0 -0.54 1 1
MAPK1 0.001 0.077 -10000 0 -0.4 18 18
TRAIL/TRAILR1/FADD/TRADD/RIP 0.047 0.079 -10000 0 -0.29 13 13
mol:ceramide 0.004 0.057 -10000 0 -0.26 18 18
FADD 0.028 0.015 -10000 0 -10000 0 0
MAPK8 -0.001 0.1 -10000 0 -0.4 17 17
TRAF2 0.034 0.012 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.027 0.017 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.033 0.073 -10000 0 -0.33 14 14
DAP3 0.028 0.013 -10000 0 -10000 0 0
CASP10 0.024 0.077 0.34 3 -0.34 5 8
JNK cascade 0.022 0.085 -10000 0 -0.4 19 19
TRAIL (trimer) 0.011 0.11 -10000 0 -0.54 19 19
TNFRSF10C 0.028 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.035 0.064 -10000 0 -0.29 9 9
TRAIL/TRAILR2/FADD 0.032 0.074 -10000 0 -0.34 14 14
cell death 0.004 0.057 -10000 0 -0.26 18 18
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.002 0.081 -10000 0 -0.4 12 12
TRAILR2 (trimer) 0.027 0.016 -10000 0 -10000 0 0
CASP8 0.02 0.057 -10000 0 -0.58 3 3
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.046 0.08 -10000 0 -0.3 14 14
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.035 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.064 0.12 0.34 6 -0.33 10 16
ERC1 0.033 0.014 0.18 3 -10000 0 3
RIP2/NOD2 0.053 0.05 0.25 3 -10000 0 3
NFKBIA 0.014 0.022 -10000 0 -0.33 1 1
BIRC2 0.03 0.011 -10000 0 -10000 0 0
IKBKB 0.029 0.013 -10000 0 -10000 0 0
RIPK2 0.029 0.021 0.18 6 -10000 0 6
IKBKG 0.02 0.13 -10000 0 -0.39 41 41
IKK complex/A20 0.042 0.14 -10000 0 -0.42 20 20
NEMO/A20/RIP2 0.029 0.021 0.18 6 -10000 0 6
XPO1 0.034 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.031 0.15 -10000 0 -0.37 50 50
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.045 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.13 -10000 0 -0.41 20 20
BCL10/MALT1/TRAF6 0.064 0.021 -10000 0 -10000 0 0
NOD2 0.058 0.06 0.18 102 -10000 0 102
NFKB1 0.036 0.007 -10000 0 -10000 0 0
RELA 0.036 0.007 -10000 0 -10000 0 0
MALT1 0.033 0.009 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.045 0.017 -10000 0 -10000 0 0
ATM 0.03 0.012 -10000 0 -10000 0 0
TNF/TNFR1A 0.05 0.021 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
PRKCA 0.031 0.013 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
UBE2D3 0.034 0.005 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.074 0.023 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.022 -10000 0 -0.32 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.008 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
IKK complex 0.034 0.14 -10000 0 -0.43 21 21
CYLD 0.03 0.012 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.037 0.14 -10000 0 -0.42 18 18
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.073 0.038 -9999 0 -0.32 1 1
HDAC3 0.033 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.049 0.01 -9999 0 -10000 0 0
GATA1/HDAC5 0.048 0.011 -9999 0 -10000 0 0
GATA2/HDAC5 0.053 0.025 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.024 0.12 -9999 0 -0.34 48 48
HDAC9 0.035 0.016 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.033 0.11 -9999 0 -0.34 39 39
HDAC4/ANKRA2 0.045 0.032 -9999 0 -0.32 3 3
HDAC5/YWHAB 0.046 0.016 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.02 -9999 0 -0.17 3 3
GATA2 0.041 0.032 -9999 0 -10000 0 0
HDAC4/RFXANK 0.048 0.012 -9999 0 -10000 0 0
BCOR 0.034 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.031 0.028 -9999 0 -0.54 1 1
HDAC5 0.033 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.047 0.024 -9999 0 -0.4 1 1
Histones 0.024 0.05 -9999 0 -0.26 5 5
ADRBK1 0.031 0.01 -9999 0 -10000 0 0
HDAC4 0.033 0.006 -9999 0 -10000 0 0
XPO1 0.034 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.045 0.033 -9999 0 -0.4 2 2
HDAC4/Ubc9 0.045 0.017 -9999 0 -10000 0 0
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.045 0.018 -9999 0 -0.17 1 1
TUBA1B 0.035 0.012 -9999 0 -10000 0 0
HDAC6 0.034 0.003 -9999 0 -10000 0 0
HDAC5/RFXANK 0.048 0.013 -9999 0 -10000 0 0
CAMK4 0.035 0.017 -9999 0 -10000 0 0
Tubulin/HDAC6 0.059 0.057 -9999 0 -0.34 9 9
SUMO1 0.034 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.032 0.008 -9999 0 -10000 0 0
GATA1 0.034 0.003 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.031 0.01 -9999 0 -10000 0 0
NR3C1 -0.011 0.15 -9999 0 -0.54 39 39
SUMO1/HDAC4 0.051 0.051 -9999 0 -0.25 3 3
SRF 0.033 0.006 -9999 0 -10000 0 0
HDAC4/YWHAB 0.046 0.015 -9999 0 -10000 0 0
Tubulin 0.041 0.061 -9999 0 -0.4 9 9
HDAC4/14-3-3 E 0.045 0.019 -9999 0 -0.17 1 1
GNB1 0.034 0.011 -9999 0 -10000 0 0
RANGAP1 0.038 0.029 -9999 0 -10000 0 0
BCL6/BCoR 0.005 0.13 -9999 0 -0.4 48 48
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.017 -9999 0 -10000 0 0
HDAC4/SRF 0.065 0.021 -9999 0 -10000 0 0
HDAC4/ER alpha -0.029 0.2 -9999 0 -0.39 110 110
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.024 0.05 -9999 0 -0.26 5 5
cell motility 0.059 0.056 -9999 0 -0.34 9 9
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.031 0.01 -9999 0 -10000 0 0
HDAC7/HDAC3 0.025 0.004 -9999 0 -10000 0 0
BCL6 -0.023 0.17 -9999 0 -0.54 49 49
HDAC4/CaMK II delta B 0.033 0.006 -9999 0 -10000 0 0
Hsp90/HDAC6 0.049 0.01 -9999 0 -10000 0 0
ESR1 -0.06 0.26 -9999 0 -0.54 106 106
HDAC6/HDAC11 0.052 0.019 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.051 0.049 -9999 0 -0.26 3 3
NPC 0.02 0.002 -9999 0 -10000 0 0
MEF2C 0.005 0.12 -9999 0 -0.54 25 25
RAN 0.034 0.005 -9999 0 -10000 0 0
HDAC4/MEF2C 0.066 0.092 -9999 0 -0.3 24 24
GNG2 0.032 0.026 -9999 0 -0.54 1 1
NCOR2 0.034 0.004 -9999 0 -10000 0 0
TUBB2A 0.023 0.077 -9999 0 -0.54 9 9
HDAC11 0.038 0.025 -9999 0 -10000 0 0
HSP90AA1 0.033 0.006 -9999 0 -10000 0 0
RANBP2 0.034 0.004 -9999 0 -10000 0 0
ANKRA2 0.03 0.037 -9999 0 -0.54 2 2
RFXANK 0.034 0.005 -9999 0 -10000 0 0
nuclear import -0.038 0.02 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

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

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.032 0.008 -10000 0 -10000 0 0
HDAC4 0.033 0.006 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.008 -10000 0 -0.13 1 1
CDKN1A -0.01 0.044 -10000 0 -0.66 2 2
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
FOXO3 -0.006 0.004 -10000 0 -10000 0 0
FOXO1 -0.023 0.17 -10000 0 -0.54 47 47
FOXO4 0.017 0.015 -10000 0 -0.28 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
TAT 0.031 0.035 -10000 0 -0.54 1 1
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0.03 -10000 0 -0.4 2 2
PPARGC1A -0.024 0.18 -10000 0 -0.54 51 51
FHL2 -0.024 0.18 -10000 0 -0.54 52 52
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.044 0.016 -10000 0 -10000 0 0
HIST2H4A -0.005 0.008 0.13 1 -10000 0 1
SIRT1/FOXO3a 0.022 0.03 -10000 0 -0.2 1 1
SIRT1 0.03 0.012 0.22 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.053 0.029 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.051 0.053 -10000 0 -0.23 3 3
apoptosis -0.061 0.022 -10000 0 -10000 0 0
SIRT1/PGC1A 0.003 0.12 -10000 0 -0.33 53 53
p53/SIRT1 0.036 0.024 0.42 1 -10000 0 1
SIRT1/FOXO4 0.032 0.045 -10000 0 -0.23 3 3
FOXO1/FHL2/SIRT1 -0.018 0.16 -10000 0 -0.34 88 88
HIST1H1E 0.039 0.043 -10000 0 -0.28 1 1
SIRT1/p300 0.044 0.015 -10000 0 -10000 0 0
muscle cell differentiation -0.018 0.026 0.34 2 -10000 0 2
TP53 0.028 0.017 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.062 0.022 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
MEF2D 0.028 0.013 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.041 0.033 -10000 0 -0.29 2 2
ACSS2 0.014 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.018 0.026 -10000 0 -0.34 2 2
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.033 0.007 -10000 0 -10000 0 0
NFATC1 0.042 0.085 0.38 2 -0.42 4 6
NFATC2 0.003 0.074 0.29 1 -0.26 15 16
NFATC3 0.013 0.007 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.03 0.062 0.26 2 -0.26 7 9
Exportin 1/Ran/NUP214 0.065 0.017 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.053 0.065 -10000 0 -0.26 2 2
BCL2/BAX -0.036 0.17 -10000 0 -0.4 94 94
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.012 -10000 0 -10000 0 0
CaM/Ca2+ 0.023 0.012 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
BAD 0.033 0.007 -10000 0 -10000 0 0
CABIN1/MEF2D 0.037 0.06 -10000 0 -0.26 6 6
Calcineurin A alpha-beta B1/BCL2 -0.074 0.22 -10000 0 -0.54 94 94
FKBP8 0.034 0.008 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.036 0.059 0.26 6 -10000 0 6
KPNB1 0.032 0.008 -10000 0 -10000 0 0
KPNA2 0.057 0.058 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
SFN 0.033 0.04 -10000 0 -0.54 2 2
MAP3K8 -0.04 0.19 -10000 0 -0.54 64 64
NFAT4/CK1 alpha 0.029 0.038 -10000 0 -0.32 1 1
MEF2D/NFAT1/Cbp/p300 0.033 0.099 -10000 0 -0.31 17 17
CABIN1 0.03 0.061 0.26 2 -0.27 7 9
CALM1 0.033 0.008 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
CAMK4 0.035 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.009 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.053 0.039 -10000 0 -0.4 2 2
YWHAB 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.032 0.027 -10000 0 -0.54 1 1
MAPK9 0.034 0.009 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
FKBP1A 0.033 0.012 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.044 0.097 0.32 1 -0.38 8 9
PRKCH 0.029 0.051 -10000 0 -0.54 4 4
CABIN1/Cbp/p300 0.04 0.031 -10000 0 -0.4 1 1
CASP3 0.033 0.008 -10000 0 -10000 0 0
PIM1 0.035 0.015 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.009 -10000 0 -10000 0 0
apoptosis -0.003 0.058 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.04 0.047 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.01 0.063 -10000 0 -10000 0 0
BAD/BCL-XL 0.047 0.013 -10000 0 -10000 0 0
PRKCD 0.034 0.016 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0.002 -10000 0 -10000 0 0
PRKCA 0.031 0.013 -10000 0 -10000 0 0
PRKCG 0.033 0.006 -10000 0 -10000 0 0
PRKCQ 0.039 0.03 -10000 0 -10000 0 0
FKBP38/BCL2 -0.035 0.17 -10000 0 -0.39 95 95
EP300 0.03 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.033 0.007 -10000 0 -10000 0 0
NFATc/JNK1 0.057 0.085 0.34 1 -0.4 4 5
CaM/Ca2+/FKBP38 0.043 0.015 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSNK1A1 0.016 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.044 0.018 -10000 0 -10000 0 0
NFATc/ERK1 0.055 0.085 0.34 1 -0.4 4 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.065 0.063 -10000 0 -0.26 2 2
NR4A1 0.025 0.14 -10000 0 -0.47 24 24
GSK3B 0.033 0.009 -10000 0 -10000 0 0
positive T cell selection 0.013 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.006 0.061 -10000 0 -0.29 6 6
RCH1/ KPNB1 0.062 0.045 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
AKAP5 0.039 0.051 -10000 0 -0.54 2 2
MEF2D 0.027 0.016 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
NFATc/p38 alpha 0.057 0.084 0.34 1 -0.4 4 5
CREBBP 0.028 0.029 -10000 0 -0.54 1 1
BCL2 -0.074 0.22 -10000 0 -0.54 94 94
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.26 0.28 -10000 0 -0.54 252 252
CLTC 0.033 0.055 -10000 0 -0.42 3 3
calcium ion-dependent exocytosis 0.012 0.041 -10000 0 -0.37 2 2
Dynamin 2/GTP 0.03 0.013 -10000 0 -10000 0 0
EXOC4 0.034 0.005 -10000 0 -10000 0 0
CD59 0.02 0.045 -10000 0 -0.3 4 4
CPE -0.042 0.13 -10000 0 -0.34 84 84
CTNNB1 0.03 0.045 -10000 0 -0.54 3 3
membrane fusion 0.012 0.035 -10000 0 -0.35 1 1
CTNND1 0.031 0.055 0.37 1 -10000 0 1
DNM2 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.043 0.25 1 -0.32 2 3
TSHR 0.015 0.028 -10000 0 -0.34 3 3
INS 0.008 0.1 -10000 0 -0.5 18 18
BIN1 0.034 0.005 -10000 0 -10000 0 0
mol:Choline 0.012 0.035 -10000 0 -0.35 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.006 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.034 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.012 -10000 0 -10000 0 0
JUP 0.021 0.036 -10000 0 -0.29 2 2
ASAP2/amphiphysin II 0.042 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.004 -10000 0 -10000 0 0
CDH1 0.007 0.066 -10000 0 -0.38 4 4
clathrin-independent pinocytosis 0.025 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.03 0.038 -10000 0 -0.54 2 2
positive regulation of endocytosis 0.025 0.004 -10000 0 -10000 0 0
EXOC2 0.04 0.031 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.036 0.053 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.031 0.011 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.045 0.081 0.35 4 -10000 0 4
positive regulation of phagocytosis 0.017 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.04 0.029 -10000 0 -0.34 2 2
ACAP1 0.011 0.034 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.039 -10000 0 -0.29 2 2
clathrin heavy chain/ACAP1 0.029 0.068 0.29 4 -0.31 6 10
JIP4/KLC1 0.056 0.024 -10000 0 -10000 0 0
EXOC1 0.034 0.005 -10000 0 -10000 0 0
exocyst 0.036 0.053 -10000 0 -0.33 4 4
RALA/GTP 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.015 -10000 0 -10000 0 0
receptor recycling 0.025 0.004 -10000 0 -10000 0 0
CTNNA1 0.032 0.055 0.37 1 -10000 0 1
NME1 0.016 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0.037 0.065 0.29 2 -0.42 3 5
IL2RA 0.027 0.047 -10000 0 -0.36 3 3
VAMP3 0.017 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.1 0.13 -10000 0 -0.32 20 20
EXOC6 0.033 0.027 -10000 0 -0.54 1 1
PLD1 0.006 0.061 -10000 0 -0.29 20 20
PLD2 0.016 0.016 -10000 0 -0.27 1 1
EXOC5 0.033 0.006 -10000 0 -10000 0 0
PIP5K1C 0.019 0.037 -10000 0 -0.42 1 1
SDC1 0.035 0.051 -10000 0 -0.36 3 3
ARF6/GDP 0.028 0.011 -10000 0 -10000 0 0
EXOC7 0.032 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.047 0.084 -10000 0 -0.36 4 4
mol:Phosphatidic acid 0.012 0.035 -10000 0 -0.35 1 1
endocytosis -0.041 0.009 -10000 0 -10000 0 0
SCAMP2 0.033 0.007 -10000 0 -10000 0 0
ADRB2 -0.11 0.15 -10000 0 -0.34 29 29
EXOC3 0.032 0.008 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.034 0.014 -10000 0 -10000 0 0
KLC1 0.033 0.006 -10000 0 -10000 0 0
AVPR2 0.032 0.068 0.28 2 -0.38 4 6
RALA 0.034 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.041 0.083 0.34 2 -0.4 2 4
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.027 0.026 -10000 0 -10000 0 0
CRKL 0.032 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DOCK1 0.03 0.045 -10000 0 -0.54 3 3
ITGA4 0.039 0.028 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.084 0.032 -10000 0 -10000 0 0
EPO 0.053 0.049 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.053 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.052 0.022 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.062 0.036 -10000 0 -10000 0 0
lamellipodium assembly -0.003 0.11 -10000 0 -0.32 40 40
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
PI3K 0.006 0.12 -10000 0 -0.4 42 42
ARF6 0.034 0.005 -10000 0 -10000 0 0
JAK2 0.042 0.034 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
MADCAM1 0.034 0.013 -10000 0 -10000 0 0
cell adhesion 0.081 0.031 -10000 0 -10000 0 0
CRKL/CBL 0.044 0.018 -10000 0 -10000 0 0
ITGB1 0.033 0.006 -10000 0 -10000 0 0
SRC 0.02 0.064 0.38 2 -0.31 11 13
ITGB7 0.034 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.061 0.067 0.25 4 -0.34 11 15
p130Cas/Crk/Dock1 0.04 0.071 0.37 1 -0.28 14 15
VCAM1 0.023 0.086 0.18 7 -0.54 11 18
RHOA 0.033 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.081 0.035 -10000 0 -10000 0 0
BCAR1 -0.007 0.061 0.39 2 -0.29 11 13
EPOR 0.034 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.11 -10000 0 -0.33 38 38
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.033 0.006 -10000 0 -10000 0 0
VDR 0.032 0.037 -10000 0 -0.54 2 2
Cbp/p300/PCAF 0.039 0.023 -10000 0 -0.34 1 1
EP300 0.032 0.008 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.001 0.088 -10000 0 -0.34 12 12
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.007 0.11 0.22 21 -0.26 54 75
RAR alpha/9cRA/Cyclin H 0.076 0.065 -10000 0 -0.27 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.001 0.1 -10000 0 -0.34 16 16
CDC2 0 0.003 -10000 0 -10000 0 0
response to UV 0.001 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.045 0.046 -10000 0 -0.45 1 1
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RXRs/RARs/NRIP1/9cRA 0.023 0.12 0.38 1 -0.52 10 11
NCOA2 0.028 0.014 -10000 0 -10000 0 0
NCOA3 0.032 0.01 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
VDR/VDR/DNA 0.032 0.037 -10000 0 -0.54 2 2
RARG 0.034 0.008 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.046 0.009 -10000 0 -10000 0 0
MAPK3 0.031 0.013 -10000 0 -10000 0 0
MAPK1 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.033 0.028 -10000 0 -0.54 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.068 0.066 -10000 0 -0.33 2 2
RARA 0.021 0.023 0.2 1 -0.24 1 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.001 0.091 -10000 0 -0.34 13 13
PRKCA 0.032 0.019 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.027 0.13 0.4 4 -0.54 9 13
RXRG 0.021 0.033 -10000 0 -0.32 3 3
RXRA 0.039 0.054 0.22 1 -0.25 5 6
RXRB 0.027 0.019 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RBP1 0.006 0.13 -10000 0 -0.54 26 26
CRBP1/9-cic-RA 0.005 0.094 -10000 0 -0.4 26 26
RARB -0.053 0.21 -10000 0 -0.54 77 77
PRKCG 0.035 0.015 -10000 0 -10000 0 0
MNAT1 0.033 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.01 0.11 -10000 0 -0.46 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.027 0.1 -10000 0 -0.43 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.095 0.25 6 -0.32 10 16
RXRs/RARs/NRIP1/9cRA/HDAC3 0.027 0.13 0.4 4 -0.56 9 13
positive regulation of DNA binding 0.059 0.055 -10000 0 -0.26 3 3
NRIP1 0.02 0.19 0.56 2 -1.1 9 11
RXRs/RARs 0.029 0.12 0.33 4 -0.43 10 14
RXRs/RXRs/DNA/9cRA 0.026 0.056 -10000 0 -0.34 2 2
PRKACA 0.034 0.005 -10000 0 -10000 0 0
CDK7 0.033 0.007 -10000 0 -10000 0 0
TFIIH 0.065 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.08 0.049 -10000 0 -10000 0 0
CCNH 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
RAR gamma2/9cRA 0.063 0.023 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.032 0.008 -9999 0 -10000 0 0
Rac1/GDP 0.03 0.013 -9999 0 -10000 0 0
DOCK1 0.03 0.045 -9999 0 -0.54 3 3
ITGA4 0.039 0.028 -9999 0 -10000 0 0
RAC1 0.034 0.005 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.053 0.022 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.031 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.069 0.024 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.059 0.022 -9999 0 -10000 0 0
lamellipodium assembly -0.03 0.16 -9999 0 -0.43 55 55
PIK3CA 0.032 0.008 -9999 0 -10000 0 0
PI3K 0.006 0.12 -9999 0 -0.4 42 42
ARF6 0.034 0.005 -9999 0 -10000 0 0
TLN1 0.033 0.006 -9999 0 -10000 0 0
PXN 0.017 0.003 -9999 0 -10000 0 0
PIK3R1 -0.019 0.16 -9999 0 -0.54 45 45
ARF6/GTP 0.067 0.032 -9999 0 -10000 0 0
cell adhesion 0.072 0.028 -9999 0 -10000 0 0
CRKL/CBL 0.044 0.018 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.058 0.023 -9999 0 -10000 0 0
ITGB1 0.033 0.006 -9999 0 -10000 0 0
ITGB7 0.034 0.004 -9999 0 -10000 0 0
ARF6/GDP 0.03 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.069 0.064 -9999 0 -0.3 11 11
p130Cas/Crk/Dock1 0.052 0.043 -9999 0 -0.34 3 3
VCAM1 0.023 0.086 -9999 0 -0.54 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.075 0.029 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.072 0.033 -9999 0 -10000 0 0
BCAR1 0.029 0.012 -9999 0 -10000 0 0
mol:GDP -0.07 0.032 -9999 0 -10000 0 0
CBL 0.03 0.011 -9999 0 -10000 0 0
PRKACA 0.034 0.005 -9999 0 -10000 0 0
GIT1 0.032 0.011 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.075 0.029 -9999 0 -10000 0 0
Rac1/GTP -0.036 0.18 -9999 0 -0.49 55 55
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.039 0.085 0.34 1 -0.34 6 7
PDGFB-D/PDGFRB/SLAP 0.04 0.027 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.041 0.017 -10000 0 -10000 0 0
AKT1 0.025 0.12 0.39 16 -10000 0 16
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.045 0.094 0.35 3 -0.36 9 12
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
FGR 0.01 0.1 -10000 0 -0.52 11 11
mol:Ca2+ 0.037 0.092 0.34 3 -0.38 10 13
MYC 0.047 0.23 0.4 17 -0.78 29 46
SHC1 0.027 0.014 -10000 0 -10000 0 0
HRAS/GDP 0.048 0.045 0.26 1 -10000 0 1
LRP1/PDGFRB/PDGFB 0.065 0.023 -10000 0 -10000 0 0
GRB10 0.029 0.051 -10000 0 -0.54 4 4
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0.036 0.093 0.34 3 -0.39 10 13
PTEN 0.025 0.068 -10000 0 -0.54 7 7
GRB2 0.033 0.017 -10000 0 -10000 0 0
GRB7 0.029 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.05 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.046 0.041 -10000 0 -0.4 4 4
cell cycle arrest 0.04 0.027 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
HIF1A 0.019 0.11 0.37 16 -0.34 1 17
GAB1 0.039 0.1 0.33 4 -0.41 7 11
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.038 0.096 0.36 5 -0.34 6 11
PDGFB-D/PDGFRB 0.06 0.036 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.048 0.018 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.029 0.079 -10000 0 -0.37 4 4
positive regulation of MAPKKK cascade 0.05 0.01 -10000 0 -10000 0 0
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
mol:IP3 0.037 0.093 0.34 3 -0.39 10 13
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.033 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.042 0.02 -10000 0 -10000 0 0
SHB 0.035 0.018 -10000 0 -10000 0 0
BLK -0.034 0.17 -10000 0 -0.4 71 71
PTPN2 0.034 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.049 0.011 -10000 0 -10000 0 0
BCAR1 0.029 0.012 -10000 0 -10000 0 0
VAV2 0.038 0.11 0.36 4 -0.42 10 14
CBL 0.03 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.05 0.015 -10000 0 -10000 0 0
LCK 0.024 0.096 -10000 0 -0.49 11 11
PDGFRB 0.034 0.009 -10000 0 -10000 0 0
ACP1 0.033 0.006 -10000 0 -10000 0 0
HCK 0.024 0.07 -10000 0 -0.61 3 3
ABL1 0.032 0.096 0.33 4 -0.39 8 12
PDGFB-D/PDGFRB/CBL 0.033 0.11 0.34 1 -0.43 13 14
PTPN1 0.036 0.028 -10000 0 -10000 0 0
SNX15 0.034 0.005 -10000 0 -10000 0 0
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT1 0.058 0.054 -10000 0 -10000 0 0
cell proliferation 0.051 0.21 0.38 21 -0.67 30 51
SLA 0.029 0.024 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.05 0.059 0.42 3 -10000 0 3
SRC 0.02 0.06 -10000 0 -0.62 2 2
PI3K -0.01 0.065 -10000 0 -0.27 20 20
PDGFB-D/PDGFRB/GRB7/SHC 0.046 0.034 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.046 0.096 0.35 3 -0.37 9 12
LYN 0.02 0.055 -10000 0 -0.41 3 3
LRP1 0.034 0.004 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
STAT5B 0.033 0.01 -10000 0 -10000 0 0
STAT5A 0.032 0.027 -10000 0 -0.54 1 1
NCK1-2/p130 Cas 0.075 0.053 -10000 0 -10000 0 0
SPHK1 0.034 0.06 -10000 0 -0.55 4 4
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.037 0.093 0.34 3 -0.39 10 13
PLCG1 0.037 0.095 0.34 3 -0.4 10 13
NHERF/PDGFRB 0.073 0.049 -10000 0 -10000 0 0
YES1 0.008 0.11 -10000 0 -0.52 16 16
cell migration 0.072 0.049 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.066 0.055 -10000 0 -10000 0 0
SLC9A3R2 0.032 0.015 -10000 0 -10000 0 0
SLC9A3R1 0.058 0.056 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.08 0.069 -10000 0 -0.31 4 4
FYN 0.005 0.1 -10000 0 -0.43 18 18
DOK1 0.035 0.049 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.009 -10000 0 -10000 0 0
PDGFB 0.033 0.015 -10000 0 -10000 0 0
RAC1 0.024 0.16 0.38 2 -0.5 29 31
PRKCD 0.035 0.051 0.26 1 -10000 0 1
FER 0.034 0.049 -10000 0 -10000 0 0
MAPKKK cascade 0.05 0.1 0.36 21 -10000 0 21
RASA1 0.034 0.049 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0.007 -10000 0 -10000 0 0
p62DOK/Csk 0.053 0.044 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.05 0.019 -10000 0 -10000 0 0
chemotaxis 0.033 0.094 0.33 4 -0.38 8 12
STAT1-3-5/STAT1-3-5 0.079 0.048 -10000 0 -0.29 1 1
Bovine Papilomavirus E5/PDGFRB 0.025 0.007 -10000 0 -10000 0 0
PTPRJ 0.035 0.016 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.008 0.069 -10000 0 -0.28 25 25
TRAF2/ASK1 0.023 0.086 -10000 0 -0.29 32 32
ATM 0.03 0.012 -10000 0 -10000 0 0
MAP2K3 -0.015 0.13 0.28 1 -0.4 29 30
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.013 0.13 0.32 1 -0.36 38 39
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.036 0.017 -10000 0 -10000 0 0
TXN 0.01 0.006 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
GADD45A 0.024 0.072 -10000 0 -0.54 8 8
GADD45B 0.031 0.037 -10000 0 -0.54 2 2
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
MAP3K6 0.033 0.007 -10000 0 -10000 0 0
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
MAP3K4 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.022 0.1 -10000 0 -0.37 29 29
TAK1/TAB family -0.002 0.021 -10000 0 -0.21 1 1
RAC1/OSM/MEKK3 0.057 0.023 -10000 0 -10000 0 0
TRAF2 0.034 0.012 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.009 0.11 -10000 0 -0.34 21 21
TRAF6 0.009 0.002 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.039 0.064 -10000 0 -0.54 4 4
CCM2 0.034 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.047 0.043 -10000 0 -0.34 4 4
MAPK11 0.032 0.009 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.042 0.091 -10000 0 -0.3 29 29
OSM/MEKK3 0.044 0.017 -10000 0 -10000 0 0
TAOK1 0.016 0.013 -10000 0 -10000 0 0
TAOK2 0.015 0.007 -10000 0 -10000 0 0
TAOK3 0.016 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.004 0.12 -10000 0 -0.54 25 25
MAP3K10 0.032 0.039 -10000 0 -0.54 2 2
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TRX/ASK1 0.01 0.081 -10000 0 -0.32 27 27
GADD45/MTK1/MTK1 0.066 0.059 -10000 0 -0.29 10 10
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.047 0.037 -10000 0 -0.29 3 3
RGS9BP 0.053 0.064 -10000 0 -0.54 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.043 0.042 0.22 1 -0.34 2 3
mol:ADP 0.008 0.019 0.14 1 -0.4 1 2
GNAT2 0.03 0.045 -10000 0 -0.54 3 3
RGS9-1/Gbeta5/R9AP 0.048 0.1 -10000 0 -0.32 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.04 0.039 -10000 0 -0.3 5 5
GRK7 0.033 0.027 -10000 0 -0.54 1 1
CNGB3 0.032 0.03 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.025 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.056 0.075 0.25 16 -0.31 2 18
Cone PDE6 0.068 0.1 -10000 0 -0.3 21 21
Cone Metarhodopsin II 0.021 0.015 -10000 0 -0.31 1 1
Na + (4 Units) 0.056 0.045 0.23 1 -0.31 2 3
GNAT2/GDP 0.056 0.096 -10000 0 -0.28 30 30
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.021 0.046 -10000 0 -0.31 5 5
Cone Transducin 0.051 0.04 -10000 0 -0.31 3 3
SLC24A2 0.033 0.01 -10000 0 -10000 0 0
GNB3/GNGT2 0.043 0.02 -10000 0 -10000 0 0
GNB3 0.032 0.011 -10000 0 -10000 0 0
GNAT2/GTP 0.022 0.034 -10000 0 -0.34 4 4
CNGA3 0.042 0.052 -10000 0 -0.54 2 2
ARR3 0.034 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.044 0.042 0.23 1 -0.34 2 3
mol:Pi 0.048 0.099 -10000 0 -0.32 28 28
Cone CNG Channel 0.063 0.062 -10000 0 -0.29 6 6
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.033 0.01 -10000 0 -10000 0 0
RGS9 0.001 0.13 -10000 0 -0.54 27 27
PDE6C 0.033 0.028 -10000 0 -0.54 1 1
GNGT2 0.031 0.011 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.032 0.03 -10000 0 -0.54 1 1
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.075 0.14 0.38 1 -0.3 27 28
CaM/Ca2+ 0.025 0.004 -10000 0 -10000 0 0
AKT1 0.035 0.016 -10000 0 -10000 0 0
AKT2 0.033 0.006 -10000 0 -10000 0 0
STXBP4 0.031 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.09 0.13 0.41 1 -0.28 51 52
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.006 0.068 -10000 0 -0.4 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
YWHAB 0.032 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.053 0.031 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.034 0.017 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.025 0.004 -10000 0 -10000 0 0
RHOQ 0.033 0.026 -10000 0 -0.54 1 1
GYS1 0.016 0.018 0.25 2 -10000 0 2
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.032 0.026 -10000 0 -0.54 1 1
TC10/GTP/CIP4/Exocyst 0.043 0.026 -10000 0 -0.34 2 2
AS160/14-3-3 0.026 0.074 -10000 0 -0.35 7 7
VAMP2 0.031 0.011 -10000 0 -10000 0 0
SLC2A4 -0.099 0.14 0.42 1 -0.31 52 53
STX4 0.031 0.01 -10000 0 -10000 0 0
GSK3B 0.027 0.014 -10000 0 -10000 0 0
SFN 0.033 0.04 -10000 0 -0.54 2 2
LNPEP 0.034 0.016 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.005 0.053 0.24 10 -10000 0 10
DAPP1 0.034 0.1 0.28 7 -0.32 19 26
Src family/SYK family/BLNK-LAT/BTK-ITK 0.045 0.14 0.39 12 -0.45 18 30
mol:DAG 0.041 0.093 0.28 31 -0.2 1 32
HRAS 0.035 0.013 -10000 0 -10000 0 0
RAP1A 0.035 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.047 0.076 -10000 0 -0.33 6 6
PLCG2 0.021 0.074 -10000 0 -0.54 8 8
PLCG1 0.032 0.008 -10000 0 -10000 0 0
ARF5 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.006 0.054 0.32 6 -10000 0 6
ARF1/GTP 0.003 0.048 0.28 8 -10000 0 8
RHOA 0.033 0.007 -10000 0 -10000 0 0
YES1 0.031 0.027 -10000 0 -0.54 1 1
RAP1A/GTP -0.004 0.054 0.24 10 -10000 0 10
ADAP1 -0.006 0.051 0.3 6 -10000 0 6
ARAP3 -0.006 0.054 0.32 6 -10000 0 6
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PREX1 0.054 0.078 -10000 0 -0.54 4 4
ARHGEF6 0.014 0.11 -10000 0 -0.54 18 18
ARHGEF7 0.031 0.012 -10000 0 -10000 0 0
ARF1 0.027 0.014 -10000 0 -10000 0 0
NRAS 0.036 0.016 -10000 0 -10000 0 0
FYN 0.029 0.037 -10000 0 -0.54 2 2
ARF6 0.034 0.005 -10000 0 -10000 0 0
FGR 0.033 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.024 0.058 0.21 19 -0.16 1 20
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.035 0.012 -10000 0 -10000 0 0
ZAP70 0.038 0.024 -10000 0 -10000 0 0
mol:IP3 0.026 0.071 0.23 23 -0.23 1 24
LYN 0.03 0.015 -10000 0 -10000 0 0
ARF1/GDP 0.038 0.074 0.43 1 -0.33 6 7
RhoA/GDP 0.05 0.057 0.3 3 -10000 0 3
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.035 0.082 0.41 4 -0.35 2 6
SRC 0.032 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.005 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PTEN 0.024 0.066 -10000 0 -0.52 7 7
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.059 0.28 11 -10000 0 11
RhoA/GTP -0.005 0.056 0.4 3 -10000 0 3
Src family/SYK family/BLNK-LAT 0.043 0.091 0.3 11 -0.36 6 17
BLK 0.039 0.043 -10000 0 -10000 0 0
PDPK1 0.031 0.01 -10000 0 -10000 0 0
CYTH1 -0.006 0.051 0.3 6 -10000 0 6
HCK 0.036 0.022 -10000 0 -10000 0 0
CYTH3 -0.006 0.051 0.3 6 -10000 0 6
CYTH2 -0.006 0.051 0.3 6 -10000 0 6
KRAS 0.035 0.017 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.015 0.034 0.3 2 -10000 0 2
SGK1 0.019 0.042 0.41 2 -10000 0 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.031 0.076 0.45 1 -0.33 7 8
SOS1 0.034 0.004 -10000 0 -10000 0 0
SYK 0.039 0.027 -10000 0 -10000 0 0
ARF6/GDP 0.033 0.063 0.32 8 -10000 0 8
mol:PI-3-4-5-P3 -0.006 0.057 0.3 10 -10000 0 10
ARAP3/RAP1A/GTP -0.004 0.054 0.24 10 -10000 0 10
VAV1 0.038 0.025 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.008 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.053 0.04 0.29 2 -10000 0 2
PLEKHA1 -0.008 0.021 -10000 0 -0.34 2 2
Rac1/GDP 0.048 0.075 -10000 0 -0.38 4 4
LAT 0.035 0.024 -10000 0 -10000 0 0
Rac1/GTP 0.027 0.08 -10000 0 -0.34 7 7
ITK -0.003 0.059 0.32 5 -0.29 2 7
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.042 0.11 0.33 22 -0.27 2 24
LCK 0.048 0.043 -10000 0 -10000 0 0
BTK -0.002 0.058 0.31 6 -10000 0 6
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.047 0.031 -10000 0 -10000 0 0
KIRREL 0.032 0.017 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.047 0.031 -10000 0 -10000 0 0
PLCG1 0.032 0.008 -10000 0 -10000 0 0
ARRB2 0.031 0.01 -10000 0 -10000 0 0
WASL 0.033 0.026 -10000 0 -0.54 1 1
Nephrin/NEPH1/podocin/CD2AP 0.071 0.046 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.031 0.027 -10000 0 -0.24 1 1
FYN 0.065 0.096 0.29 69 -0.24 2 71
mol:Ca2+ 0.066 0.046 -10000 0 -10000 0 0
mol:DAG 0.067 0.047 -10000 0 -10000 0 0
NPHS2 0.032 0.017 -10000 0 -10000 0 0
mol:IP3 0.067 0.047 -10000 0 -10000 0 0
regulation of endocytosis 0.053 0.043 -10000 0 -0.22 2 2
Nephrin/NEPH1/podocin/Cholesterol 0.055 0.038 -10000 0 -10000 0 0
establishment of cell polarity 0.047 0.031 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.083 0.052 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.056 0.045 -10000 0 -0.23 2 2
NPHS1 0.048 0.031 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.056 0.043 -10000 0 -0.24 2 2
TJP1 0.032 0.027 -10000 0 -0.54 1 1
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0.007 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.068 0.048 -10000 0 -10000 0 0
CD2AP 0.033 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.068 0.049 -10000 0 -10000 0 0
GRB2 0.033 0.017 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.056 0.12 0.3 65 -0.3 14 79
cytoskeleton organization 0.032 0.053 0.26 8 -10000 0 8
Nephrin/NEPH1 0.04 0.026 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.057 0.042 -10000 0 -0.37 1 1
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.076 0.054 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.064 -10000 0 -0.31 1 1
SUMO1 0.034 0.005 -10000 0 -10000 0 0
ZFPM1 0.029 0.014 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.02 -10000 0 -0.17 3 3
FKBP3 0.034 0.005 -10000 0 -10000 0 0
Histones 0.076 0.049 -10000 0 -10000 0 0
YY1/LSF 0.031 0.057 -10000 0 -0.26 9 9
SMG5 0.029 0.016 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.031 0.025 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.042 0.044 -10000 0 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
RELA 0.028 0.043 -10000 0 -0.23 7 7
HDAC1/Smad7 0.064 0.019 -10000 0 -10000 0 0
RANGAP1 0.038 0.029 -10000 0 -10000 0 0
HDAC3/TR2 0.044 0.041 -10000 0 -0.29 1 1
NuRD/MBD3 Complex 0.039 0.06 -10000 0 -0.32 5 5
NF kappa B1 p50/RelA 0.043 0.068 0.4 1 -0.33 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.041 0.032 -10000 0 -10000 0 0
GATA1 0.034 0.003 -10000 0 -10000 0 0
Mad/Max 0.048 0.013 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.029 0.093 -10000 0 -0.38 12 12
RBBP7 0.037 0.021 -10000 0 -10000 0 0
NPC 0.02 0.002 -10000 0 -10000 0 0
RBBP4 0.033 0.006 -10000 0 -10000 0 0
MAX 0.033 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
NFKBIA 0.028 0.019 -10000 0 -0.27 1 1
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.027 0.054 -10000 0 -0.29 6 6
SIN3 complex 0.078 0.032 -10000 0 -10000 0 0
SMURF1 0.034 0.005 -10000 0 -10000 0 0
CHD3 0.031 0.015 -10000 0 -10000 0 0
SAP30 0.033 0.009 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.031 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.031 0.05 -10000 0 -0.36 2 2
YY1/HDAC2 0.034 0.047 -10000 0 -0.23 6 6
YY1/HDAC1 0.034 0.05 -10000 0 -0.24 7 7
NuRD/MBD2 Complex (MeCP1) 0.039 0.057 -10000 0 -0.25 5 5
PPARG -0.21 0.16 -10000 0 -0.31 337 337
HDAC8/hEST1B 0.057 0.028 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.045 0.039 -10000 0 -10000 0 0
MBD3L2 0.032 0.026 -10000 0 -0.54 1 1
ubiquitin-dependent protein catabolic process 0.063 0.019 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
NuRD/MBD3/MBD3L2 Complex 0.04 0.08 -10000 0 -0.37 7 7
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.03 0.013 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
YY1 0.016 0.015 -10000 0 -0.28 1 1
HDAC8 0.034 0.002 -10000 0 -10000 0 0
SMAD7 0.033 0.007 -10000 0 -10000 0 0
NCOR2 0.034 0.004 -10000 0 -10000 0 0
MXD1 0.034 0.007 -10000 0 -10000 0 0
STAT3 0.023 0.019 -10000 0 -0.33 1 1
NFKB1 0.034 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.034 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.049 0.058 -10000 0 -0.28 4 4
YY1/SAP30/HDAC1 0.05 0.053 -10000 0 -0.26 2 2
EP300 0.032 0.008 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.023 0.019 -10000 0 -0.32 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.019 -10000 0 -0.27 1 1
histone deacetylation 0.039 0.06 -10000 0 -0.27 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.033 0.042 -10000 0 -10000 0 0
nuclear export -0.056 0.028 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GATAD2B 0.028 0.013 -10000 0 -10000 0 0
GATAD2A 0.037 0.02 -10000 0 -10000 0 0
GATA2/HDAC3 0.049 0.044 -10000 0 -10000 0 0
GATA1/HDAC1 0.049 0.009 -10000 0 -10000 0 0
GATA1/HDAC3 0.045 0.038 -10000 0 -10000 0 0
CHD4 0.032 0.008 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.05 0.021 -10000 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.028 0.063 -10000 0 -0.31 10 10
NuRD Complex 0.041 0.076 -10000 0 -0.33 5 5
positive regulation of chromatin silencing 0.072 0.047 -10000 0 -10000 0 0
SIN3B 0.035 0.014 -10000 0 -10000 0 0
MTA2 0.033 0.006 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.052 0.05 -10000 0 -0.25 3 3
HDAC complex 0.081 0.031 -10000 0 -10000 0 0
GATA1/Fog1 0.042 0.02 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.063 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
negative regulation of cell growth 0.025 0.072 -10000 0 -0.33 14 14
NuRD/MBD2/PRMT5 Complex 0.039 0.057 -10000 0 -0.25 5 5
Ran/GTP/Exportin 1 0.051 0.049 -10000 0 -0.26 3 3
NF kappa B/RelA/I kappa B alpha 0.031 0.047 -10000 0 -0.32 1 1
SIN3/HDAC complex/NCoR1 0.021 0.064 -10000 0 -0.31 11 11
TFCP2 0.032 0.036 -10000 0 -0.54 2 2
NR2C1 0.033 0.026 -10000 0 -0.54 1 1
MBD3 0.033 0.007 -10000 0 -10000 0 0
MBD2 0.034 0.011 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.05 0.013 -10000 0 -10000 0 0
FBXW11 0.033 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.032 0.021 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.052 -10000 0 -0.26 1 1
NFKBIA 0.033 0.037 -10000 0 -0.28 1 1
MAPK14 0.034 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.03 0.016 -10000 0 -10000 0 0
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.037 0.022 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.032 0.018 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.031 0.015 -10000 0 -10000 0 0
PIK3CA 0.032 0.008 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.022 0.015 0.26 1 -10000 0 1
PIK3R1 -0.019 0.16 -10000 0 -0.54 45 45
NFKB1 0.014 0.007 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.04 0.05 -10000 0 -0.22 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.042 0.057 -10000 0 -0.29 2 2
SRC 0.032 0.008 -10000 0 -10000 0 0
PI3K 0.006 0.12 -10000 0 -0.4 42 42
NF kappa B1 p50/RelA 0.04 0.05 -10000 0 -0.22 3 3
IKBKB 0.029 0.013 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -10000 0 0
SYK 0.039 0.027 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.018 0.099 -10000 0 -0.28 35 35
cell death 0.04 0.055 -10000 0 -0.28 2 2
NF kappa B1 p105/c-Rel 0.032 0.021 -10000 0 -10000 0 0
LCK 0.048 0.043 -10000 0 -10000 0 0
BCL3 0.035 0.014 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.03 0.012 -10000 0 -10000 0 0
ELF1 0.045 0.029 -10000 0 -10000 0 0
CCNA2 0.08 0.067 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
JAK3 0.034 0.005 -10000 0 -10000 0 0
PIK3R1 -0.018 0.16 -10000 0 -0.54 45 45
JAK1 0.034 0.007 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.067 0.11 0.33 4 -0.38 6 10
SHC1 0.028 0.014 -10000 0 -10000 0 0
SP1 0.036 0.05 -10000 0 -0.36 8 8
IL2RA 0.036 0.057 -10000 0 -10000 0 0
IL2RB 0.036 0.022 -10000 0 -10000 0 0
SOS1 0.035 0.004 -10000 0 -10000 0 0
IL2RG 0.044 0.034 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.047 0.15 0.37 3 -0.73 12 15
PTPN11 0.035 0.004 -10000 0 -10000 0 0
CCND2 0.009 0.11 -10000 0 -0.77 9 9
LCK 0.049 0.043 -10000 0 -10000 0 0
GRB2 0.034 0.017 -10000 0 -10000 0 0
IL2 0.033 0.027 -10000 0 -0.54 1 1
CDK6 0.028 0.064 -10000 0 -0.54 6 6
CCND3 0.067 0.11 0.47 3 -0.45 1 4
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.046 0.055 -10000 0 -0.29 8 8
BIRC5 0.11 0.073 -10000 0 -10000 0 0
NFKBIA 0.023 0.041 0.27 5 -10000 0 5
CPEB1 0.019 0.092 -10000 0 -0.54 13 13
AKT1 0.024 0.041 0.3 3 -10000 0 3
NDEL1 0.031 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.04 0.034 -10000 0 -10000 0 0
NDEL1/TACC3 0.094 0.065 -10000 0 -10000 0 0
GADD45A 0.024 0.072 -10000 0 -0.54 8 8
GSK3B 0.005 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.056 0.049 -10000 0 -10000 0 0
MDM2 0.033 0.012 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.11 0.059 -10000 0 -10000 0 0
TP53 0.023 0.058 -10000 0 -10000 0 0
DLG7 0.023 0.032 -10000 0 -10000 0 0
AURKAIP1 0.034 0.013 -10000 0 -10000 0 0
ARHGEF7 0.031 0.012 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.1 0.069 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.04 0.034 -10000 0 -10000 0 0
AURKA 0.033 0.041 -10000 0 -10000 0 0
AURKB 0.044 0.053 -10000 0 -10000 0 0
CDC25B 0.036 0.046 -10000 0 -10000 0 0
G2/M transition checkpoint 0.01 0.024 -10000 0 -10000 0 0
mRNA polyadenylation 0.03 0.059 -10000 0 -0.28 13 13
Aurora A/CPEB 0.031 0.06 -10000 0 -0.28 13 13
Aurora A/TACC1/TRAP/chTOG 0.053 0.089 -10000 0 -0.29 18 18
BRCA1 0.036 0.021 -10000 0 -10000 0 0
centrosome duplication 0.056 0.049 -10000 0 -10000 0 0
regulation of centrosome cycle 0.091 0.063 -10000 0 -10000 0 0
spindle assembly 0.051 0.087 -10000 0 -0.29 18 18
TDRD7 0.034 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.071 0.27 5 -10000 0 5
CENPA 0.061 0.056 0.16 64 -0.23 1 65
Aurora A/PP2A 0.052 0.037 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.029 0.036 0.27 1 -10000 0 1
negative regulation of DNA binding 0.023 0.058 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.043 0.02 -10000 0 -10000 0 0
RASA1 0.033 0.011 -10000 0 -10000 0 0
Ajuba/Aurora A 0.016 0.028 -10000 0 -10000 0 0
mitotic prometaphase 0.006 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.041 -10000 0 -10000 0 0
TACC1 0.001 0.12 -10000 0 -0.54 24 24
TACC3 0.094 0.072 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.069 0.037 -10000 0 -10000 0 0
Aurora A/RasGAP 0.05 0.036 -10000 0 -10000 0 0
OAZ1 0.033 0.007 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.005 0.026 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.059 0.043 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.11 0.059 -10000 0 -10000 0 0
PPP2R5D 0.033 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.062 0.25 3 -10000 0 3
PAK1 0.043 0.045 -10000 0 -10000 0 0
CKAP5 0.035 0.015 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.045 0.04 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.078 0.054 0.24 19 -10000 0 19
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.017 0.029 -10000 0 -0.31 3 3
AURKB 0.056 0.057 -10000 0 -10000 0 0
AURKC 0.035 0.019 -10000 0 -10000 0 0
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.012 0.018 0.14 11 -10000 0 11
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.053 0.028 -10000 0 -10000 0 0
STXBP1 0.034 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.023 0.03 -10000 0 -0.16 1 1
RAB3GAP2/RIMS1/UNC13B 0.057 0.037 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.041 0.034 -10000 0 -10000 0 0
mol:ACh 0 0.031 0.092 12 -0.12 10 22
RAB3GAP2 0.028 0.014 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.041 0.054 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.023 0.03 -10000 0 -0.16 1 1
UNC13B 0.034 0.014 -10000 0 -10000 0 0
CHRNA1 0.034 0.01 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.052 0.077 0.17 13 -0.33 9 22
SNAP25 0.007 0.035 0.093 20 -0.3 5 25
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 0.069 0.1 -10000 0 -0.54 8 8
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.033 0.014 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.041 0.054 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.01 0.033 -10000 0 -0.34 5 5
ADCY5 -0.006 0.022 -10000 0 -0.34 1 1
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.003 0.019 -10000 0 -10000 0 0
ADCY1 -0.006 0.009 -10000 0 -10000 0 0
ADCY2 -0.009 0.043 -10000 0 -0.34 7 7
ADCY3 -0.007 0.007 -10000 0 -10000 0 0
ADCY8 -0.004 0.014 -10000 0 -10000 0 0
PRKCE 0.009 0.001 -10000 0 -10000 0 0
ADCY9 -0.004 0.016 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.035 0.069 0.27 7 -10000 0 7
Ephrin A reverse signaling

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

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

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

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.034 0.004 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.031 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.013 -10000 0 -10000 0 0
HIF1A/p53 0.046 0.06 -10000 0 -0.27 7 7
HIF1A 0.03 0.05 -10000 0 -0.27 6 6
COPS5 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.07 0.05 -10000 0 -10000 0 0
FIH (dimer) 0.034 0.005 -10000 0 -10000 0 0
CDKN2A 0.052 0.053 -10000 0 -10000 0 0
ARNT/IPAS 0.04 0.021 -10000 0 -10000 0 0
HIF1AN 0.034 0.005 -10000 0 -10000 0 0
GNB2L1 0.033 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.033 0.056 -10000 0 -0.28 7 7
CUL2 0.034 0.009 -10000 0 -10000 0 0
OS9 0.033 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.03 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.049 0.059 -10000 0 -0.28 7 7
PHD1-3/OS9 0.076 0.057 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.057 0.064 -10000 0 -0.32 1 1
VHL 0.035 0.018 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
HIF1A/JAB1 0.04 0.059 -10000 0 -0.28 6 6
EGLN3 0.06 0.057 -10000 0 -10000 0 0
EGLN2 0.035 0.016 -10000 0 -10000 0 0
EGLN1 0.027 0.014 -10000 0 -10000 0 0
TP53 0.031 0.014 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.044 0.066 -10000 0 -0.47 6 6
ARNT 0.027 0.014 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.032 0.008 -10000 0 -10000 0 0
HIF1A/p19ARF 0.059 0.068 0.26 3 -0.26 6 9
Rapid glucocorticoid signaling

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

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

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

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.015 0.035 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.035 0.052 0.15 7 -0.17 4 11
AP2 0.049 0.017 0.25 1 -10000 0 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.043 0.015 -10000 0 -10000 0 0
CLTB 0.033 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.019 -10000 0 -10000 0 0
CD4 0.032 0.009 -10000 0 -10000 0 0
CLTA 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP 0.015 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.012 0.021 0.18 5 -10000 0 5
mol:Choline 0.008 0.02 -10000 0 -0.2 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.015 -10000 0 -10000 0 0
DDEF1 0.008 0.02 -10000 0 -0.2 1 1
ARF1/GDP 0.002 0.022 -10000 0 -10000 0 0
AP2M1 0.034 0.009 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.008 -10000 0 -10000 0 0
Rac/GTP 0.028 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.033 0.024 -10000 0 -10000 0 0
ARFIP2 0.021 0.026 -10000 0 -10000 0 0
COPA 0.028 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.016 0.032 -10000 0 -0.2 3 3
ARF1/GTP/ARHGAP10 0.018 0.01 -10000 0 -10000 0 0
GGA3 0.032 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.016 0.041 -10000 0 -0.23 9 9
AP2A1 0.034 0.012 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.032 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.018 0.05 -10000 0 -0.24 14 14
Arfaptin 2/Rac/GDP 0.041 0.016 -10000 0 -10000 0 0
CYTH2 -0.001 0.002 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.021 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.025 0.032 -10000 0 -10000 0 0
PLD2 0.008 0.02 -10000 0 -0.2 1 1
ARF-GAP1/v-SNARE 0.009 0.008 -10000 0 -10000 0 0
PIP5K1A 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP/Membrin/GBF1/p115 0.016 0.024 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.02 -10000 0 -0.2 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.008 -10000 0 -10000 0 0
GOSR2 0.013 0.018 -10000 0 -0.26 1 1
USO1 0.012 0.024 -10000 0 -0.31 2 2
GBF1 0.013 0.02 -10000 0 -0.31 1 1
ARF1/GTP/Arfaptin 2 0.035 0.022 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.062 0.025 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.032 0.027 -10000 0 -0.54 1 1
SMAD2 -0.007 0.051 -10000 0 -0.28 4 4
SMAD3 0.027 0.045 0.29 2 -10000 0 2
SMAD3/SMAD4 0.058 0.065 -10000 0 -0.46 3 3
SMAD4/Ubc9/PIASy 0.058 0.034 -10000 0 -0.34 1 1
SMAD2/SMAD2/SMAD4 0.064 0.074 -10000 0 -0.32 1 1
PPM1A 0.033 0.006 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.009 0.057 -10000 0 -0.3 4 4
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
TRAP-1/SMAD4 0.047 0.025 -10000 0 -0.4 1 1
MAPK3 0.032 0.009 -10000 0 -10000 0 0
MAPK1 0.032 0.008 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
CTDSP1 0.034 0.005 -10000 0 -10000 0 0
CTDSP2 0.033 0.006 -10000 0 -10000 0 0
CTDSPL 0.031 0.037 -10000 0 -0.54 2 2
KPNB1 0.032 0.008 -10000 0 -10000 0 0
TGFBRAP1 0.034 0.004 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
NUP153 0.033 0.006 -10000 0 -10000 0 0
KPNA2 0.057 0.058 -10000 0 -10000 0 0
PIAS4 0.035 0.015 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.048 0.022 -10000 0 -10000 0 0
ATM 0.03 0.012 -10000 0 -10000 0 0
UBE2D3 0.034 0.005 -10000 0 -10000 0 0
PRKDC 0.031 0.019 -10000 0 -10000 0 0
ATR 0.033 0.006 -10000 0 -10000 0 0
UBE2L3 0.032 0.008 -10000 0 -10000 0 0
FANCD2 0.024 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.089 0.058 0.32 1 -10000 0 1
XRCC5 0.034 0.005 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.049 0.033 -10000 0 -10000 0 0
MRE11A 0.03 0.011 -10000 0 -10000 0 0
DNA-PK 0.056 0.03 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.026 0.11 -10000 0 -0.47 11 11
FANCF 0.033 0.006 -10000 0 -10000 0 0
BRCA1 0.036 0.021 -10000 0 -10000 0 0
CCNE1 0.058 0.055 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.067 0.046 0.25 8 -10000 0 8
FANCG 0.034 0.011 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.052 0.024 -10000 0 -10000 0 0
FANCE 0.033 0.027 -10000 0 -0.54 1 1
FANCC 0.035 0.016 -10000 0 -10000 0 0
NBN 0.028 0.015 -10000 0 -10000 0 0
FANCA 0.061 0.063 -10000 0 -10000 0 0
DNA repair 0.075 0.1 0.33 9 -0.4 2 11
BRCA1/BARD1/ubiquitin 0.052 0.024 -10000 0 -10000 0 0
BARD1/DNA-PK 0.072 0.039 -10000 0 -10000 0 0
FANCL 0.034 0.004 -10000 0 -10000 0 0
mRNA polyadenylation -0.047 0.022 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.073 -10000 0 -0.31 3 3
BRCA1/BACH1/BARD1/TopBP1 0.068 0.028 0.25 1 -10000 0 1
BRCA1/BARD1/P53 0.078 0.037 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.063 0.031 -10000 0 -10000 0 0
BRCA1/BACH1 0.036 0.021 -10000 0 -10000 0 0
BARD1 0.037 0.022 -10000 0 -10000 0 0
PCNA 0.037 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.069 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.067 0.028 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.12 0.069 0.35 2 -10000 0 2
BARD1/DNA-PK/P53 0.077 0.05 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.052 0.024 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.048 0.039 -10000 0 -0.32 2 2
FA complex 0.043 0.054 -10000 0 -0.3 2 2
BARD1/EWS 0.049 0.02 -10000 0 -10000 0 0
RBBP8 0.013 0.028 -10000 0 -0.4 2 2
TP53 0.031 0.014 -10000 0 -10000 0 0
TOPBP1 0.034 0.012 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.075 0.036 -10000 0 -10000 0 0
BRCA1/BARD1 0.097 0.063 0.34 1 -10000 0 1
CSTF1 0.031 0.01 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.027 0.016 -10000 0 -10000 0 0
CDK2 0.037 0.021 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.072 -10000 0 -10000 0 0
RAD50 0.033 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.052 0.024 -10000 0 -10000 0 0
EWSR1 0.032 0.008 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.033 0.006 -9999 0 -9999 0 0
ITGB7 0.034 0.004 -9999 0 -9999 0 0
ITGA4 0.039 0.028 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.053 0.022 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.052 0.022 -9999 0 -9999 0 0
Glypican 2 network

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

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

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

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

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

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

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.048 0.015 -10000 0 -9999 0 0
FBXW11 0.033 0.006 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.006 -10000 0 -9999 0 0
CHUK 0.034 0.005 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.094 0.035 -10000 0 -9999 0 0
NFKB1 0.034 0.005 -10000 0 -9999 0 0
MAP3K14 0.033 0.007 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.051 0.016 -10000 0 -9999 0 0
RELB 0.036 0.019 -10000 0 -9999 0 0
NFKB2 0.035 0.012 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.047 0.017 0.23 1 -9999 0 1
regulation of B cell activation 0.046 0.017 0.22 1 -9999 0 1
Inferred Pathway Levels Matrix

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

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

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/2327737/2.GDAC_MergeDataFiles.Finished/BRCA-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/BRCA-TP/2401337/1.Gistic2_Analysis.Finished/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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