PARADIGM pathway analysis of mRNA expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1NK3BZN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Breast Invasive Carcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1NK3BZN
Overview
Introduction

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

Summary

There were 53 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Signaling mediated by p38-alpha and p38-beta 249
Signaling events mediated by Stem cell factor receptor (c-Kit) 222
Endothelins 159
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 152
EGFR-dependent Endothelin signaling events 146
Class IB PI3K non-lipid kinase events 126
IGF1 pathway 118
FOXM1 transcription factor network 113
Arf6 signaling events 110
Nongenotropic Androgen signaling 96
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 249 10980 44 -0.6 0.034 1000 -1000 -0.005 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 222 17363 78 -1 0.32 1000 -1000 -0.03 -1000
Endothelins 159 15357 96 -0.81 0.17 1000 -1000 -0.023 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 152 10385 68 -0.88 0.45 1000 -1000 -0.05 -1000
EGFR-dependent Endothelin signaling events 146 3081 21 -0.31 0.048 1000 -1000 -0.032 -1000
Class IB PI3K non-lipid kinase events 126 378 3 -0.11 -1000 1000 -1000 -0.022 -1000
IGF1 pathway 118 6731 57 -0.27 0.11 1000 -1000 -0.033 -1000
FOXM1 transcription factor network 113 5777 51 -0.12 0.71 1000 -1000 0.011 -1000
Arf6 signaling events 110 6854 62 -0.31 0.081 1000 -1000 -0.001 -1000
Nongenotropic Androgen signaling 96 5014 52 -0.57 0.3 1000 -1000 -0.017 -1000
Glucocorticoid receptor regulatory network 86 9916 114 -0.95 0.29 1000 -1000 -0.049 -1000
Signaling events mediated by PTP1B 80 6115 76 -0.37 0.19 1000 -1000 -0.031 -1000
S1P1 pathway 77 2797 36 -0.62 0.045 1000 -1000 -0.022 -1000
Calcium signaling in the CD4+ TCR pathway 74 2310 31 -0.35 0.039 1000 -1000 -0.031 -1000
PDGFR-alpha signaling pathway 70 3106 44 -0.7 0.063 1000 -1000 -0.029 -1000
BMP receptor signaling 68 5581 81 -0.4 0.11 1000 -1000 -0.027 -1000
Ephrin B reverse signaling 68 3299 48 -0.18 0.061 1000 -1000 -0.033 -1000
HIF-1-alpha transcription factor network 67 5139 76 -0.4 0.07 1000 -1000 -0.008 -1000
Ras signaling in the CD4+ TCR pathway 65 1119 17 -0.2 0.033 1000 -1000 -0.003 -1000
Plasma membrane estrogen receptor signaling 59 5119 86 -0.25 0.17 1000 -1000 -0.046 -1000
IL6-mediated signaling events 56 4234 75 -0.37 0.073 1000 -1000 -0.016 -1000
IL4-mediated signaling events 55 5041 91 -0.51 0.14 1000 -1000 -0.11 -1000
EPHB forward signaling 55 4675 85 -0.18 0.15 1000 -1000 -0.057 -1000
FAS signaling pathway (CD95) 53 2520 47 -0.88 0.06 1000 -1000 -0.023 -1000
IL23-mediated signaling events 51 3083 60 -0.79 0.065 1000 -1000 -0.004 -1000
Integrins in angiogenesis 49 4171 84 -0.39 0.13 1000 -1000 -0.034 -1000
S1P4 pathway 49 1226 25 -0.17 0.045 1000 -1000 -0.011 -1000
PLK1 signaling events 48 4107 85 -0.035 0.17 1000 -1000 -0.021 -1000
Visual signal transduction: Rods 47 2470 52 -0.43 0.074 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 46 4486 97 -0.36 0.04 1000 -1000 -0.045 -1000
Aurora B signaling 43 2881 67 -0.38 0.24 1000 -1000 -0.027 -1000
Signaling events mediated by the Hedgehog family 41 2142 52 -0.14 0.067 1000 -1000 -0.013 -1000
Glypican 1 network 41 2004 48 -0.39 0.07 1000 -1000 -0.022 -1000
E-cadherin signaling in keratinocytes 40 1731 43 -0.27 0.035 1000 -1000 -0.023 -1000
Nectin adhesion pathway 39 2485 63 -0.075 0.054 1000 -1000 -0.027 -1000
S1P5 pathway 39 679 17 -0.17 0.067 1000 -1000 -0.004 -1000
Insulin Pathway 39 2923 74 -0.28 0.091 1000 -1000 -0.028 -1000
p75(NTR)-mediated signaling 38 4785 125 -0.13 0.093 1000 -1000 -0.039 -1000
Stabilization and expansion of the E-cadherin adherens junction 37 2738 74 -0.27 0.074 1000 -1000 -0.056 -1000
TCGA08_retinoblastoma 37 297 8 -0.022 0.057 1000 -1000 -0.002 -1000
Presenilin action in Notch and Wnt signaling 36 2212 61 -0.38 0.1 1000 -1000 -0.043 -1000
ErbB4 signaling events 35 2439 69 -0.36 0.14 1000 -1000 -0.017 -1000
LPA receptor mediated events 35 3656 102 -0.35 0.094 1000 -1000 -0.062 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 33 2889 85 -0.54 0.046 1000 -1000 -0.029 -1000
Signaling events regulated by Ret tyrosine kinase 33 2734 82 -0.1 0.11 1000 -1000 -0.047 -1000
ErbB2/ErbB3 signaling events 31 2036 65 -0.35 0.047 1000 -1000 -0.04 -1000
IL27-mediated signaling events 31 1588 51 -0.37 0.065 1000 -1000 -0.037 -1000
Neurotrophic factor-mediated Trk receptor signaling 31 3732 120 -0.25 0.12 1000 -1000 -0.039 -1000
Syndecan-1-mediated signaling events 29 1010 34 -0.042 0.11 1000 -1000 -0.014 -1000
TCGA08_rtk_signaling 29 772 26 -0.27 0.042 1000 -1000 -0.024 -1000
FOXA2 and FOXA3 transcription factor networks 28 1294 46 -0.74 0.05 1000 -1000 -0.011 -1000
Regulation of nuclear SMAD2/3 signaling 27 3682 136 -0.37 0.075 1000 -1000 -0.039 -1000
Syndecan-2-mediated signaling events 27 1908 69 -0.32 0.13 1000 -1000 -0.028 -1000
amb2 Integrin signaling 26 2187 82 -0.53 0.13 1000 -1000 -0.015 -1000
TCR signaling in naïve CD8+ T cells 26 2497 93 -0.04 0.082 1000 -1000 -0.042 -1000
Canonical Wnt signaling pathway 26 1348 51 -0.38 0.16 1000 -1000 -0.028 -1000
S1P3 pathway 26 1126 42 -0.17 0.062 1000 -1000 -0.023 -1000
Coregulation of Androgen receptor activity 25 1931 76 -0.23 0.053 1000 -1000 -0.016 -1000
IL1-mediated signaling events 25 1559 62 -0.051 0.067 1000 -1000 -0.019 -1000
RXR and RAR heterodimerization with other nuclear receptor 25 1312 52 -0.38 0.1 1000 -1000 -0.016 -1000
mTOR signaling pathway 24 1320 53 -0.051 0.044 1000 -1000 -0.041 -1000
Syndecan-3-mediated signaling events 24 857 35 -0.37 0.074 1000 -1000 -0.02 -1000
Angiopoietin receptor Tie2-mediated signaling 24 2127 88 -0.39 0.13 1000 -1000 -0.054 -1000
IL12-mediated signaling events 23 2060 87 -0.83 0.088 1000 -1000 -0.034 -1000
Osteopontin-mediated events 23 886 38 -0.35 0.14 1000 -1000 -0.008 -1000
Ceramide signaling pathway 23 1774 76 -0.25 0.083 1000 -1000 -0.01 -1000
HIF-2-alpha transcription factor network 23 1017 43 -0.22 0.26 1000 -1000 -0.1 -1000
Thromboxane A2 receptor signaling 22 2347 105 -0.27 0.066 1000 -1000 -0.036 -1000
Reelin signaling pathway 21 1231 56 -0.056 0.084 1000 -1000 -0.026 -1000
TCGA08_p53 21 150 7 -0.009 0.028 1000 -1000 -0.002 -1000
Regulation of p38-alpha and p38-beta 21 1145 54 -0.32 0.071 1000 -1000 -0.038 -1000
Regulation of Telomerase 20 2057 102 -0.35 0.087 1000 -1000 -0.036 -1000
Syndecan-4-mediated signaling events 20 1389 67 -0.39 0.15 1000 -1000 -0.025 -1000
Regulation of Androgen receptor activity 20 1467 70 -0.43 0.078 1000 -1000 -0.034 -1000
Signaling mediated by p38-gamma and p38-delta 18 279 15 -0.006 0.034 1000 -1000 -0.032 -1000
Noncanonical Wnt signaling pathway 16 418 26 -0.016 0.04 1000 -1000 -0.032 -1000
Cellular roles of Anthrax toxin 16 625 39 -0.063 0.038 1000 -1000 -0.017 -1000
IL2 signaling events mediated by PI3K 16 949 58 -0.12 0.049 1000 -1000 -0.024 -1000
E-cadherin signaling in the nascent adherens junction 16 1264 76 -0.041 0.059 1000 -1000 -0.052 -1000
Caspase cascade in apoptosis 15 1162 74 -0.16 0.049 1000 -1000 -0.021 -1000
Hedgehog signaling events mediated by Gli proteins 15 1010 65 -0.17 0.077 1000 -1000 -0.028 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 15 687 45 -0.007 0.06 1000 -1000 -0.022 -1000
Signaling events mediated by PRL 15 531 34 -0.31 0.051 1000 -1000 -0.026 -1000
E-cadherin signaling events 15 77 5 0.006 0.034 1000 -1000 0.018 -1000
Wnt signaling 13 92 7 -0.016 0.04 1000 -1000 -0.018 -1000
BCR signaling pathway 13 1351 99 -0.15 0.093 1000 -1000 -0.044 -1000
IFN-gamma pathway 12 862 68 -0.02 0.099 1000 -1000 -0.036 -1000
Class I PI3K signaling events mediated by Akt 12 823 68 -0.15 0.06 1000 -1000 -0.023 -1000
ceramide signaling pathway 12 634 49 -0.072 0.053 1000 -1000 -0.014 -1000
PLK2 and PLK4 events 11 33 3 0.016 0.055 1000 -1000 -0.003 -1000
EPO signaling pathway 11 611 55 -0.091 0.068 1000 -1000 -0.011 -1000
Sphingosine 1-phosphate (S1P) pathway 10 284 28 -0.17 0.053 1000 -1000 -0.007 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 10 558 54 -0.041 0.082 1000 -1000 -0.025 -1000
FoxO family signaling 10 683 64 0 0.15 1000 -1000 -0.02 -1000
Signaling events mediated by VEGFR1 and VEGFR2 10 1295 125 -0.38 0.075 1000 -1000 -0.033 -1000
JNK signaling in the CD4+ TCR pathway 9 166 17 -0.04 0.089 1000 -1000 -0.014 -1000
VEGFR1 specific signals 9 529 56 -0.38 0.075 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class III 8 323 40 -0.061 0.062 1000 -1000 -0.034 -1000
TRAIL signaling pathway 8 418 48 -0.002 0.046 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class II 7 564 75 -0.058 0.066 1000 -1000 -0.029 -1000
Circadian rhythm pathway 7 171 22 -0.021 0.1 1000 -1000 -0.022 -1000
Paxillin-independent events mediated by a4b1 and a4b7 7 265 37 -0.02 0.085 1000 -1000 -0.019 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 7 624 83 -0.072 0.066 1000 -1000 -0.014 -1000
Retinoic acid receptors-mediated signaling 7 452 58 -0.055 0.08 1000 -1000 -0.005 -1000
Paxillin-dependent events mediated by a4b1 6 231 36 -0.07 0.075 1000 -1000 -0.032 -1000
Class I PI3K signaling events 6 439 73 -0.008 0.059 1000 -1000 -0.023 -1000
Arf6 trafficking events 6 492 71 -0.26 0.056 1000 -1000 -0.028 -1000
p38 MAPK signaling pathway 6 295 44 -0.016 0.066 1000 -1000 -0.014 -1000
Nephrin/Neph1 signaling in the kidney podocyte 5 172 34 -0.047 0.083 1000 -1000 -0.025 -1000
Visual signal transduction: Cones 5 199 38 0 0.069 1000 -1000 0 -1000
Insulin-mediated glucose transport 5 177 32 -0.099 0.053 1000 -1000 -0.011 -1000
PDGFR-beta signaling pathway 5 560 97 -0.035 0.08 1000 -1000 -0.044 -1000
Canonical NF-kappaB pathway 4 171 39 0 0.074 1000 -1000 -0.016 -1000
Aurora A signaling 4 289 60 0 0.12 1000 -1000 -0.007 -1000
Signaling events mediated by HDAC Class I 4 501 104 -0.21 0.082 1000 -1000 -0.035 -1000
Atypical NF-kappaB pathway 4 142 31 -0.02 0.048 1000 -1000 -0.003 -1000
IL2 signaling events mediated by STAT5 4 108 22 -0.02 0.081 1000 -1000 -0.015 -1000
LPA4-mediated signaling events 2 30 12 -0.01 0.035 1000 -1000 -0.02 -1000
Arf6 downstream pathway 2 118 43 -0.09 0.092 1000 -1000 -0.032 -1000
Effects of Botulinum toxin 2 72 26 0 0.07 1000 -1000 0 -1000
Ephrin A reverse signaling 1 7 7 0 0.044 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 1 27 27 0 0.078 1000 -1000 -0.027 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 1 52 33 0 0.075 1000 -1000 -0.031 -1000
Rapid glucocorticoid signaling 1 25 20 0 0.043 1000 -1000 0 -1000
Arf1 pathway 1 66 54 -0.001 0.062 1000 -1000 -0.008 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 22 23 -0.007 0.064 1000 -1000 -0.014 -1000
BARD1 signaling events 0 49 57 -0.075 0.12 1000 -1000 -0.045 -1000
a4b1 and a4b7 Integrin signaling 0 0 5 0.033 0.054 1000 -1000 0.023 -1000
Aurora C signaling 0 4 7 0 0.078 1000 -1000 -0.009 -1000
Glypican 2 network 0 0 4 0 0.032 1000 -1000 0 -1000
Alternative NF-kappaB pathway 0 2 13 0 0.094 1000 -1000 0 -1000
Total 4426 268828 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 0.4 4 -1 306 310
MKNK1 0.034 0.006 -10000 0 -10000 0 0
MAPK14 -0.2 0.2 -10000 0 -0.36 306 306
ATF2/c-Jun -0.26 0.32 -10000 0 -0.69 144 144
MAPK11 -0.19 0.2 -10000 0 -0.36 286 286
MITF -0.24 0.23 -10000 0 -0.42 308 308
MAPKAPK5 -0.23 0.22 -10000 0 -0.41 308 308
KRT8 -0.22 0.22 -10000 0 -0.39 304 304
MAPKAPK3 0.034 0.012 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.016 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.31 0.32 -10000 0 -0.55 309 309
CEBPB -0.22 0.23 0.3 1 -0.41 283 284
SLC9A1 -0.24 0.23 -10000 0 -0.42 304 304
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.24 0.24 -10000 0 -0.42 306 306
p38alpha-beta/MNK1 -0.25 0.28 -10000 0 -0.45 309 309
JUN -0.26 0.31 -10000 0 -0.68 144 144
PPARGC1A -0.28 0.29 0.28 1 -0.48 314 315
USF1 -0.21 0.22 0.33 4 -0.39 292 296
RAB5/GDP/GDI1 -0.17 0.18 -10000 0 -0.31 301 301
NOS2 -0.24 0.22 -10000 0 -0.41 308 308
DDIT3 -0.23 0.22 -10000 0 -0.41 306 306
RAB5A 0.034 0.005 -10000 0 -10000 0 0
HSPB1 -0.19 0.18 -10000 0 -0.34 272 272
p38alpha-beta/HBP1 -0.25 0.28 -10000 0 -0.45 306 306
CREB1 -0.25 0.24 -10000 0 -0.43 307 307
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.24 0.24 0.24 1 -0.42 293 294
RPS6KA4 -0.23 0.23 -10000 0 -0.41 304 304
PLA2G4A -0.36 0.27 -10000 0 -0.52 356 356
GDI1 -0.23 0.22 -10000 0 -0.41 308 308
TP53 -0.31 0.3 -10000 0 -0.54 297 297
RPS6KA5 -0.25 0.23 -10000 0 -0.42 315 315
ESR1 -0.29 0.27 0.32 1 -0.43 358 359
HBP1 0.034 0.005 -10000 0 -10000 0 0
MEF2C -0.26 0.26 -10000 0 -0.44 313 313
MEF2A -0.23 0.23 0.3 1 -0.41 304 305
EIF4EBP1 -0.25 0.25 -10000 0 -0.44 302 302
KRT19 -0.22 0.23 0.33 1 -0.39 300 301
ELK4 -0.21 0.22 0.33 2 -0.4 287 289
ATF6 -0.22 0.22 0.33 4 -0.39 295 299
ATF1 -0.25 0.24 -10000 0 -0.43 309 309
p38alpha-beta/MAPKAPK2 -0.22 0.24 -10000 0 -0.42 288 288
p38alpha-beta/MAPKAPK3 -0.25 0.28 -10000 0 -0.45 308 308
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 -0.38 369 369
CRKL -0.32 0.17 -10000 0 -0.4 389 389
HRAS -0.23 0.15 -10000 0 -0.35 215 215
mol:PIP3 -0.27 0.17 -10000 0 -0.39 280 280
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 -0.42 400 400
FOXO3 -0.27 0.16 -10000 0 -0.37 322 322
AKT1 -0.3 0.18 -10000 0 -0.39 354 354
BAD -0.28 0.16 -10000 0 -0.37 331 331
megakaryocyte differentiation -0.32 0.17 -10000 0 -0.41 398 398
GSK3B -0.28 0.16 -10000 0 -0.38 273 273
RAF1 -0.19 0.13 -10000 0 -0.32 51 51
SHC1 0.027 0.014 -10000 0 -10000 0 0
STAT3 -0.33 0.18 -10000 0 -0.42 396 396
STAT1 -0.81 0.43 -10000 0 -1 406 406
HRAS/SPRED1 -0.19 0.14 -10000 0 -0.33 53 53
cell proliferation -0.33 0.17 -10000 0 -0.41 400 400
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 -0.4 399 399
HRAS/SPRED2 -0.19 0.14 -10000 0 -0.32 52 52
LYN/TEC/p62DOK -0.29 0.18 -10000 0 -0.4 335 335
MAPK3 -0.13 0.098 -10000 0 -0.3 9 9
STAP1 -0.32 0.18 -10000 0 -0.41 396 396
GRAP2 0.034 0.019 -10000 0 -10000 0 0
JAK2 -0.68 0.37 -10000 0 -0.85 406 406
STAT1 (dimer) -0.79 0.42 -10000 0 -0.99 406 406
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.28 0.19 -10000 0 -0.4 322 322
actin filament polymerization -0.33 0.17 -10000 0 -0.41 403 403
LYN 0.03 0.015 0.18 2 -10000 0 2
STAP1/STAT5A (dimer) -0.47 0.26 -10000 0 -0.58 407 407
PIK3R1 -0.021 0.17 -10000 0 -0.55 47 47
CBL/CRKL/GRB2 -0.28 0.17 -10000 0 -0.38 341 341
PI3K -0.32 0.2 -10000 0 -0.42 364 364
PTEN 0.026 0.067 -10000 0 -0.54 7 7
SCF/KIT/EPO/EPOR -0.95 0.51 -10000 0 -1.2 403 403
MAPK8 -0.33 0.18 -10000 0 -0.42 400 400
STAT3 (dimer) -0.33 0.17 -10000 0 -0.41 396 396
positive regulation of transcription -0.11 0.083 -10000 0 -0.26 6 6
mol:GDP -0.24 0.16 -10000 0 -0.36 220 220
PIK3C2B -0.3 0.18 -10000 0 -0.42 315 315
CBL/CRKL -0.3 0.16 -10000 0 -0.38 377 377
FER -0.33 0.18 -10000 0 -0.42 400 400
SH2B3 -0.33 0.18 -10000 0 -0.42 401 401
PDPK1 -0.24 0.17 -10000 0 -0.37 245 245
SNAI2 -0.34 0.2 -10000 0 -0.45 362 362
positive regulation of cell proliferation -0.58 0.3 -10000 0 -0.73 408 408
KITLG -0.011 0.07 -10000 0 -0.56 2 2
cell motility -0.58 0.3 -10000 0 -0.73 408 408
PTPN6 0.05 0.021 0.2 4 -10000 0 4
EPOR -0.23 0.19 -10000 0 -1.1 13 13
STAT5A (dimer) -0.48 0.26 -10000 0 -0.6 408 408
SOCS1 0.032 0.012 -10000 0 -10000 0 0
cell migration 0.32 0.17 0.41 397 -10000 0 397
SOS1 0.034 0.004 -10000 0 -10000 0 0
EPO 0.01 0.064 0.18 7 -10000 0 7
VAV1 0.038 0.025 -10000 0 -10000 0 0
GRB10 -0.34 0.18 -10000 0 -0.42 400 400
PTPN11 0.047 0.009 -10000 0 -10000 0 0
SCF/KIT -0.35 0.19 -10000 0 -0.44 403 403
GO:0007205 0.018 0.009 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.29 12 12
CBL 0.03 0.011 -10000 0 -10000 0 0
KIT -1 0.53 -10000 0 -1.3 403 403
MAP2K2 -0.15 0.11 -10000 0 -0.29 12 12
SHC/Grb2/SOS1 -0.27 0.18 -10000 0 -0.4 278 278
STAT5A -0.5 0.26 -10000 0 -0.62 408 408
GRB2 0.034 0.018 -10000 0 -10000 0 0
response to radiation -0.34 0.2 0.27 1 -0.44 362 363
SHC/GRAP2 0.039 0.026 -10000 0 -10000 0 0
PTPRO -0.33 0.18 -10000 0 -0.42 398 398
SH2B2 -0.33 0.18 -10000 0 -0.42 403 403
DOK1 0.036 0.016 0.18 6 -10000 0 6
MATK -0.33 0.18 -10000 0 -0.42 397 397
CREBBP -0.082 0.075 -10000 0 -0.19 63 63
BCL2 -0.43 0.51 -10000 0 -1.4 110 110
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.1 0.17 -10000 0 -0.34 146 146
PTK2B 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.17 0.29 -10000 0 -0.72 79 79
EDN1 -0.16 0.25 -10000 0 -0.54 154 154
EDN3 -0.39 0.25 -10000 0 -0.54 375 375
EDN2 0.098 0.078 -10000 0 -0.54 1 1
HRAS/GDP -0.25 0.23 -10000 0 -0.45 243 243
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.18 -10000 0 -0.34 167 167
ADCY4 -0.083 0.15 0.34 2 -0.3 145 147
ADCY5 -0.08 0.15 0.35 1 -0.3 141 142
ADCY6 -0.081 0.15 0.34 2 -0.3 142 144
ADCY7 -0.077 0.15 0.34 2 -0.29 141 143
ADCY1 -0.081 0.15 -10000 0 -0.3 141 141
ADCY2 -0.082 0.16 0.34 2 -0.3 144 146
ADCY3 -0.081 0.15 0.35 1 -0.3 144 145
ADCY8 -0.067 0.14 0.35 1 -0.3 105 106
ADCY9 -0.075 0.14 -10000 0 -0.3 125 125
arachidonic acid secretion -0.52 0.34 -10000 0 -0.69 376 376
ETB receptor/Endothelin-1/Gq/GTP -0.21 0.21 -10000 0 -0.36 300 300
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 -0.092 0.16 -10000 0 -0.32 145 145
ETA receptor/Endothelin-1/Gs/GTP -0.088 0.15 -10000 0 -0.31 148 148
mol:GTP -0.007 0.008 -10000 0 -10000 0 0
COL3A1 -0.1 0.17 -10000 0 -0.35 140 140
EDNRB -0.21 0.29 -10000 0 -0.54 224 224
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.099 0.17 -10000 0 -0.35 141 141
CYSLTR1 -0.1 0.18 0.38 2 -0.35 142 144
SLC9A1 -0.068 0.12 -10000 0 -0.23 141 141
mol:GDP -0.27 0.25 -10000 0 -0.46 260 260
SLC9A3 -0.39 0.39 -10000 0 -0.69 280 280
RAF1 -0.36 0.27 -10000 0 -0.51 333 333
JUN -0.25 0.43 -10000 0 -1 112 112
JAK2 -0.1 0.17 -10000 0 -0.35 143 143
mol:IP3 -0.21 0.22 -10000 0 -0.4 221 221
ETA receptor/Endothelin-1 -0.12 0.2 -10000 0 -0.4 149 149
PLCB1 -0.048 0.2 -10000 0 -0.55 70 70
PLCB2 0.024 0.014 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.29 0.19 -10000 0 -0.4 376 376
FOS -0.68 0.43 -10000 0 -0.96 365 365
Gai/GDP -0.2 0.36 -10000 0 -0.95 83 83
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.26 0.26 -10000 0 -0.52 211 211
BCAR1 0.029 0.013 -10000 0 -10000 0 0
PRKCB1 -0.21 0.21 -10000 0 -0.38 248 248
GNAQ -0.008 0.009 -10000 0 -10000 0 0
GNAZ 0.026 0.062 -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 -0.43 245 245
ETA receptor/Endothelin-1/Gq/GTP -0.097 0.15 -10000 0 -0.3 142 142
MAPK14 -0.22 0.22 -10000 0 -0.39 268 268
TRPC6 -0.18 0.31 -10000 0 -0.77 79 79
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 -0.54 183 183
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.23 -10000 0 -0.4 290 290
ETB receptor/Endothelin-2 -0.11 0.22 -10000 0 -0.32 244 244
ETB receptor/Endothelin-3 -0.42 0.27 -10000 0 -0.53 414 414
ETB receptor/Endothelin-1 -0.27 0.28 -10000 0 -0.48 300 300
MAPK3 -0.61 0.39 -10000 0 -0.84 367 367
MAPK1 -0.62 0.41 -10000 0 -0.86 368 368
Rac1/GDP -0.25 0.23 -10000 0 -0.44 250 250
cAMP biosynthetic process -0.031 0.15 0.4 5 -0.35 28 33
MAPK8 -0.18 0.3 -10000 0 -0.63 124 124
SRC 0.032 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.28 0.29 -10000 0 -0.49 276 276
p130Cas/CRK/Src/PYK2 -0.27 0.29 -10000 0 -0.56 205 205
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.25 0.23 -10000 0 -0.45 244 244
COL1A2 -0.23 0.27 0.39 2 -0.47 239 241
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.071 0.077 0.26 3 -0.35 4 7
mol:DAG -0.21 0.22 -10000 0 -0.41 221 221
MAP2K2 -0.47 0.32 -10000 0 -0.64 371 371
MAP2K1 -0.47 0.32 0.36 1 -0.64 371 372
EDNRA 0.006 0.057 -10000 0 -0.44 3 3
positive regulation of muscle contraction -0.091 0.14 -10000 0 -0.31 141 141
Gq family/GDP -0.21 0.22 -10000 0 -0.41 224 224
HRAS/GTP -0.26 0.24 -10000 0 -0.44 278 278
PRKCH -0.21 0.21 -10000 0 -0.42 210 210
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA -0.2 0.21 -10000 0 -0.42 191 191
PRKCB -0.21 0.21 -10000 0 -0.38 252 252
PRKCE -0.21 0.21 -10000 0 -0.42 202 202
PRKCD -0.21 0.21 -10000 0 -0.42 203 203
PRKCG -0.21 0.21 0.3 1 -0.41 211 212
regulation of vascular smooth muscle contraction -0.81 0.51 -10000 0 -1.1 365 365
PRKCQ -0.2 0.21 -10000 0 -0.42 198 198
PLA2G4A -0.59 0.4 -10000 0 -0.79 376 376
GNA14 0.026 0.073 -10000 0 -0.55 4 4
GNA15 0.021 0.031 -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 -0.092 0.16 -10000 0 -0.32 147 147
MMP1 0.17 0.15 0.41 84 -10000 0 84
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 0.031 -10000 0 -10000 0 0
NFATC2 -0.081 0.23 0.47 5 -0.54 58 63
NFATC3 -0.15 0.17 0.32 1 -0.32 217 218
CD40LG -0.67 0.53 0.79 4 -1 334 338
ITCH -0.064 0.14 -10000 0 -0.52 1 1
CBLB -0.067 0.14 -10000 0 -0.86 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.24 0.31 0.74 7 -0.68 75 82
JUNB 0.031 0.044 -10000 0 -0.54 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.077 0.17 -10000 0 -0.3 190 190
T cell anergy -0.13 0.21 -10000 0 -0.4 178 178
TLE4 -0.065 0.2 -10000 0 -0.55 45 45
Jun/NFAT1-c-4/p21SNFT -0.58 0.55 0.69 3 -0.96 317 320
AP-1/NFAT1-c-4 -0.8 0.68 0.92 5 -1.2 336 341
IKZF1 -0.044 0.17 0.46 10 -0.45 29 39
T-helper 2 cell differentiation -0.12 0.28 -10000 0 -0.78 45 45
AP-1/NFAT1 -0.3 0.3 0.53 6 -0.51 295 301
CALM1 -0.036 0.11 -10000 0 -0.31 1 1
EGR2 -0.8 0.76 0.7 4 -1.5 268 272
EGR3 -0.88 0.76 0.76 2 -1.4 322 324
NFAT1/FOXP3 -0.03 0.18 0.46 9 -0.4 48 57
EGR1 -0.43 0.23 -10000 0 -0.54 414 414
JUN -0.067 0.22 0.26 1 -0.54 89 90
EGR4 0.001 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.089 -10000 0 -0.17 190 190
GBP3 -0.078 0.24 0.44 2 -0.64 58 60
FOSL1 0.035 0.01 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.54 0.53 0.67 3 -0.91 313 316
DGKA -0.051 0.16 0.47 1 -0.41 45 46
CREM 0.033 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.76 0.55 -10000 0 -1.1 347 347
CTLA4 -0.023 0.16 0.42 15 -0.39 27 42
NFAT1-c-4 (dimer)/EGR1 -0.78 0.57 -10000 0 -1.1 352 352
NFAT1-c-4 (dimer)/EGR4 -0.56 0.52 0.67 1 -0.92 318 319
FOS -0.35 0.27 0.26 1 -0.54 344 345
IFNG -0.096 0.3 0.56 8 -0.76 50 58
T cell activation -0.39 0.34 0.69 3 -0.7 210 213
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 0.74 300 -0.66 3 303
TNF -0.67 0.48 -10000 0 -0.97 348 348
FASLG -0.88 0.78 0.86 3 -1.4 332 335
TBX21 0.028 0.15 0.29 12 -0.54 30 42
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.043 0.036 0.24 6 -10000 0 6
PTPN1 -0.047 0.16 0.42 1 -0.45 29 30
NFAT1-c-4/ICER1 -0.55 0.53 0.61 1 -0.92 316 317
GATA3 0.035 0.16 -10000 0 -0.54 33 33
T-helper 1 cell differentiation -0.094 0.3 0.56 8 -0.74 50 58
IL2RA -0.25 0.31 0.74 6 -0.59 131 137
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.051 0.16 -10000 0 -0.43 38 38
E2F1 0.055 0.048 0.24 2 -10000 0 2
PPARG -0.38 0.26 -10000 0 -0.54 369 369
SLC3A2 -0.049 0.16 -10000 0 -0.43 38 38
IRF4 0.039 0.028 -10000 0 -10000 0 0
PTGS2 -0.77 0.57 0.73 4 -1.1 354 358
CSF2 -0.67 0.53 0.79 4 -1 334 338
JunB/Fra1/NFAT1-c-4 -0.53 0.52 0.6 2 -0.9 314 316
IL4 -0.12 0.29 -10000 0 -0.82 45 45
IL5 -0.68 0.52 0.73 4 -1 336 340
IL2 -0.39 0.35 0.69 3 -0.72 208 211
IL3 -0.088 0.15 -10000 0 -0.91 13 13
RNF128 -0.21 0.33 -10000 0 -0.63 191 191
NFATC1 -0.45 0.41 0.66 3 -0.75 300 303
CDK4 0.28 0.28 0.54 168 -0.64 2 170
PTPRK -0.087 0.24 -10000 0 -0.62 65 65
IL8 -0.66 0.53 0.74 5 -1 330 335
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 -0.54 269 269
EGF/EGFR -0.3 0.26 -9999 0 -0.44 366 366
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.19 0.21 -9999 0 -0.36 270 270
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 -0.54 164 164
EGF/EGFR dimer/SHC -0.23 0.23 -9999 0 -0.41 285 285
mol:GDP -0.19 0.21 -9999 0 -0.36 270 270
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.14 0.26 -9999 0 -0.54 153 153
GRB2/SOS1 0.048 0.019 -9999 0 -10000 0 0
HRAS/GTP -0.18 0.19 -9999 0 -0.34 259 259
SHC1 0.027 0.014 -9999 0 -10000 0 0
HRAS/GDP -0.18 0.2 -9999 0 -0.35 259 259
FRAP1 -0.2 0.17 -9999 0 -0.34 267 267
EGF/EGFR dimer -0.31 0.26 -9999 0 -0.47 357 357
SOS1 0.034 0.004 -9999 0 -10000 0 0
GRB2 0.034 0.018 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.088 0.21 -9999 0 -0.39 160 160
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 0.54 126 -10000 0 126
PI3K Class IB/PDE3B -0.11 0.25 -10000 0 -0.54 126 126
PDE3B -0.11 0.25 -10000 0 -0.54 126 126
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.034 0.007 -10000 0 -10000 0 0
PTK2 0.027 0.014 -10000 0 -10000 0 0
CRKL -0.17 0.2 -10000 0 -0.35 244 244
GRB2/SOS1/SHC 0.051 0.034 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
IRS1/Crk -0.16 0.21 -10000 0 -0.34 259 259
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.21 -10000 0 -0.36 221 221
AKT1 -0.16 0.19 0.23 1 -0.47 96 97
BAD -0.16 0.18 0.22 1 -0.45 91 92
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.17 0.2 -10000 0 -0.34 259 259
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.21 -10000 0 -0.34 258 258
RAF1 -0.12 0.18 -10000 0 -0.46 73 73
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.22 -10000 0 -0.34 225 225
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.17 0.23 -10000 0 -0.37 259 259
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.18 0.23 1 -0.46 89 90
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.099 0.16 0.33 1 -0.39 63 64
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.18 -10000 0 -0.32 169 169
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.07 0.18 -10000 0 -0.3 160 160
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 -0.34 257 257
Crk/p130 Cas/Paxillin -0.13 0.21 -10000 0 -0.33 238 238
IGF1R -0.049 0.14 -10000 0 -0.65 21 21
IGF1 -0.27 0.3 -10000 0 -0.57 253 253
IRS2/Crk -0.22 0.26 -10000 0 -0.42 267 267
PI3K -0.15 0.24 -10000 0 -0.37 242 242
apoptosis 0.11 0.15 0.39 66 -0.28 2 68
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
PRKCD -0.18 0.23 -10000 0 -0.4 234 234
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 -0.41 68 70
PRKCZ -0.16 0.19 0.22 1 -0.35 221 222
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.17 -10000 0 -0.42 65 65
PTPN1 0.037 0.03 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.19 0.23 -10000 0 -0.41 245 245
BCAR1 0.029 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.094 0.19 -10000 0 -0.33 176 176
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 -0.34 257 257
GRB10 0.03 0.051 -10000 0 -0.54 4 4
PTPN11 -0.17 0.2 -10000 0 -0.34 258 258
IRS1 -0.18 0.22 -10000 0 -0.37 259 259
IRS2 -0.23 0.26 -10000 0 -0.43 278 278
IGF-1R heterotetramer/IGF1 -0.2 0.26 -10000 0 -0.45 247 247
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDPK1 -0.16 0.21 -10000 0 -0.36 224 224
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PRKD1 -0.22 0.28 -10000 0 -0.47 241 241
SHC1 0.027 0.014 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.57 0.46 1.1 117 -1 2 119
PLK1 0.23 0.2 0.72 22 -10000 0 22
BIRC5 0.37 0.25 0.7 111 -0.66 3 114
HSPA1B 0.57 0.46 1.1 145 -0.95 3 148
MAP2K1 0.17 0.13 0.34 130 -10000 0 130
BRCA2 0.6 0.49 1.2 143 -0.94 3 146
FOXM1 0.62 0.61 1.3 160 -1.2 3 163
XRCC1 0.57 0.47 1.1 122 -1 2 124
FOXM1B/p19 0.079 0.3 0.92 9 -0.93 5 14
Cyclin D1/CDK4 0.49 0.46 1 121 -0.87 10 131
CDC2 0.63 0.52 1.2 155 -1 3 158
TGFA 0.45 0.52 1 124 -0.93 20 144
SKP2 0.58 0.47 1.2 109 -1 2 111
CCNE1 0.087 0.063 0.23 42 -10000 0 42
CKS1B 0.62 0.5 1.2 147 -1 2 149
RB1 0.28 0.35 0.73 130 -0.76 8 138
FOXM1C/SP1 0.5 0.45 0.98 127 -1 7 134
AURKB 0.21 0.31 0.66 64 -0.8 22 86
CENPF 0.7 0.53 1.2 176 -1.3 1 177
CDK4 0.092 0.061 0.23 22 -10000 0 22
MYC 0.32 0.44 0.95 90 -0.87 10 100
CHEK2 0.17 0.13 0.34 131 -10000 0 131
ONECUT1 0.5 0.48 1 139 -0.87 7 146
CDKN2A -0.017 0.078 -10000 0 -0.23 15 15
LAMA4 0.56 0.48 1.1 135 -0.96 6 141
FOXM1B/HNF6 0.5 0.5 1.1 122 -1 7 129
FOS -0.12 0.65 1.1 45 -1 77 122
SP1 0.031 0.033 -10000 0 -0.27 2 2
CDC25B 0.58 0.47 1.1 135 -0.94 3 138
response to radiation 0.12 0.094 0.24 127 -10000 0 127
CENPB 0.57 0.46 1.1 129 -0.94 3 132
CENPA 0.64 0.51 1.2 166 -0.94 3 169
NEK2 0.71 0.52 1.2 189 -1.2 1 190
HIST1H2BA 0.57 0.46 1.1 125 -0.94 3 128
CCNA2 0.11 0.077 0.23 62 -10000 0 62
EP300 0.032 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.61 0.52 1.2 138 -1.1 3 141
CCNB2 0.63 0.51 1.2 151 -0.94 3 154
CCNB1 0.64 0.54 1.3 156 -1 3 159
ETV5 0.54 0.52 1.1 132 -1.1 12 144
ESR1 0.38 0.61 1.1 120 -0.95 17 137
CCND1 0.51 0.51 1.1 142 -0.9 10 152
GSK3A 0.14 0.1 0.31 80 -10000 0 80
Cyclin A-E1/CDK1-2 0.21 0.13 0.38 133 -10000 0 133
CDK2 0.071 0.036 0.23 9 -10000 0 9
G2/M transition of mitotic cell cycle 0.14 0.12 0.28 170 -10000 0 170
FOXM1B/Cbp/p300 0.3 0.38 0.85 34 -1 3 37
GAS1 0.28 0.71 1.1 110 -1 63 173
MMP2 0.56 0.48 1.1 133 -1.2 6 139
RB1/FOXM1C 0.46 0.46 0.97 137 -0.96 7 144
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 -0.26 247 247
EGFR -0.27 0.29 -10000 0 -0.54 269 269
EPHA2 0.026 0.062 -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 -0.47 357 357
ARRB2 0.015 0.029 -10000 0 -0.33 3 3
mol:GTP 0.013 0.029 0.12 26 -10000 0 26
ARRB1 0.03 0.027 -10000 0 -0.54 1 1
FBXO8 0.033 0.007 -10000 0 -10000 0 0
TSHR 0.029 0.045 -10000 0 -0.54 3 3
EGF -0.15 0.27 -10000 0 -0.54 164 164
somatostatin receptor activity 0 0 -10000 0 -0.001 250 250
ARAP2 0 0 -10000 0 0 257 257
mol:GDP -0.14 0.14 -10000 0 -0.27 218 218
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 250 250
ITGA2B 0.033 0.012 -10000 0 -10000 0 0
ARF6 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.059 -10000 0 -0.32 6 6
ADAP1 0 0 -10000 0 0 153 153
KIF13B 0.027 0.029 -10000 0 -0.54 1 1
HGF/MET 0.006 0.13 -10000 0 -0.4 50 50
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.14 0.12 -10000 0 -0.25 243 243
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.26 0.24 -10000 0 -0.41 349 349
ADRB2 -0.26 0.29 -10000 0 -0.54 263 263
receptor agonist activity 0 0 -10000 0 0 214 214
actin filament binding 0 0 -10000 0 0 264 264
SRC 0.032 0.008 -10000 0 -10000 0 0
ITGB3 0.035 0.019 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -0.001 161 161
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 171 171
ARF6/GDP -0.03 0.084 -10000 0 -0.27 29 29
ARF6/GDP/GULP/ACAP1 -0.16 0.18 -10000 0 -0.35 202 202
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 0 254 254
LHCGR/beta Arrestin2 0.022 0.048 -10000 0 -0.47 3 3
EFNA1 0.028 0.016 -10000 0 -10000 0 0
HGF 0.034 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 216 216
CYTH2 -0.002 0.002 -10000 0 -0.004 263 263
NCK1 0.034 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 155 155
endosomal lumen acidification 0 0 0.001 5 0 159 164
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.072 0.22 -10000 0 -0.54 94 94
GNAQ/ARNO -0.003 0.003 -10000 0 -0.007 149 149
mol:Phosphatidic acid 0 0 -10000 0 0 254 254
PIP3-E 0 0 -10000 0 0 311 311
MET -0.023 0.17 -10000 0 -0.54 50 50
GNA14 0.043 0.068 -10000 0 -0.54 4 4
GNA15 0.036 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 -0.001 210 210
GNA11 0.033 0.006 -10000 0 -10000 0 0
LHCGR 0.032 0.046 -10000 0 -0.54 3 3
AGTR1 -0.18 0.3 -10000 0 -0.54 207 207
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 -0.32 355 355
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 0.011 0.13 -10000 0 -0.32 66 66
regulation of S phase of mitotic cell cycle -0.045 0.13 -10000 0 -0.3 91 91
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 0.008 -10000 0 -10000 0 0
PELP1 0.029 0.01 -10000 0 -10000 0 0
AKT1 0.011 0.014 0.14 6 -10000 0 6
MAP2K1 -0.11 0.11 -10000 0 -0.36 61 61
T-DHT/AR -0.033 0.14 0.12 2 -0.4 67 69
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.003 -10000 0 -0.007 359 359
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 -0.54 183 183
mol:GDP -0.079 0.16 -10000 0 -0.38 100 100
cell proliferation -0.3 0.21 -10000 0 -0.43 323 323
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
FOS -0.57 0.37 -10000 0 -0.8 365 365
mol:Ca2+ -0.037 0.038 -10000 0 -0.075 231 231
MAPK3 -0.21 0.16 -10000 0 -0.37 160 160
MAPK1 -0.16 0.15 -10000 0 -0.4 82 82
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 -0.003 0.002 -10000 0 -0.004 336 336
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 -0.004 336 336
HRAS/GTP -0.059 0.12 -10000 0 -0.33 65 65
actin cytoskeleton reorganization 0.015 0.095 -10000 0 -0.28 44 44
SRC 0.03 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.003 0.002 -10000 0 -0.004 336 336
PI3K 0.007 0.11 -10000 0 -0.34 44 44
apoptosis 0.3 0.22 0.42 360 -10000 0 360
T-DHT/AR/PELP1 -0.014 0.13 -10000 0 -0.35 67 67
HRAS/GDP -0.069 0.17 -10000 0 -0.39 92 92
CREB1 -0.32 0.23 -10000 0 -0.46 360 360
RAC1-CDC42/GTP 0.025 0.1 -10000 0 -0.29 44 44
AR -0.043 0.2 0.18 2 -0.55 66 68
GNB1 0.034 0.011 -10000 0 -10000 0 0
RAF1 -0.086 0.11 -10000 0 -0.34 61 61
RAC1-CDC42/GDP -0.032 0.17 -10000 0 -0.4 78 78
T-DHT/AR/PELP1/Src -0.004 0.13 -10000 0 -0.33 67 67
MAP2K2 -0.12 0.11 -10000 0 -0.36 61 61
T-DHT/AR/PELP1/Src/PI3K -0.046 0.13 -10000 0 -0.3 91 91
GNAZ 0.025 0.062 -10000 0 -0.54 6 6
SHBG 0.03 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.11 0.19 -10000 0 -0.47 80 80
mol:T-DHT -0.001 0.002 -10000 0 -0.005 74 74
RAC1 0.034 0.005 -10000 0 -10000 0 0
GNRH1 -0.001 0.056 0.14 1 -0.4 10 11
Gi family/GTP -0.1 0.14 -10000 0 -0.26 189 189
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 0.41 1 -0.85 30 31
SUMO2 0.001 0.025 -10000 0 -10000 0 0
STAT1 (dimer) 0.072 0.069 0.28 25 -10000 0 25
FKBP4 0.037 0.026 -10000 0 -10000 0 0
FKBP5 0.025 0.082 -10000 0 -0.54 10 10
GR alpha/HSP90/FKBP51/HSP90 0.13 0.14 0.33 45 -0.36 4 49
PRL -0.06 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.52 178 -10000 0 178
RELA -0.096 0.12 0.28 3 -0.26 34 37
FGG 0.23 0.23 0.45 228 -10000 0 228
GR beta/TIF2 0.11 0.14 0.32 73 -0.36 3 76
IFNG -0.39 0.34 0.48 3 -0.68 243 246
apoptosis -0.25 0.18 -10000 0 -0.56 36 36
CREB1 0.058 0.041 -10000 0 -10000 0 0
histone acetylation 0.036 0.14 0.39 41 -0.32 10 51
BGLAP -0.092 0.14 -10000 0 -0.46 13 13
GR/PKAc 0.15 0.14 0.34 52 -0.31 3 55
NF kappa B1 p50/RelA -0.16 0.2 0.48 3 -0.32 174 177
SMARCD1 0.034 0.004 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.21 212 -10000 0 212
GATA3 0.043 0.16 -10000 0 -0.54 33 33
AKT1 0.028 0.024 -10000 0 -10000 0 0
CSF2 -0.008 0.11 0.4 3 -0.37 2 5
GSK3B 0.001 0.027 -10000 0 -10000 0 0
NR1I3 -0.19 0.16 -10000 0 -0.54 11 11
CSN2 0.19 0.19 0.38 199 -10000 0 199
BRG1/BAF155/BAF170/BAF60A 0.084 0.027 -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 0.022 0.12 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.011 0.006 -10000 0 -10000 0 0
SFN 0.032 0.04 -10000 0 -0.54 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.14 0.14 0.35 28 -0.4 2 30
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.65 0.33 -10000 0 -0.8 426 426
JUN -0.21 0.24 0.38 2 -0.48 174 176
IL4 -0.12 0.15 -10000 0 -0.53 8 8
CDK5R1 0.028 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 -0.5 330 330
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.15 0.14 0.35 32 -0.36 3 35
cortisol/GR alpha (monomer) 0.29 0.31 0.57 235 -10000 0 235
NCOA2 0.028 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.42 0.26 -10000 0 -0.58 359 359
AP-1/NFAT1-c-4 -0.58 0.41 -10000 0 -0.82 349 349
AFP -0.18 0.2 -10000 0 -0.6 21 21
SUV420H1 0.032 0.01 -10000 0 -10000 0 0
IRF1 0.21 0.18 0.48 61 -10000 0 61
TP53 0.046 0.034 -10000 0 -0.51 1 1
PPP5C 0.036 0.017 -10000 0 -10000 0 0
KRT17 -0.9 0.65 -10000 0 -1.4 327 327
KRT14 -0.82 0.63 -10000 0 -1.3 324 324
TBP 0.039 0.011 -10000 0 -10000 0 0
CREBBP 0.18 0.15 0.3 288 -0.29 1 289
HDAC1 0.028 0.012 -10000 0 -10000 0 0
HDAC2 0.029 0.022 -10000 0 -10000 0 0
AP-1 -0.58 0.41 -10000 0 -0.82 349 349
MAPK14 0.01 0.023 -10000 0 -10000 0 0
MAPK10 -0.011 0.082 -10000 0 -0.55 10 10
MAPK11 -0.001 0.025 -10000 0 -10000 0 0
KRT5 -0.95 0.63 -10000 0 -1.3 356 356
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 0.072 0.069 0.28 25 -10000 0 25
CGA -0.084 0.16 0.41 2 -0.46 14 16
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.19 0.34 208 -0.35 2 210
MAPK3 0 0.024 -10000 0 -10000 0 0
MAPK1 0.009 0.023 -10000 0 -10000 0 0
ICAM1 -0.26 0.25 0.51 4 -0.49 205 209
NFKB1 -0.095 0.11 0.28 3 -0.24 36 39
MAPK8 -0.15 0.19 0.57 1 -0.35 172 173
MAPK9 0.009 0.024 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.19 -10000 0 -0.57 40 40
BAX 0.028 0.076 -10000 0 -10000 0 0
POMC -0.14 0.19 0.57 1 -0.76 10 11
EP300 0.18 0.14 0.29 285 -10000 0 285
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.52 194 -10000 0 194
proteasomal ubiquitin-dependent protein catabolic process 0.09 0.11 0.29 66 -10000 0 66
SGK1 0.23 0.17 0.36 310 -0.43 1 311
IL13 -0.29 0.25 0.5 1 -0.64 87 88
IL6 -0.75 0.48 0.62 1 -1 376 377
PRKACG 0.033 0.026 -10000 0 -0.54 1 1
IL5 -0.24 0.2 -10000 0 -0.65 32 32
IL2 -0.42 0.32 -10000 0 -0.69 260 260
CDK5 0.032 0.024 -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 0.45 10 -0.49 205 215
CDK5R1/CDK5 0.037 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.096 0.18 0.43 3 -0.38 35 38
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.5 223 -10000 0 223
SMARCA4 0.035 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.17 0.16 0.34 175 -10000 0 175
NF kappa B1 p50/RelA/Cbp -0.005 0.19 0.46 32 -0.32 10 42
JUN (dimer) -0.21 0.24 0.38 2 -0.47 174 176
YWHAH 0.033 0.014 -10000 0 -10000 0 0
VIPR1 -0.11 0.16 -10000 0 -0.51 31 31
NR3C1 0.19 0.2 0.39 181 -0.45 5 186
NR4A1 0.014 0.12 -10000 0 -0.55 24 24
TIF2/SUV420H1 0.039 0.023 -10000 0 -10000 0 0
MAPKKK cascade -0.25 0.18 -10000 0 -0.56 36 36
cortisol/GR alpha (dimer)/Src-1 0.27 0.26 0.51 238 -10000 0 238
PBX1 0.043 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 -0.72 115 117
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.16 0.34 174 -10000 0 174
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.5 223 -10000 0 223
mol:cortisol 0.18 0.17 0.32 249 -10000 0 249
MMP1 -0.023 0.35 -10000 0 -0.94 53 53
Signaling events mediated by PTP1B

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.006 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.24 0.21 -10000 0 -0.4 257 257
PTP1B/AKT1 -0.16 0.15 0.25 1 -0.29 215 216
FYN 0.03 0.037 -10000 0 -0.54 2 2
p210 bcr-abl/PTP1B -0.19 0.16 0.25 1 -0.31 265 266
EGFR -0.29 0.28 -10000 0 -0.56 269 269
EGF/EGFR -0.36 0.26 -10000 0 -0.5 361 361
CSF1 0.034 0.008 -10000 0 -10000 0 0
AKT1 0.035 0.017 -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 -0.32 192 193
Insulin Receptor/Insulin -0.11 0.13 -10000 0 -0.36 42 42
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 -0.31 238 239
EGF -0.18 0.26 -10000 0 -0.56 164 164
YES1 0.032 0.027 -10000 0 -0.54 1 1
CAV1 -0.37 0.23 -10000 0 -0.49 368 368
TXN 0.028 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.19 0.18 -10000 0 -0.34 238 238
cell migration 0.19 0.16 0.31 265 -0.25 1 266
STAT3 0.031 0.007 -10000 0 -10000 0 0
PRLR 0.074 0.064 -10000 0 -10000 0 0
ITGA2B 0.032 0.011 -10000 0 -10000 0 0
CSF1R 0.034 0.006 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.081 0.049 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.17 0.16 0.24 1 -0.31 237 238
Crk/p130 Cas -0.17 0.16 -10000 0 -0.31 209 209
DOK1 -0.15 0.14 0.27 1 -0.34 97 98
JAK2 -0.081 0.14 -10000 0 -0.53 31 31
Jak2/Leptin Receptor/Leptin -0.25 0.2 -10000 0 -0.44 225 225
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
PTPN1 -0.19 0.16 0.25 1 -0.31 265 266
LYN 0.03 0.015 0.18 2 -10000 0 2
CDH2 0.057 0.055 -10000 0 -10000 0 0
SRC -0.051 0.12 -10000 0 -0.67 15 15
ITGB3 0.033 0.018 -10000 0 -10000 0 0
CAT1/PTP1B -0.14 0.18 0.36 1 -0.42 89 90
CAPN1 0.031 0.014 -10000 0 -10000 0 0
CSK 0.034 0.011 -10000 0 -10000 0 0
PI3K -0.12 0.16 -10000 0 -0.41 63 63
mol:H2O2 -0.005 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.22 0.19 -10000 0 -0.4 209 209
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 0.044 -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 -0.54 321 321
BCAR1 0.029 0.013 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.034 0.018 -10000 0 -10000 0 0
mol:NADPH -0.006 0.004 -10000 0 -10000 0 0
TRPV6 -0.006 0.15 0.42 2 -0.4 41 43
PRL 0.037 0.009 -10000 0 -10000 0 0
SOCS3 0 0.25 -10000 0 -1.3 17 17
SPRY2 -0.32 0.28 -10000 0 -0.55 304 304
Insulin Receptor/Insulin/IRS1 0.015 0.13 -10000 0 -0.35 59 59
CSF1/CSF1R -0.17 0.16 -10000 0 -0.31 186 186
Ras protein signal transduction 0.09 0.18 0.66 39 -10000 0 39
IRS1 -0.034 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 -0.55 237 237
STAT5B -0.14 0.16 0.26 1 -0.35 98 99
STAT5A -0.14 0.16 0.26 1 -0.35 100 101
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.18 0.16 0.24 1 -0.31 239 240
CSN2 0.079 0.062 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
LAT -0.035 0.076 -10000 0 -0.64 3 3
YBX1 0.044 0.028 -10000 0 -10000 0 0
LCK 0.048 0.044 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
NOX4 0.051 0.055 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.051 0.038 -10000 0 -10000 0 0
PDGFRB 0.029 0.007 -10000 0 -10000 0 0
SPHK1 -0.042 0.14 -10000 0 -0.9 11 11
mol:S1P -0.045 0.14 0.3 1 -0.82 11 12
S1P1/S1P/Gi -0.29 0.29 0.33 5 -0.49 307 312
GNAO1 0.003 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.25 0.26 0.41 3 -0.45 289 292
PLCG1 -0.27 0.27 0.32 7 -0.47 298 305
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.007 -10000 0 -10000 0 0
GNAI2 0.004 0.029 -10000 0 -10000 0 0
GNAI3 0.005 0.029 -10000 0 -10000 0 0
GNAI1 -0.19 0.27 -10000 0 -0.56 183 183
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.004 0.04 -10000 0 -10000 0 0
S1P1/S1P -0.066 0.13 0.28 8 -0.66 11 19
negative regulation of cAMP metabolic process -0.28 0.28 0.33 5 -0.48 307 312
MAPK3 -0.37 0.35 0.36 9 -0.63 311 320
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 0.029 0.011 -10000 0 -10000 0 0
PLCB2 -0.055 0.12 0.32 6 -0.57 11 17
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.065 0.1 -10000 0 -0.54 11 11
receptor internalization -0.065 0.12 0.24 5 -0.6 11 16
PTGS2 -0.62 0.53 0.43 4 -1 315 319
Rac1/GTP -0.064 0.1 -10000 0 -0.54 11 11
RHOA 0.033 0.007 -10000 0 -10000 0 0
VEGFA 0.045 0.048 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.28 0.28 0.33 5 -0.48 307 312
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 0.37 5 -0.68 315 320
S1P1/S1P/PDGFB-D/PDGFRB -0.08 0.14 0.34 8 -0.62 11 19
ABCC1 0.032 0.023 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.008 0.058 0.26 9 -0.35 2 11
NFATC2 0.009 0.055 0.25 10 -0.34 1 11
NFATC3 0.012 0.052 0.26 9 -10000 0 9
CD40LG -0.22 0.29 0.6 15 -0.51 191 206
PTGS2 -0.32 0.36 0.58 15 -0.62 265 280
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 0.019 -10000 0 -10000 0 0
JUN -0.067 0.22 -10000 0 -0.54 89 89
mol:Ca2+ -0.003 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.012 -10000 0 -10000 0 0
FOSL1 0.034 0.01 -10000 0 -10000 0 0
CREM 0.033 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.033 0.17 0.45 15 -0.34 61 76
FOS -0.35 0.27 -10000 0 -0.54 344 344
IFNG -0.2 0.31 0.64 18 -0.51 186 204
AP-1/NFAT1-c-4 -0.26 0.34 0.71 11 -0.58 201 212
FASLG -0.19 0.29 0.67 15 -0.48 180 195
NFAT1-c-4/ICER1 0.015 0.098 0.35 16 -0.28 1 17
IL2RA -0.21 0.3 0.62 16 -0.51 187 203
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSF2 -0.22 0.3 0.62 16 -0.51 192 208
JunB/Fra1/NFAT1-c-4 0.039 0.11 0.41 9 -0.29 4 13
IL4 -0.22 0.29 0.58 15 -0.51 190 205
IL2 -0.009 0.14 -10000 0 -0.97 11 11
IL3 -0.009 0.13 -10000 0 -0.74 13 13
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
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.09 0.18 -10000 0 -0.58 61 61
PDGF/PDGFRA/CRKL -0.054 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 0.033 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.055 0.14 -10000 0 -0.41 64 64
AP1 -0.7 0.45 -10000 0 -0.97 366 366
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 -0.055 0.14 -10000 0 -0.42 62 62
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.084 0.13 -10000 0 -0.45 56 56
CAV3 0.031 0.037 -10000 0 -0.54 2 2
CAV1 -0.38 0.26 -10000 0 -0.54 365 365
SHC/Grb2/SOS1 0.017 0.12 -10000 0 -0.33 44 44
PDGF/PDGFRA/Shf -0.053 0.14 -10000 0 -0.4 64 64
FOS -0.69 0.44 -10000 0 -0.95 366 366
JUN -0.13 0.16 -10000 0 -0.46 86 86
oligodendrocyte development -0.055 0.14 -10000 0 -0.42 62 62
GRB2 0.034 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:DAG -0.085 0.14 -10000 0 -0.45 56 56
PDGF/PDGFRA -0.09 0.18 -10000 0 -0.58 61 61
actin cytoskeleton reorganization -0.052 0.14 -10000 0 -0.4 64 64
SRF 0.031 0.014 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
PI3K -0.028 0.18 -10000 0 -0.42 82 82
PDGF/PDGFRA/Crk/C3G 0.002 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 -0.36 55 56
SHB 0.035 0.018 -10000 0 -10000 0 0
SHF 0.034 0.013 -10000 0 -10000 0 0
CSNK2A1 0.063 0.025 -10000 0 -10000 0 0
GO:0007205 -0.092 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 -0.052 0.14 -10000 0 -0.4 64 64
PDGF/PDGFRA/Caveolin-1 -0.34 0.24 -10000 0 -0.46 376 376
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
ELK1 -0.11 0.13 0.23 2 -0.44 60 62
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.054 0.14 -10000 0 -0.41 63 63
JAK-STAT cascade -0.065 0.13 -10000 0 -0.4 63 63
cell proliferation -0.053 0.14 -10000 0 -0.4 64 64
BMP receptor signaling

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.11 0.079 -10000 0 -0.3 3 3
SMAD6-7/SMURF1 0.064 0.02 -10000 0 -10000 0 0
NOG 0.031 0.031 -10000 0 -0.54 1 1
SMAD9 -0.088 0.24 -10000 0 -0.68 62 62
SMAD4 0.032 0.026 -10000 0 -0.54 1 1
SMAD5 -0.1 0.19 -10000 0 -0.44 83 83
BMP7/USAG1 -0.24 0.2 -10000 0 -0.39 313 313
SMAD5/SKI -0.094 0.19 -10000 0 -0.43 79 79
SMAD1 0.004 0.09 -10000 0 -0.45 9 9
BMP2 -0.23 0.29 -10000 0 -0.54 230 230
SMAD1/SMAD1/SMAD4 0.03 0.087 -10000 0 -0.43 6 6
BMPR1A 0.031 0.044 -10000 0 -0.54 3 3
BMPR1B 0.088 0.071 -10000 0 -10000 0 0
BMPR1A-1B/BAMBI 0.081 0.13 -10000 0 -0.3 38 38
AHSG 0.033 0.007 -10000 0 -10000 0 0
CER1 0.032 0.011 -10000 0 -10000 0 0
BMP2-4/CER1 -0.17 0.23 -10000 0 -0.38 261 261
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.18 -10000 0 -0.4 93 93
BMP2-4 (homodimer) -0.21 0.25 -10000 0 -0.43 277 277
RGMB 0.033 0.007 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.02 0.19 -10000 0 -0.28 168 168
RGMA -0.053 0.2 -10000 0 -0.54 76 76
SMURF1 0.034 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.18 -10000 0 -0.4 112 112
BMP2-4/USAG1 -0.4 0.27 -10000 0 -0.51 408 408
SMAD6/SMURF1/SMAD5 -0.095 0.19 -10000 0 -0.43 78 78
SOSTDC1 -0.37 0.26 -10000 0 -0.54 359 359
BMP7/BMPR2/BMPR1A-1B 0.11 0.072 -10000 0 -0.32 3 3
SKI 0.033 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) -0.16 0.27 -10000 0 -0.54 168 168
HFE2 0.031 0.038 -10000 0 -0.54 2 2
ZFYVE16 0.033 0.007 -10000 0 -10000 0 0
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
BMP2-4/CHRD -0.17 0.23 -10000 0 -0.38 261 261
SMAD5/SMAD5/SMAD4 -0.096 0.19 -10000 0 -0.44 79 79
MAPK1 0.032 0.008 -10000 0 -10000 0 0
TAK1/TAB family -0.089 0.17 -10000 0 -0.36 100 100
BMP7 (homodimer) 0.043 0.043 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
BMP6/FETUA -0.098 0.21 -10000 0 -0.4 164 164
SMAD1/SKI 0.015 0.095 -10000 0 -0.45 7 7
SMAD6 0.033 0.007 -10000 0 -10000 0 0
CTDSP2 0.034 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA -0.17 0.23 -10000 0 -0.38 261 261
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.048 0.046 -10000 0 -10000 0 0
BMPR2 (homodimer) 0.034 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.06 0.038 -10000 0 -0.34 2 2
BMPR1A-1B (homodimer) 0.084 0.063 -10000 0 -0.4 3 3
CHRDL1 -0.3 0.28 -10000 0 -0.54 301 301
ENDOFIN/SMAD1 0.015 0.097 -10000 0 -0.44 9 9
SMAD6-7/SMURF1/SMAD1 0.048 0.1 -10000 0 -0.48 6 6
SMAD6/SMURF1 0.034 0.005 -10000 0 -10000 0 0
BAMBI 0.017 0.16 -10000 0 -0.54 36 36
SMURF2 0.031 0.013 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.36 0.31 -10000 0 -0.54 354 354
BMP2-4/GREM1 -0.16 0.24 0.25 2 -0.37 266 268
SMAD7 0.033 0.007 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.078 0.23 -10000 0 -0.66 60 60
SMAD1/SMAD6 0.015 0.098 -10000 0 -0.5 6 6
TAK1/SMAD6 0.047 0.015 -10000 0 -10000 0 0
BMP7 0.043 0.043 -10000 0 -10000 0 0
BMP6 -0.16 0.27 -10000 0 -0.54 168 168
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.11 0.19 -10000 0 -0.4 110 110
PPM1A 0.033 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.012 0.093 -10000 0 -0.5 6 6
SMAD7/SMURF1 0.048 0.013 -10000 0 -10000 0 0
CTDSPL 0.031 0.036 -10000 0 -0.54 2 2
PPP1CA 0.034 0.021 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.034 0.005 -10000 0 -10000 0 0
PPP1R15A 0.032 0.036 -10000 0 -0.54 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.11 0.18 -10000 0 -0.39 111 111
CHRD 0.036 0.021 -10000 0 -10000 0 0
BMPR2 0.034 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.21 -10000 0 -0.45 114 114
BMP4 -0.04 0.2 -10000 0 -0.54 67 67
FST 0.032 0.039 -10000 0 -0.54 2 2
BMP2-4/NOG -0.16 0.22 -10000 0 -0.38 246 246
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.11 0.075 -10000 0 -0.3 3 3
Ephrin B reverse 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
EFNB2 0.026 0.058 -10000 0 -0.54 5 5
EPHB2 0.042 0.037 -10000 0 -10000 0 0
EFNB1 0.015 0.028 -10000 0 -0.4 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.049 0.18 -10000 0 -0.28 180 180
Ephrin B2/EPHB1-2 -0.075 0.19 -10000 0 -0.31 191 191
neuron projection morphogenesis -0.061 0.16 -10000 0 -0.27 180 180
Ephrin B1/EPHB1-2/Tiam1 -0.06 0.18 -10000 0 -0.3 186 186
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 56 56
YES1 -0.069 0.26 -10000 0 -0.79 56 56
Ephrin B1/EPHB1-2/NCK2 -0.06 0.18 -10000 0 -0.3 188 188
PI3K -0.045 0.22 -10000 0 -0.6 57 57
mol:GDP -0.06 0.18 -10000 0 -0.29 186 186
ITGA2B 0.033 0.012 -10000 0 -10000 0 0
endothelial cell proliferation 0.038 0.046 -10000 0 -0.31 7 7
FYN -0.071 0.26 -10000 0 -0.79 56 56
MAP3K7 -0.058 0.19 -10000 0 -0.6 56 56
FGR -0.065 0.26 -10000 0 -0.79 56 56
TIAM1 0.035 0.012 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RGS3 0.034 0.005 -10000 0 -10000 0 0
cell adhesion -0.047 0.2 -10000 0 -0.56 54 54
LYN -0.065 0.25 -10000 0 -0.78 56 56
Ephrin B1/EPHB1-2/Src Family Kinases -0.07 0.24 -10000 0 -0.73 57 57
Ephrin B1/EPHB1-2 -0.062 0.2 -10000 0 -0.64 56 56
SRC -0.064 0.25 -10000 0 -0.78 57 57
ITGB3 0.035 0.019 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 192 192
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 -0.078 0.26 -10000 0 -0.8 56 56
HCK -0.064 0.25 -10000 0 -0.78 56 56
regulation of stress fiber formation 0.061 0.18 0.29 188 -10000 0 188
MAPK8 -0.056 0.18 -10000 0 -0.55 56 56
Ephrin B1/EPHB1-2/RGS3 -0.061 0.18 -10000 0 -0.3 183 183
endothelial cell migration -0.051 0.17 0.26 1 -0.51 59 60
NCK2 0.034 0.007 -10000 0 -10000 0 0
PTPN13 -0.027 0.2 -10000 0 -0.65 47 47
regulation of focal adhesion formation 0.061 0.18 0.29 188 -10000 0 188
chemotaxis 0.061 0.18 0.3 183 -10000 0 183
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.054 0.17 -10000 0 -0.28 180 180
angiogenesis -0.061 0.2 -10000 0 -0.64 56 56
LCK -0.061 0.26 -10000 0 -0.78 57 57
HIF-1-alpha transcription factor network

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
PKM2 0.005 0.43 0.81 1 -0.74 74 75
HDAC7 0.007 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.003 0.37 0.83 4 -0.71 46 50
SMAD4 0.033 0.027 -10000 0 -0.54 1 1
ID2 0.002 0.43 -10000 0 -0.74 73 73
AP1 -0.33 0.27 -10000 0 -0.49 350 350
ABCG2 -0.014 0.44 -10000 0 -0.75 81 81
HIF1A 0.022 0.13 0.33 2 -0.44 6 8
TFF3 -0.049 0.44 -10000 0 -0.75 87 87
GATA2 0.021 0.049 -10000 0 -10000 0 0
AKT1 0.02 0.13 0.34 3 -0.2 16 19
response to hypoxia -0.004 0.11 0.25 13 -0.16 59 72
MCL1 -0.029 0.39 -10000 0 -0.73 72 72
NDRG1 -0.017 0.4 0.88 1 -0.74 68 69
SERPINE1 0.012 0.44 0.85 7 -0.74 74 81
FECH -0.002 0.42 -10000 0 -0.73 75 75
FURIN 0.006 0.43 -10000 0 -0.74 75 75
NCOA2 0.035 0.024 -10000 0 -10000 0 0
EP300 0.033 0.17 0.45 16 -0.29 35 51
HMOX1 0.009 0.44 0.87 4 -0.73 75 79
BHLHE40 -0.053 0.4 0.72 4 -0.73 75 79
BHLHE41 -0.053 0.4 0.72 4 -0.73 75 79
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.042 0.16 -10000 0 -0.44 2 2
ENG 0.045 0.14 0.46 1 -0.41 2 3
JUN -0.075 0.22 -10000 0 -0.55 89 89
RORA -0.006 0.43 -10000 0 -0.74 79 79
ABCB1 -0.29 0.47 -10000 0 -0.94 162 162
TFRC 0.007 0.43 0.87 5 -0.74 74 79
CXCR4 0.01 0.43 0.87 1 -0.73 76 77
TF -0.006 0.44 -10000 0 -0.76 78 78
CITED2 -0.005 0.43 -10000 0 -0.74 76 76
HIF1A/ARNT -0.069 0.44 0.97 1 -0.87 62 63
LDHA -0.01 0.13 -10000 0 -0.71 14 14
ETS1 -0.002 0.43 -10000 0 -0.74 75 75
PGK1 0.007 0.43 0.82 4 -0.74 74 78
NOS2 -0.053 0.4 0.72 4 -0.73 75 79
ITGB2 0.007 0.43 0.82 8 -0.73 76 84
ALDOA 0.004 0.42 -10000 0 -0.74 72 72
Cbp/p300/CITED2 -0.012 0.43 0.82 2 -0.81 60 62
FOS -0.36 0.27 -10000 0 -0.55 344 344
HK2 0.003 0.43 -10000 0 -0.73 77 77
SP1 -0.019 0.094 -10000 0 -0.24 35 35
GCK 0.065 0.22 0.67 3 -0.52 2 5
HK1 0.005 0.43 -10000 0 -0.74 74 74
NPM1 0.001 0.43 -10000 0 -0.74 75 75
EGLN1 -0.023 0.4 -10000 0 -0.73 73 73
CREB1 0.04 0.01 -10000 0 -10000 0 0
PGM1 0 0.43 -10000 0 -0.74 74 74
SMAD3 0.034 0.01 -10000 0 -10000 0 0
EDN1 -0.4 0.6 0.62 1 -1.2 163 164
IGFBP1 0.002 0.43 -10000 0 -0.74 75 75
VEGFA 0.069 0.36 0.81 19 -0.61 44 63
HIF1A/JAB1 0.04 0.1 0.31 5 -0.41 4 9
CP -0.063 0.51 0.84 5 -0.8 118 123
CXCL12 -0.087 0.48 -10000 0 -0.8 113 113
COPS5 0.034 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4 0.048 0.028 -10000 0 -0.25 3 3
BNIP3 -0.001 0.43 0.85 1 -0.74 76 77
EGLN3 0.02 0.44 0.85 9 -0.74 73 82
CA9 0.015 0.44 0.84 7 -0.73 77 84
TERT -0.012 0.42 -10000 0 -0.74 72 72
ENO1 0.003 0.43 -10000 0 -0.74 73 73
PFKL 0.002 0.43 -10000 0 -0.74 73 73
NCOA1 0.035 0.027 -10000 0 -0.54 1 1
ADM -0.1 0.5 -10000 0 -0.78 132 132
ARNT 0.02 0.098 -10000 0 -10000 0 0
HNF4A 0.036 0.009 -10000 0 -10000 0 0
ADFP -0.053 0.4 0.72 4 -0.73 75 79
SLC2A1 0.07 0.36 0.81 16 -0.6 46 62
LEP -0.14 0.48 -10000 0 -0.8 131 131
HIF1A/ARNT/Cbp/p300 -0.02 0.36 0.82 2 -0.71 50 52
EPO 0.069 0.32 0.78 14 -0.62 23 37
CREBBP 0.04 0.16 0.45 15 -0.28 14 29
HIF1A/ARNT/Cbp/p300/HDAC7 -0.012 0.35 0.8 5 -0.7 45 50
PFKFB3 -0.005 0.42 -10000 0 -0.75 72 72
NT5E -0.004 0.44 -10000 0 -0.75 78 78
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.2 0.19 -9999 0 -0.35 217 217
MAP3K8 -0.048 0.19 -9999 0 -0.55 65 65
FOS -0.098 0.12 -9999 0 -0.36 28 28
PRKCA -0.006 0.028 -9999 0 -10000 0 0
PTPN7 -0.002 0.044 -9999 0 -10000 0 0
HRAS 0.032 0.013 -9999 0 -10000 0 0
PRKCB -0.013 0.009 -9999 0 -0.018 361 361
NRAS 0.033 0.016 -9999 0 -10000 0 0
RAS family/GTP 0.029 0.038 -9999 0 -10000 0 0
MAPK3 -0.029 0.075 -9999 0 -0.61 3 3
MAP2K1 -0.055 0.089 -9999 0 -0.28 42 42
ELK1 -0.015 0.037 -9999 0 -10000 0 0
BRAF -0.016 0.037 -9999 0 -0.25 6 6
mol:GTP -0.004 0.003 -9999 0 -0.006 364 364
MAPK1 -0.052 0.12 -9999 0 -0.45 28 28
RAF1 -0.016 0.035 -9999 0 -0.25 5 5
KRAS 0.032 0.018 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.009 0.16 -10000 0 -0.3 104 104
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.44 158 158
AKT1 -0.18 0.37 -10000 0 -0.79 132 132
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.18 0.38 -10000 0 -0.8 132 132
mol:Ca2+ -0.032 0.12 0.26 3 -0.28 68 71
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
E2/ER alpha (dimer)/Striatin -0.018 0.17 0.23 1 -0.34 104 105
SHC1 0.027 0.014 -10000 0 -10000 0 0
apoptosis 0.17 0.35 0.75 132 -10000 0 132
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 -0.45 138 139
regulation of stress fiber formation 0.016 0.12 -10000 0 -0.25 20 20
E2/ERA-ERB (dimer) -0.021 0.17 -10000 0 -0.34 108 108
KRAS 0.034 0.018 -10000 0 -10000 0 0
G13/GTP -0.018 0.15 -10000 0 -0.31 99 99
pseudopodium formation -0.016 0.12 0.25 20 -10000 0 20
E2/ER alpha (dimer)/PELP1 -0.024 0.17 -10000 0 -0.34 106 106
GRB2 0.034 0.018 -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 -0.5 139 139
E2/ER beta (dimer) 0.024 0.005 -10000 0 -10000 0 0
mol:GDP -0.045 0.18 0.23 12 -0.39 105 117
mol:NADP -0.14 0.25 -10000 0 -0.5 139 139
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 -0.035 0.12 0.26 3 -0.29 67 70
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
PLCB1 -0.036 0.13 -10000 0 -0.29 72 72
PLCB2 0.002 0.087 -10000 0 -0.46 8 8
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
mol:L-citrulline -0.14 0.25 -10000 0 -0.5 139 139
RHOA 0.033 0.007 -10000 0 -10000 0 0
Gai/GDP -0.14 0.28 -10000 0 -0.73 81 81
JNK cascade 0.024 0.005 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
ESR2 0.033 0.007 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.058 0.26 -10000 0 -0.54 106 106
Gq family/GDP/Gbeta gamma 0.008 0.16 -10000 0 -0.82 15 15
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.029 0.14 -10000 0 -0.58 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.22 0.31 1 -0.45 109 110
GNAZ 0.026 0.062 -10000 0 -0.54 6 6
E2/ER alpha (dimer) -0.044 0.18 -10000 0 -0.39 110 110
STRN 0.034 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 -0.54 183 183
HBEGF -0.11 0.23 0.37 7 -0.56 58 65
cAMP biosynthetic process -0.02 0.13 -10000 0 -0.28 102 102
SRC -0.14 0.23 0.3 4 -0.43 141 145
PI3K 0.005 0.13 -10000 0 -0.4 44 44
GNB1 0.034 0.011 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.019 0.18 -10000 0 -0.37 86 86
SOS1 0.034 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.21 0.21 -10000 0 -0.42 211 211
Gs family/GTP -0.011 0.14 -10000 0 -0.28 102 102
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.061 0.025 -10000 0 -10000 0 0
vasodilation -0.14 0.24 -10000 0 -0.48 140 140
mol:DAG -0.035 0.12 0.26 3 -0.29 67 70
Gs family/GDP/Gbeta gamma -0.04 0.16 -10000 0 -0.36 84 84
MSN -0.018 0.12 0.26 20 -10000 0 20
Gq family/GTP 0.003 0.093 -10000 0 -0.36 14 14
mol:PI-3-4-5-P3 -0.18 0.36 -10000 0 -0.76 132 132
NRAS 0.036 0.016 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.14 0.24 0.48 140 -10000 0 140
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
RhoA/GDP -0.026 0.19 0.24 12 -0.37 104 116
NOS3 -0.15 0.26 -10000 0 -0.53 139 139
GNA11 0.033 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.13 0.27 -10000 0 -0.57 130 130
E2/ER alpha (dimer)/PELP1/Src -0.14 0.24 0.31 3 -0.47 139 142
ruffle organization -0.016 0.12 0.25 20 -10000 0 20
ROCK2 -0.016 0.13 0.27 20 -10000 0 20
GNA14 0.043 0.068 -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 -0.097 0.22 0.39 8 -0.55 56 64
MMP2 -0.14 0.22 0.3 6 -0.54 65 71
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.023 0.3 0.68 3 -0.76 25 28
CRP 0.002 0.32 0.74 5 -0.76 25 30
cell cycle arrest -0.052 0.34 0.69 4 -0.74 54 58
TIMP1 -0.012 0.28 0.66 9 -0.62 33 42
IL6ST 0.038 0.084 -10000 0 -0.54 9 9
Rac1/GDP -0.088 0.22 0.42 7 -0.44 80 87
AP1 -0.16 0.24 0.55 2 -0.53 88 90
GAB2 0.033 0.015 -10000 0 -10000 0 0
TNFSF11 -0.005 0.32 0.67 10 -0.7 33 43
HSP90B1 0.043 0.14 -10000 0 -0.89 7 7
GAB1 0.035 0.027 -10000 0 -0.54 1 1
MAPK14 -0.13 0.2 -10000 0 -0.54 61 61
AKT1 0.032 0.092 0.34 1 -0.42 6 7
FOXO1 0.005 0.13 -10000 0 -0.43 17 17
MAP2K6 -0.12 0.2 0.36 3 -0.45 86 89
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.055 0.24 0.48 10 -0.48 67 77
MITF -0.11 0.21 0.37 4 -0.43 94 98
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 -0.16 0.49 -10000 0 -1.3 74 74
CEBPB 0.038 0.03 -10000 0 -0.54 1 1
GRB2/SOS1/GAB family/SHP2 -0.001 0.14 0.4 1 -0.48 22 23
STAT3 -0.071 0.36 0.69 4 -0.81 54 58
STAT1 0.035 0.12 -10000 0 -0.85 7 7
CEBPD -0.08 0.44 0.68 4 -1 71 75
PIK3CA 0.034 0.009 -10000 0 -10000 0 0
PI3K 0.007 0.13 -10000 0 -0.4 44 44
JUN -0.067 0.22 -10000 0 -0.54 89 89
PIAS3/MITF -0.1 0.2 0.38 2 -0.43 80 82
MAPK11 -0.12 0.2 -10000 0 -0.53 61 61
STAT3 (dimer)/FOXO1 -0.086 0.33 0.62 6 -0.69 65 71
GRB2/SOS1/GAB family -0.082 0.18 0.37 2 -0.44 47 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.19 0.3 5 -0.41 102 107
GRB2 0.036 0.019 -10000 0 -10000 0 0
JAK2 0.032 0.011 -10000 0 -10000 0 0
LBP 0.01 0.28 0.66 14 -0.65 19 33
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
JAK1 0.038 0.013 -10000 0 -10000 0 0
MYC -0.014 0.38 0.72 9 -1 37 46
FGG -0.025 0.3 0.7 3 -0.71 34 37
macrophage differentiation -0.052 0.34 0.69 4 -0.74 54 58
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.19 -10000 0 -0.3 269 269
JUNB -0.03 0.3 0.64 3 -0.73 32 35
FOS -0.35 0.27 -10000 0 -0.54 344 344
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.36 9 -0.44 100 109
STAT1/PIAS1 -0.073 0.23 0.42 10 -0.43 78 88
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.097 -10000 0 -0.4 11 11
STAT3 (dimer) -0.069 0.35 0.69 4 -0.8 53 57
PRKCD -0.033 0.26 0.55 11 -0.54 55 66
IL6R 0.03 0.031 -10000 0 -0.55 1 1
SOCS3 -0.15 0.24 -10000 0 -0.92 27 27
gp130 (dimer)/JAK1/JAK1/LMO4 0.073 0.12 0.3 4 -0.32 31 35
Rac1/GTP -0.077 0.23 0.43 9 -0.45 77 86
HCK 0.037 0.022 -10000 0 -10000 0 0
MAPKKK cascade 0.022 0.16 -10000 0 -0.57 24 24
bone resorption -0.002 0.31 0.66 12 -0.66 33 45
IRF1 -0.023 0.31 0.71 4 -0.75 27 31
mol:GDP -0.1 0.21 0.4 9 -0.43 90 99
SOS1 0.038 0.009 -10000 0 -10000 0 0
VAV1 -0.1 0.22 0.4 9 -0.44 90 99
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.2 -10000 0 -0.57 62 62
PTPN11 0.021 0.093 -10000 0 -0.81 5 5
IL6/IL6RA -0.23 0.2 -10000 0 -0.36 329 329
gp130 (dimer)/TYK2/TYK2/LMO4 0.067 0.11 0.29 1 -0.33 27 28
gp130 (dimer)/JAK2/JAK2/LMO4 0.063 0.11 0.29 1 -0.32 30 31
IL6 -0.37 0.27 0.22 1 -0.54 365 366
PIAS3 0.033 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 0.036 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.14 0.17 0.29 3 -0.3 189 192
LMO4 0.029 0.12 0.24 4 -0.54 21 25
STAT3 (dimer)/PIAS3 -0.066 0.33 0.65 4 -0.73 57 61
MCL1 0.07 0.12 0.52 2 -10000 0 2
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.62 0.96 1 -1.2 91 92
STAT6 (cleaved dimer) -0.23 0.54 -10000 0 -1.1 107 107
IGHG1 0.026 0.3 0.62 17 -0.6 10 27
IGHG3 -0.15 0.58 0.78 3 -1.1 109 112
AKT1 -0.026 0.35 0.65 1 -0.75 31 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.028 0.28 0.6 3 -0.86 13 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.024 0.37 0.64 6 -0.77 35 41
THY1 -0.14 0.62 1 5 -1.1 101 106
MYB -0.006 0.16 -10000 0 -0.54 40 40
HMGA1 0.037 0.022 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.003 0.4 0.73 13 -0.64 57 70
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.001 0.34 0.63 6 -0.82 17 23
SP1 0.057 0.044 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.007 0.057 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.16 0.59 0.84 1 -1.1 105 106
SOCS1 -0.06 0.41 0.76 1 -0.71 83 84
SOCS3 -0.015 0.39 0.7 1 -1.1 21 22
FCER2 -0.14 0.52 0.89 4 -0.88 82 86
PARP14 0.042 0.032 -10000 0 -10000 0 0
CCL17 -0.12 0.64 1 10 -1.1 101 111
GRB2 0.034 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.03 0.29 0.59 8 -0.71 13 21
T cell proliferation -0.18 0.62 -10000 0 -1.1 108 108
IL4R/JAK1 -0.15 0.61 -10000 0 -1.1 97 97
EGR2 -0.51 0.86 0.98 4 -1.3 251 255
JAK2 0.03 0.089 -10000 0 -10000 0 0
JAK3 0.035 0.019 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
JAK1 0.035 0.047 -10000 0 -10000 0 0
COL1A2 0.038 0.31 0.67 8 -1.2 9 17
CCL26 -0.14 0.62 1.1 5 -1.1 102 107
IL4R -0.14 0.68 1.1 7 -1.2 98 105
PTPN6 0.015 0.044 0.19 3 -10000 0 3
IL13RA2 -0.15 0.63 0.97 4 -1.1 108 112
IL13RA1 0.031 0.091 -10000 0 -10000 0 0
IRF4 0.064 0.21 0.71 3 -0.68 7 10
ARG1 0.048 0.26 0.72 4 -1.1 4 8
CBL -0.015 0.36 0.66 6 -0.6 60 66
GTF3A 0.1 0.066 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL13RA1/JAK2 0.05 0.13 0.37 4 -10000 0 4
IRF4/BCL6 0.028 0.21 -10000 0 -0.66 9 9
CD40LG 0.048 0.033 0.31 2 -10000 0 2
MAPK14 -0.014 0.38 0.67 5 -0.66 53 58
mitosis -0.02 0.34 0.65 1 -0.7 31 32
STAT6 -0.15 0.76 1.2 15 -1.3 107 122
SPI1 0.043 0.033 -10000 0 -0.24 1 1
RPS6KB1 -0.003 0.33 0.65 5 -0.72 23 28
STAT6 (dimer) -0.15 0.76 1.2 15 -1.3 107 122
STAT6 (dimer)/PARP14 -0.17 0.64 -10000 0 -1.2 107 107
mast cell activation -0.006 0.027 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.018 0.36 0.64 4 -0.75 37 41
FRAP1 -0.026 0.35 0.65 1 -0.74 32 33
LTA -0.14 0.62 0.93 3 -1.1 102 105
FES 0.031 0.037 -10000 0 -0.54 2 2
T-helper 1 cell differentiation 0.14 0.74 1.2 107 -1.2 15 122
CCL11 -0.11 0.61 0.89 5 -1.1 102 107
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.01 0.34 0.63 3 -0.87 17 20
IL2RG 0.044 0.042 0.22 11 -10000 0 11
IL10 -0.1 0.63 1 11 -1.1 94 105
IRS1 -0.034 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 117 117
IL4 0.045 0.3 0.79 7 -1.1 13 20
IL5 -0.14 0.62 1 4 -1.1 98 102
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.061 0.55 0.98 14 -0.87 94 108
COL1A1 0.12 0.4 0.76 42 -0.93 24 66
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.16 0.62 -10000 0 -1.2 90 90
IL2R gamma/JAK3 0.063 0.039 -10000 0 -10000 0 0
TFF3 -0.27 0.73 0.93 3 -1.3 142 145
ALOX15 -0.14 0.62 0.93 3 -1.2 94 97
MYBL1 0.049 0.054 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.094 0.54 0.81 7 -0.89 106 113
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 -0.042 0.36 0.62 5 -0.7 42 47
mol:PI-3-4-5-P3 -0.025 0.35 0.66 1 -0.75 31 32
PI3K -0.032 0.37 0.66 1 -0.81 31 32
DOK2 0.025 0.039 -10000 0 -0.54 2 2
ETS1 0.002 0.06 0.2 1 -0.51 1 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.039 0.28 0.57 9 -0.68 11 20
ITGB3 -0.14 0.62 0.97 4 -1.1 104 108
PIGR -0.39 0.84 1 11 -1.3 214 225
IGHE -0.042 0.1 0.17 16 -0.26 27 43
MAPKKK cascade 0.041 0.27 0.57 9 -0.67 11 20
BCL6 -0.026 0.17 -10000 0 -0.55 51 51
OPRM1 -0.14 0.62 0.93 3 -1.1 102 105
RETNLB -0.14 0.62 0.93 3 -1.1 95 98
SELP -0.29 0.82 0.98 10 -1.4 161 171
AICDA -0.14 0.59 0.94 1 -1.1 101 102
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 0.11 0.12 0.27 177 -10000 0 177
Ephrin B/EPHB2/RasGAP 0.081 0.067 -10000 0 -0.3 7 7
ITSN1 0.034 0.005 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.044 0.027 -10000 0 -0.34 2 2
Ephrin B1/EPHB1 -0.1 0.19 -10000 0 -0.34 194 194
HRAS/GDP -0.083 0.16 -10000 0 -0.38 48 48
Ephrin B/EPHB1/GRB7 -0.056 0.18 -10000 0 -0.31 159 159
Endophilin/SYNJ1 0.018 0.05 0.26 1 -0.28 7 8
KRAS 0.034 0.018 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.056 0.19 -10000 0 -0.31 174 174
endothelial cell migration 0.026 0.11 -10000 0 -0.3 47 47
GRB2 0.034 0.018 -10000 0 -10000 0 0
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.008 0.064 0.3 5 -0.29 5 10
HRAS 0.034 0.013 -10000 0 -10000 0 0
RRAS 0.017 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 -0.095 0.16 0.36 2 -0.29 190 192
lamellipodium assembly -0.11 0.12 -10000 0 -0.27 177 177
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.063 0.15 -10000 0 -0.29 126 126
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
EPHB2 0.043 0.037 -10000 0 -10000 0 0
EPHB3 0.035 0.016 -10000 0 -10000 0 0
EPHB1 -0.18 0.28 -10000 0 -0.54 192 192
EPHB4 0.035 0.032 -10000 0 -0.54 1 1
mol:GDP -0.084 0.14 -10000 0 -0.39 48 48
Ephrin B/EPHB2 0.067 0.059 -10000 0 -0.3 7 7
Ephrin B/EPHB3 0.061 0.054 -10000 0 -0.3 7 7
JNK cascade -0.092 0.16 0.39 4 -0.3 183 187
Ephrin B/EPHB1 -0.071 0.18 -10000 0 -0.3 190 190
RAP1/GDP -0.062 0.14 -10000 0 -0.36 41 41
EFNB2 0.026 0.058 -10000 0 -0.54 5 5
EFNB3 0.031 0.011 -10000 0 -10000 0 0
EFNB1 0.032 0.036 -10000 0 -0.54 2 2
Ephrin B2/EPHB1-2 -0.077 0.19 -10000 0 -0.32 191 191
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.062 0.17 -10000 0 -0.35 44 44
Rap1/GTP -0.075 0.15 -10000 0 -0.27 159 159
axon guidance 0.048 0.033 0.23 2 -0.34 1 3
MAPK3 -0.047 0.14 0.26 1 -0.38 32 33
MAPK1 -0.054 0.14 -10000 0 -0.38 33 33
Rac1/GDP -0.075 0.14 -10000 0 -0.37 45 45
actin cytoskeleton reorganization -0.077 0.12 -10000 0 -0.31 34 34
CDC42/GDP -0.074 0.14 -10000 0 -0.36 47 47
PI3K 0.031 0.12 -10000 0 -0.31 47 47
EFNA5 0.033 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 0.019 0.068 -10000 0 -0.3 8 8
CDC42 0.033 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.077 0.14 -10000 0 -0.27 153 153
PTK2 0.15 0.27 0.67 104 -10000 0 104
MAP4K4 -0.093 0.16 0.39 4 -0.3 183 187
SRC 0.033 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 -0.055 0.14 0.45 5 -0.34 14 19
MAP2K1 -0.06 0.14 -10000 0 -0.4 34 34
WASL 0.033 0.026 -10000 0 -0.54 1 1
Ephrin B1/EPHB1-2/NCK1 -0.062 0.2 -10000 0 -0.32 191 191
cell migration -0.065 0.17 0.32 5 -0.43 37 42
NRAS 0.036 0.016 -10000 0 -10000 0 0
SYNJ1 0.018 0.051 0.26 1 -0.28 7 8
PXN 0.034 0.003 -10000 0 -10000 0 0
TF -0.014 0.068 0.25 1 -0.28 22 23
HRAS/GTP -0.062 0.17 -10000 0 -0.28 178 178
Ephrin B1/EPHB1-2 -0.073 0.19 -10000 0 -0.31 191 191
cell adhesion mediated by integrin -0.009 0.049 0.26 7 -0.2 11 18
RAC1 0.034 0.005 -10000 0 -10000 0 0
mol:GTP -0.062 0.18 -10000 0 -0.29 181 181
RAC1-CDC42/GTP -0.088 0.14 -10000 0 -0.27 176 176
RASA1 0.034 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.064 0.14 -10000 0 -0.36 44 44
ruffle organization -0.097 0.14 0.41 3 -0.47 8 11
NCK1 0.034 0.005 -10000 0 -10000 0 0
receptor internalization -0.006 0.05 0.25 1 -0.27 7 8
Ephrin B/EPHB2/KALRN 0.082 0.066 -10000 0 -0.3 7 7
ROCK1 0.024 0.038 -10000 0 -0.31 2 2
RAS family/GDP -0.085 0.095 -10000 0 -0.31 29 29
Rac1/GTP -0.089 0.15 -10000 0 -0.28 177 177
Ephrin B/EPHB1/Src/Paxillin -0.087 0.16 -10000 0 -0.28 180 180
FAS signaling pathway (CD95)

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.02 0.093 0.22 64 -10000 0 64
RFC1 0.02 0.088 0.21 64 -10000 0 64
PRKDC 0.04 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 -0.024 0.091 0.34 3 -0.32 16 19
MAP2K4 -0.18 0.19 -10000 0 -0.42 110 110
mol:ceramide -0.075 0.12 0.27 1 -0.38 31 32
GSN -0.058 0.17 0.23 23 -0.34 107 130
FASLG/FAS/FADD/FAF1/Caspase 8 -0.032 0.097 0.32 3 -0.32 15 18
FAS -0.047 0.14 -10000 0 -0.56 33 33
BID -0.022 0.021 -10000 0 -10000 0 0
MAP3K1 -0.093 0.14 0.27 2 -0.44 27 29
MAP3K7 0.025 0.01 -10000 0 -10000 0 0
RB1 0.021 0.086 0.21 67 -10000 0 67
CFLAR 0.04 0.026 -10000 0 -0.52 1 1
HGF/MET -0.01 0.17 -10000 0 -0.36 90 90
ARHGDIB 0.023 0.096 0.23 68 -10000 0 68
FADD -0.008 0.028 -10000 0 -10000 0 0
actin filament polymerization 0.058 0.17 0.34 108 -0.23 23 131
NFKB1 -0.1 0.12 -10000 0 -0.65 8 8
MAPK8 -0.32 0.25 -10000 0 -0.45 371 371
DFFA 0.02 0.088 0.21 68 -10000 0 68
DNA fragmentation during apoptosis 0.019 0.089 0.21 28 -10000 0 28
FAS/FADD/MET -0.031 0.15 -10000 0 -0.39 65 65
CFLAR/RIP1 0.06 0.027 -10000 0 -0.37 1 1
FAIM3 0.034 0.029 -10000 0 -10000 0 0
FAF1 -0.017 0.033 -10000 0 -10000 0 0
PARP1 0.025 0.1 0.24 73 -10000 0 73
DFFB 0.019 0.089 0.21 53 -10000 0 53
CHUK -0.1 0.11 -10000 0 -0.61 8 8
FASLG 0.001 0.061 -10000 0 -0.55 1 1
FAS/FADD -0.033 0.1 -10000 0 -0.42 28 28
HGF 0.035 0.01 -10000 0 -10000 0 0
LMNA 0.022 0.1 0.42 15 -10000 0 15
CASP6 0.021 0.09 0.21 69 -10000 0 69
CASP10 -0.012 0.03 -10000 0 -10000 0 0
CASP3 0.02 0.1 0.26 68 -0.22 17 85
PTPN13 -0.019 0.17 -10000 0 -0.54 47 47
CASP8 -0.027 0.021 -10000 0 -10000 0 0
IL6 -0.88 0.56 -10000 0 -1.2 380 380
MET -0.022 0.17 -10000 0 -0.54 50 50
ICAD/CAD 0.011 0.075 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.076 0.13 0.27 1 -0.38 31 32
activation of caspase activity by cytochrome c -0.022 0.021 -10000 0 -10000 0 0
PAK2 0.017 0.099 0.23 74 -10000 0 74
BCL2 -0.07 0.22 -10000 0 -0.54 93 93
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.28 0.53 1 5 -1.2 65 70
IL23A -0.24 0.48 1.1 6 -1 50 56
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.46 0.76 2 -1 64 66
positive regulation of T cell mediated cytotoxicity -0.27 0.52 1.1 8 -1.1 65 73
ITGA3 -0.23 0.47 0.99 5 -1 55 60
IL17F -0.18 0.35 0.7 9 -0.66 69 78
IL12B 0.007 0.082 0.31 6 -10000 0 6
STAT1 (dimer) -0.26 0.5 0.92 5 -1.1 63 68
CD4 -0.24 0.47 1 4 -1 57 61
IL23 -0.24 0.46 0.95 5 -1 51 56
IL23R -0.019 0.21 0.82 3 -1.1 10 13
IL1B -0.25 0.49 1.1 6 -1 58 64
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.47 0.94 7 -0.98 55 62
TYK2 0.003 0.06 0.27 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 -0.006 0.16 0.2 2 -0.54 42 44
IL12RB1 0.004 0.06 0.27 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 -0.023 0.22 0.69 3 -1 10 13
positive regulation of chronic inflammatory response -0.27 0.52 1.1 8 -1.1 65 73
natural killer cell activation 0.001 0.014 0.08 2 -0.061 6 8
JAK2 0.004 0.076 0.32 4 -10000 0 4
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
NFKB1 0.034 0.009 -10000 0 -10000 0 0
RELA 0.034 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.23 0.44 0.92 6 -0.95 52 58
ALOX12B -0.24 0.46 1 4 -0.99 59 63
CXCL1 -0.64 0.73 1 8 -1.2 298 306
T cell proliferation -0.27 0.52 1.1 8 -1.1 65 73
NFKBIA 0.033 0.01 -10000 0 -10000 0 0
IL17A -0.12 0.3 0.65 12 -0.53 53 65
PI3K -0.28 0.47 0.82 1 -1 78 79
IFNG 0.022 0.074 0.18 64 -0.12 6 70
STAT3 (dimer) -0.26 0.46 0.77 2 -0.98 74 76
IL18R1 0.04 0.03 -10000 0 -0.54 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.34 0.77 11 -0.69 39 50
IL18/IL18R 0.065 0.14 0.28 27 -0.34 42 69
macrophage activation -0.013 0.028 0.078 19 -0.044 18 37
TNF -0.25 0.48 1.1 5 -1.1 50 55
STAT3/STAT4 -0.26 0.48 0.81 2 -1 67 69
STAT4 (dimer) -0.27 0.5 0.88 5 -1.1 68 73
IL18 0.047 0.046 -10000 0 -10000 0 0
IL19 -0.2 0.47 0.95 7 -0.99 52 59
STAT5A (dimer) -0.27 0.49 0.88 4 -1.1 66 70
STAT1 0.059 0.055 -10000 0 -10000 0 0
SOCS3 0.018 0.087 -10000 0 -0.54 12 12
CXCL9 -0.22 0.5 1.1 6 -1.1 54 60
MPO -0.23 0.47 1 4 -0.98 59 63
positive regulation of humoral immune response -0.27 0.52 1.1 8 -1.1 65 73
IL23/IL23R/JAK2/TYK2 -0.28 0.54 1.1 8 -1.2 62 70
IL6 -0.79 0.67 0.94 6 -1.2 368 374
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
IL2 0.049 0.039 0.25 1 -0.52 1 2
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.014 0.08 2 -0.061 6 8
CD3E -0.24 0.46 0.99 5 -1 55 60
keratinocyte proliferation -0.27 0.52 1.1 8 -1.1 65 73
NOS2 -0.25 0.46 0.88 8 -0.96 66 74
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.06 0.035 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.23 0.18 -10000 0 -0.34 367 367
PTK2 -0.047 0.12 0.4 2 -0.47 7 9
IGF1R 0.011 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 0.033 0.008 -10000 0 -10000 0 0
CDKN1B -0.1 0.13 -10000 0 -0.57 27 27
VEGFA 0.05 0.047 -10000 0 -10000 0 0
ILK -0.087 0.096 -10000 0 -0.47 16 16
ROCK1 0.034 0.006 -10000 0 -10000 0 0
AKT1 -0.082 0.089 -10000 0 -0.45 15 15
PTK2B 0.027 0.051 0.3 6 -0.3 1 7
alphaV/beta3 Integrin/JAM-A -0.16 0.17 -10000 0 -0.3 271 271
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 0.031 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.25 -10000 0 -0.38 258 258
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.039 0.06 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Syndecan-1 0.089 0.053 -10000 0 -0.34 1 1
PI4KA 0.033 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.3 0.25 -10000 0 -0.5 268 268
PI4 Kinase 0.039 0.022 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.1 0.068 -10000 0 -0.34 4 4
RPS6KB1 -0.28 0.23 0.59 1 -0.51 202 203
TLN1 0.033 0.006 -10000 0 -10000 0 0
MAPK3 -0.36 0.29 -10000 0 -0.56 322 322
GPR124 0.008 0.1 -10000 0 -0.54 17 17
MAPK1 -0.38 0.29 -10000 0 -0.56 340 340
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
alphaV/beta3 Integrin/Tumstatin 0.066 0.029 -10000 0 -0.34 1 1
cell adhesion 0.034 0.093 -10000 0 -0.3 31 31
ANGPTL3 0.033 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.072 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
TGFBR2 -0.004 0.14 -10000 0 -0.54 34 34
ITGB3 0.035 0.019 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
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 0.022 0.08 -10000 0 -0.54 10 10
alphaV/beta3 Integrin/CD47 0.057 0.064 -10000 0 -0.34 11 11
VCL 0.034 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.056 0.096 0.25 2 -0.34 23 25
CSF1 0.034 0.008 -10000 0 -10000 0 0
PIK3C2A -0.084 0.091 -10000 0 -0.46 13 13
PI4 Kinase/Pyk2 -0.15 0.13 -10000 0 -0.51 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.089 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 0.013 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
F11R -0.23 0.2 -10000 0 -0.4 295 295
alphaV/beta3 Integrin/Lactadherin 0.047 0.089 -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 0.068 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.056 0.048 0.29 1 -0.3 1 2
SDC1 0.073 0.065 -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 -0.034 0.19 -10000 0 -0.54 60 60
FAK1/Paxillin -0.032 0.12 0.38 3 -0.38 7 10
cell migration -0.033 0.1 0.36 3 -0.35 7 10
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PI3K -0.17 0.18 -10000 0 -0.31 269 269
SPP1 0.091 0.087 -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 0.027 -10000 0 -0.54 1 1
COL4A3 0.034 0.006 -10000 0 -10000 0 0
angiogenesis -0.37 0.28 -10000 0 -0.56 321 321
Rac1/GTP 0.031 0.068 -10000 0 -0.28 18 18
EDIL3 0.024 0.13 -10000 0 -0.54 22 22
cell proliferation 0.038 0.1 -10000 0 -0.34 33 33
S1P4 pathway

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:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.03 0.012 -9999 0 -10000 0 0
CDC42/GTP -0.067 0.14 -9999 0 -0.23 189 189
PLCG1 -0.073 0.13 -9999 0 -0.33 54 54
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.033 0.01 -9999 0 -10000 0 0
GNAI3 0.034 0.005 -9999 0 -10000 0 0
G12/G13 0.045 0.017 -9999 0 -10000 0 0
cell migration -0.067 0.14 -9999 0 -0.23 189 189
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 -0.07 0.13 -9999 0 -0.34 49 49
MAPK1 -0.077 0.13 -9999 0 -0.24 184 184
S1P/S1P5/Gi -0.081 0.14 -9999 0 -0.25 186 186
GNAI1 -0.17 0.28 -9999 0 -0.54 183 183
CDC42/GDP 0.024 0.006 -9999 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -9999 0 -10000 0 0
RHOA 0.034 0.051 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.081 0.14 -9999 0 -0.25 186 186
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.026 0.062 -9999 0 -0.54 6 6
S1P/S1P4/G12/G13 0.039 0.014 -9999 0 -10000 0 0
GNA12 0.034 0.005 -9999 0 -10000 0 0
GNA13 0.031 0.01 -9999 0 -10000 0 0
CDC42 0.033 0.007 -9999 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.035 0.043 0.12 5 -0.11 55 60
BUB1B 0.094 0.063 0.17 103 -10000 0 103
PLK1 0.046 0.035 0.11 54 -10000 0 54
PLK1S1 0.023 0.019 0.06 45 -10000 0 45
KIF2A 0.038 0.037 0.27 4 -10000 0 4
regulation of mitotic centrosome separation 0.046 0.035 0.11 54 -10000 0 54
GOLGA2 0.034 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.1 0.062 0.16 225 -10000 0 225
WEE1 0.049 0.077 -10000 0 -0.32 14 14
cytokinesis 0.13 0.082 0.22 113 -0.39 1 114
PP2A-alpha B56 0.14 0.11 -10000 0 -0.46 6 6
AURKA 0.051 0.04 0.14 11 -0.16 2 13
PICH/PLK1 0.13 0.095 0.24 174 -10000 0 174
CENPE 0.084 0.067 0.16 163 -10000 0 163
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 0.039 0.12 120 -10000 0 120
PAK1 0.043 0.044 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.007 -10000 0 -10000 0 0
CLSPN 0.044 0.054 0.14 14 -0.2 12 26
GORASP1 0.033 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 39 -10000 0 39
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.023 0.019 0.06 45 -10000 0 45
G2 phase of mitotic cell cycle 0.001 0.003 0.016 7 -10000 0 7
STAG2 0.034 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.021 0.092 -10000 0 -0.5 15 15
spindle elongation 0.046 0.035 0.11 54 -10000 0 54
ODF2 0.037 0.015 -10000 0 -10000 0 0
BUB1 0.12 0.12 -10000 0 -0.47 10 10
TPT1 0.014 0.059 0.13 1 -0.17 39 40
CDC25C 0.083 0.067 0.16 15 -0.21 12 27
CDC25B 0.048 0.041 -10000 0 -10000 0 0
SGOL1 0.036 0.043 0.11 55 -0.12 5 60
RHOA 0.033 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.091 0.067 0.24 27 -0.21 1 28
CDC14B -0.002 0.065 -10000 0 -0.4 13 13
CDC20 0.083 0.069 -10000 0 -10000 0 0
PLK1/PBIP1 0.074 0.055 0.14 178 -10000 0 178
mitosis -0.001 0.003 0.033 2 -10000 0 2
FBXO5 0.038 0.044 0.16 23 -0.12 1 24
CDC2 0.005 0.004 0.016 32 -10000 0 32
NDC80 0.11 0.074 0.18 282 -10000 0 282
metaphase plate congression 0.027 0.057 -10000 0 -0.21 24 24
ERCC6L 0.12 0.094 0.24 167 -10000 0 167
NLP/gamma Tubulin 0.025 0.025 0.09 12 -0.094 2 14
microtubule cytoskeleton organization 0.014 0.059 0.13 1 -0.17 39 40
G2/M transition DNA damage checkpoint 0 0.003 0.013 10 -10000 0 10
PPP1R12A 0.035 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.013 10 -10000 0 10
PLK1/PRC1-2 0.17 0.099 0.27 224 -10000 0 224
GRASP65/GM130/RAB1/GTP/PLK1 0.083 0.034 -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 0.033 0.098 66 -10000 0 66
mitotic prometaphase 0.001 0.005 0.021 25 -10000 0 25
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.045 -10000 0 -10000 0 0
microtubule-based process 0.12 0.066 0.18 230 -10000 0 230
Golgi organization 0.046 0.035 0.11 54 -10000 0 54
Cohesin/SA2 0.055 0.027 0.16 2 -10000 0 2
PPP1CB/MYPT1 0.051 0.01 -10000 0 -10000 0 0
KIF20A 0.13 0.071 -10000 0 -10000 0 0
APC/C/CDC20 0.094 0.066 0.18 149 -10000 0 149
PPP2R1A 0.034 0.006 -10000 0 -10000 0 0
chromosome segregation 0.073 0.054 0.14 178 -10000 0 178
PRC1 0.1 0.074 -10000 0 -10000 0 0
ECT2 0.072 0.074 0.2 94 -10000 0 94
C13orf34 0.039 0.031 0.099 47 -10000 0 47
NUDC 0.027 0.057 -10000 0 -0.21 24 24
regulation of attachment of spindle microtubules to kinetochore 0.093 0.063 0.17 106 -10000 0 106
spindle assembly 0.036 0.03 0.11 25 -10000 0 25
spindle stabilization 0.023 0.019 0.06 45 -10000 0 45
APC/C/HCDH1 0.021 0.059 -10000 0 -0.34 13 13
MKLP2/PLK1 0.12 0.066 0.18 230 -10000 0 230
CCNB1 0.087 0.07 -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 -0.16 13 14
G2/M transition of mitotic cell cycle 0.061 0.064 0.21 27 -0.21 1 28
MLF1IP 0.071 0.066 0.14 247 -10000 0 247
INCENP 0.047 0.04 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
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 0.058 0.04 -10000 0 -0.34 1 1
PDE6G/GNAT1/GTP 0.042 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.033 0.007 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.09 0.17 -10000 0 -0.29 205 205
mol:Na + -0.09 0.17 -10000 0 -0.28 214 214
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.049 0.1 -10000 0 -0.32 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.084 0.19 -10000 0 -0.29 195 195
CNGB1 0.029 0.012 -10000 0 -10000 0 0
RDH5 -0.43 0.23 -10000 0 -0.54 412 412
SAG 0.055 0.06 -10000 0 -0.54 1 1
mol:Ca2+ -0.12 0.15 0.36 6 -0.51 7 13
Na + (4 Units) -0.091 0.16 -10000 0 -0.28 145 145
RGS9 0.001 0.13 -10000 0 -0.54 27 27
GNB1/GNGT1 0.071 0.045 0.26 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 0.067 0.061 -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 -0.54 412 412
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 -0.4 412 412
SLC24A1 0.033 0.006 -10000 0 -10000 0 0
CNGA1 -0.21 0.29 -10000 0 -0.54 219 219
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 0.054 0.065 -10000 0 -0.54 2 2
Metarhodopsin II/Transducin 0.037 0.038 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.055 0.064 -10000 0 -0.34 12 12
PDE6A/B 0.038 0.071 -10000 0 -0.4 12 12
mol:Pi 0.048 0.1 -10000 0 -0.32 28 28
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.079 0.043 0.24 1 -10000 0 1
PDE6B 0.021 0.089 -10000 0 -0.54 12 12
PDE6A 0.034 0.009 -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 0.066 0.11 -10000 0 -0.3 25 25
GUCA1A 0.024 0.077 -10000 0 -0.54 9 9
GC2/GCAP Family 0.074 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
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.036 0.19 -10000 0 -0.54 61 61
LAT2 -0.029 0.13 -10000 0 -0.35 47 47
AP1 -0.19 0.23 -10000 0 -0.46 162 162
mol:PIP3 0.006 0.19 0.37 21 -0.42 46 67
IKBKB 0.022 0.14 0.31 36 -0.27 33 69
AKT1 -0.006 0.2 0.34 74 -0.47 27 101
IKBKG 0.004 0.13 0.28 22 -0.27 35 57
MS4A2 -0.056 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 0.011 0.15 0.36 11 -0.4 25 36
mol:Ca2+ 0.014 0.16 0.32 30 -0.32 45 75
LYN 0.032 0.018 0.18 1 -10000 0 1
CBLB -0.029 0.13 -10000 0 -0.36 45 45
SHC1 0.027 0.014 -10000 0 -10000 0 0
RasGAP/p62DOK -0.091 0.18 -10000 0 -0.31 204 204
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.011 0.2 0.34 66 -0.35 82 148
PTPN13 -0.038 0.19 -10000 0 -0.59 27 27
PTPN11 0.033 0.022 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.002 0.16 0.36 19 -0.35 27 46
SYK 0.04 0.027 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.039 0.15 -10000 0 -0.42 49 49
LAT -0.026 0.12 0.22 1 -0.35 44 45
PAK2 0.009 0.16 0.38 10 -0.43 25 35
NFATC2 -0.011 0.057 -10000 0 -0.69 1 1
HRAS 0.005 0.16 0.32 9 -0.45 27 36
GAB2 0.03 0.012 -10000 0 -10000 0 0
PLA2G1B 0.009 0.11 -10000 0 -0.83 7 7
Fc epsilon R1 -0.036 0.19 -10000 0 -0.42 94 94
Antigen/IgE/Fc epsilon R1 -0.031 0.17 -10000 0 -0.38 94 94
mol:GDP -0.023 0.15 0.28 2 -0.45 28 30
JUN -0.067 0.22 -10000 0 -0.54 89 89
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.55 47 47
FOS -0.36 0.27 -10000 0 -0.54 344 344
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.026 0.13 -10000 0 -0.35 52 52
CHUK 0.004 0.13 0.28 23 -0.26 37 60
KLRG1 -0.024 0.12 -10000 0 -0.32 45 45
VAV1 -0.028 0.13 0.22 1 -0.35 46 47
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 -0.027 0.11 -10000 0 -0.3 45 45
BTK -0.024 0.15 -10000 0 -0.46 29 29
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.047 0.17 -10000 0 -0.38 83 83
GAB2/PI3K/SHP2 -0.062 0.15 -10000 0 -0.39 61 61
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.032 0.13 -10000 0 -0.35 52 52
RAF1 0.008 0.12 -10000 0 -0.9 7 7
Fc epsilon R1/FcgammaRIIB/SHIP -0.019 0.18 -10000 0 -0.36 94 94
FCER1G 0.031 0.021 -10000 0 -10000 0 0
FCER1A -0.044 0.19 -10000 0 -0.55 63 63
Antigen/IgE/Fc epsilon R1/Fyn -0.02 0.17 -10000 0 -0.36 92 92
MAPK3 0.01 0.11 -10000 0 -0.86 7 7
MAPK1 0.004 0.11 -10000 0 -0.82 7 7
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.016 0.2 -10000 0 -0.57 42 42
DUSP1 -0.2 0.28 -10000 0 -0.54 208 208
NF-kappa-B/RelA 0.014 0.082 0.18 12 -0.18 22 34
actin cytoskeleton reorganization -0.013 0.18 -10000 0 -0.58 22 22
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.012 0.17 -10000 0 -0.45 36 36
FER -0.028 0.12 -10000 0 -0.35 48 48
RELA 0.034 0.005 -10000 0 -10000 0 0
ITK -0.002 0.069 -10000 0 -0.34 14 14
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG1 0 0.16 0.33 6 -0.46 26 32
cytokine secretion -0.005 0.046 -10000 0 -10000 0 0
SPHK1 -0.026 0.12 -10000 0 -0.36 41 41
PTK2 -0.015 0.18 -10000 0 -0.62 22 22
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.039 0.16 -10000 0 -0.44 50 50
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.029 0.22 0.37 15 -0.51 51 66
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 -0.076 0.32 -10000 0 -0.86 71 71
Fc epsilon R1/FcgammaRIIB -0.019 0.19 -10000 0 -0.38 94 94
mol:Choline -0.011 0.2 0.34 66 -0.34 82 148
SHC/Grb2/SOS1 0.01 0.14 -10000 0 -0.39 25 25
FYN 0.03 0.037 -10000 0 -0.54 2 2
DOK1 0.036 0.016 -10000 0 -10000 0 0
PXN -0.014 0.17 -10000 0 -0.56 21 21
HCLS1 -0.028 0.13 0.22 1 -0.35 45 46
PRKCB -0.003 0.16 0.32 22 -0.35 44 66
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 -0.3 45 45
LCP2 0.037 0.023 -10000 0 -10000 0 0
PLA2G4A -0.16 0.2 -10000 0 -0.35 219 219
RASA1 0.034 0.012 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.011 0.2 0.34 66 -0.34 82 148
IKK complex 0.023 0.12 0.28 35 -0.22 20 55
WIPF1 0.037 0.022 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.049 0.077 0.25 33 -10000 0 33
STMN1 0.054 0.084 0.29 45 -10000 0 45
Aurora B/RasGAP/Survivin 0.11 0.077 0.27 1 -10000 0 1
Chromosomal passenger complex/Cul3 protein complex -0.071 0.13 0.23 9 -0.33 27 36
BIRC5 0.12 0.076 0.19 10 -10000 0 10
DES -0.012 0.13 -10000 0 -0.56 24 24
Aurora C/Aurora B/INCENP 0.075 0.052 -10000 0 -10000 0 0
Aurora B/TACC1 0.025 0.087 -10000 0 -0.31 26 26
Aurora B/PP2A 0.058 0.042 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.019 0.022 0.14 3 -10000 0 3
mitotic metaphase/anaphase transition -0.003 0.004 -10000 0 -10000 0 0
NDC80 0.1 0.1 0.28 84 -10000 0 84
Cul3 protein complex -0.23 0.18 -10000 0 -0.35 364 364
KIF2C 0.14 0.1 0.23 257 -10000 0 257
PEBP1 0.039 0.027 -10000 0 -0.55 1 1
KIF20A 0.12 0.07 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.056 0.041 -10000 0 -10000 0 0
SEPT1 0.035 0.023 -10000 0 -10000 0 0
SMC2 0.04 0.03 -10000 0 -10000 0 0
SMC4 0.046 0.042 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.063 0.16 0.32 12 -0.42 32 44
PSMA3 0.033 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.005 -10000 0 -10000 0 0
H3F3B 0.031 0.037 -10000 0 -10000 0 0
AURKB 0.05 0.054 -10000 0 -10000 0 0
AURKC 0.036 0.019 -10000 0 -10000 0 0
CDCA8 0.11 0.074 -10000 0 -10000 0 0
cytokinesis 0.18 0.15 0.35 200 -10000 0 200
Aurora B/Septin1 0.18 0.15 0.38 130 -10000 0 130
AURKA 0.077 0.068 -10000 0 -10000 0 0
INCENP 0.053 0.041 -10000 0 -10000 0 0
KLHL13 -0.38 0.26 -10000 0 -0.54 370 370
BUB1 0.15 0.053 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.13 0.099 0.3 75 -10000 0 75
EVI5 0.036 0.026 -10000 0 -0.53 1 1
RhoA/GTP 0.22 0.14 0.35 214 -10000 0 214
SGOL1 0.073 0.065 -10000 0 -10000 0 0
CENPA 0.14 0.12 0.28 189 -10000 0 189
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.058 0.042 -10000 0 -10000 0 0
NCAPD2 0.035 0.021 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.059 0.041 -10000 0 -10000 0 0
RHOA 0.033 0.007 -10000 0 -10000 0 0
NCAPH 0.079 0.067 -10000 0 -10000 0 0
NPM1 0.026 0.11 -10000 0 -0.76 4 4
RASA1 0.034 0.012 -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 0.24 0.15 0.37 256 -10000 0 256
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
NSUN2 0.027 0.093 0.26 1 -0.75 2 3
MYLK -0.071 0.17 -10000 0 -0.34 139 139
KIF23 0.12 0.075 0.19 17 -10000 0 17
VIM -0.007 0.13 -10000 0 -0.39 47 47
RACGAP1 0.081 0.066 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.025 0.11 -10000 0 -0.48 12 12
Chromosomal passenger complex 0.16 0.13 0.28 245 -10000 0 245
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 0.034 0.006 -10000 0 -10000 0 0
CUL3 0.032 0.036 -10000 0 -0.54 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.045 0.24 0.59 2 -0.55 77 79
IHH 0.021 0.075 -10000 0 -0.2 1 1
SHH Np/Cholesterol/GAS1 -0.068 0.15 -10000 0 -0.31 126 126
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.067 0.15 0.31 126 -10000 0 126
SMO/beta Arrestin2 -0.002 0.19 0.41 2 -0.47 31 33
SMO -0.016 0.18 0.44 2 -0.48 35 37
AKT1 -0.021 0.19 0.31 1 -0.59 37 38
ARRB2 0.031 0.01 -10000 0 -10000 0 0
BOC -0.091 0.24 -10000 0 -0.54 111 111
ADRBK1 0.032 0.01 -10000 0 -10000 0 0
heart looping -0.016 0.18 0.44 2 -0.47 35 37
STIL 0.042 0.15 0.39 17 -0.34 7 24
DHH N/PTCH2 0.049 0.01 -10000 0 -10000 0 0
DHH N/PTCH1 0.006 0.16 0.38 2 -0.32 82 84
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DHH 0.034 0.004 -10000 0 -10000 0 0
PTHLH -0.11 0.39 0.52 6 -0.9 94 100
determination of left/right symmetry -0.016 0.18 0.44 2 -0.47 35 37
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
skeletal system development -0.11 0.39 0.52 6 -0.89 94 100
IHH N/Hhip 0.038 0.053 -10000 0 -10000 0 0
DHH N/Hhip 0.05 0.011 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.016 0.18 0.44 2 -0.47 35 37
pancreas development 0.034 0.011 -10000 0 -10000 0 0
HHAT 0.024 0.059 -10000 0 -0.54 5 5
PI3K 0.005 0.13 -10000 0 -0.4 44 44
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.14 0.27 -10000 0 -0.54 158 158
somite specification -0.016 0.18 0.44 2 -0.47 35 37
SHH Np/Cholesterol/PTCH1 -0.01 0.12 -10000 0 -0.37 9 9
SHH Np/Cholesterol/PTCH2 0.024 0.037 -10000 0 -0.31 5 5
SHH Np/Cholesterol/Megalin -0.056 0.14 -10000 0 -0.32 110 110
SHH 0.01 0.043 -10000 0 -0.4 5 5
catabolic process -0.009 0.18 0.47 2 -0.36 86 88
SMO/Vitamin D3 0.01 0.17 0.41 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 -0.061 0.2 0.35 9 -0.51 38 47
SHH Np/Cholesterol/BOC -0.038 0.13 -10000 0 -0.31 86 86
SHH Np/Cholesterol/CDO 0.019 0.049 -10000 0 -0.35 7 7
mesenchymal cell differentiation -0.024 0.038 0.31 5 -10000 0 5
mol:Vitamin D3 0.027 0.16 0.41 17 -0.37 9 26
IHH N/PTCH2 0.038 0.052 -10000 0 -10000 0 0
CDON 0.027 0.045 -10000 0 -0.54 3 3
IHH N/PTCH1 -0.001 0.18 0.47 2 -0.36 86 88
Megalin/LRPAP1 -0.071 0.2 -10000 0 -0.4 139 139
PTCH2 0.034 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.014 0.034 -10000 0 -0.31 5 5
PTCH1 -0.009 0.18 0.47 2 -0.36 86 88
HHIP 0.034 0.011 -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 -0.35 325 325
fibroblast growth factor receptor signaling pathway -0.22 0.18 -10000 0 -0.35 325 325
LAMA1 0.033 0.01 -10000 0 -10000 0 0
PRNP 0.017 0.094 -10000 0 -0.54 14 14
GPC1/SLIT2 -0.009 0.15 -10000 0 -0.39 66 66
SMAD2 -0.001 0.084 0.28 1 -0.31 32 33
GPC1/PrPc/Cu2+ 0.033 0.064 -10000 0 -0.34 14 14
GPC1/Laminin alpha1 0.048 0.017 -10000 0 -10000 0 0
TDGF1 0.033 0.007 -10000 0 -10000 0 0
CRIPTO/GPC1 0.048 0.015 -10000 0 -10000 0 0
APP/GPC1 0.045 0.048 -10000 0 -0.4 5 5
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 0.04 0.1 -10000 0 -0.34 34 34
SERPINC1 0.032 0.024 -10000 0 -10000 0 0
FYN 0.018 0.025 -10000 0 -0.34 2 2
FGR 0.02 0.01 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.024 0.084 0.29 2 -0.36 10 12
SLIT2 -0.039 0.19 -10000 0 -0.54 64 64
GPC1/NRG -0.002 0.13 -10000 0 -0.34 60 60
NRG1 -0.019 0.16 -10000 0 -0.54 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.07 0.039 -10000 0 -10000 0 0
LYN 0.018 0.013 -10000 0 -10000 0 0
mol:Spermine 0.009 0.01 -10000 0 -10000 0 0
cell growth -0.22 0.18 -10000 0 -0.35 325 325
BMP signaling pathway -0.034 0.013 -10000 0 -10000 0 0
SRC 0.019 0.009 -10000 0 -10000 0 0
TGFBR1 0.036 0.016 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.033 0.2 -10000 0 -0.54 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 0.047 -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 -0.54 380 380
FGFR1 0.018 0.076 -10000 0 -0.54 9 9
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
TGFBR2 -0.004 0.14 -10000 0 -0.54 34 34
cell death 0.045 0.048 -10000 0 -0.4 5 5
ATIII/GPC1 0.043 0.026 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.006 0.16 -10000 0 -0.38 74 74
LCK 0.031 0.033 -10000 0 -10000 0 0
neuron differentiation -0.002 0.13 -10000 0 -0.34 60 60
PrPc/Cu2+ 0.013 0.069 -10000 0 -0.4 14 14
APP 0.03 0.06 -10000 0 -0.54 5 5
TGFBR2 (dimer) -0.004 0.14 -10000 0 -0.54 34 34
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.025 0.12 0.24 1 -0.34 42 43
adherens junction organization -0.026 0.13 0.23 1 -0.42 26 27
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 0.32 3 -0.38 102 105
FMN1 -0.025 0.12 -10000 0 -0.31 54 54
mol:IP3 -0.025 0.1 -10000 0 -0.29 43 43
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.024 0.12 -10000 0 -0.32 54 54
CTNNB1 0.03 0.051 -10000 0 -0.54 4 4
AKT1 -0.021 0.11 -10000 0 -0.36 17 17
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.028 0.18 -10000 0 -0.52 39 39
CTNND1 0.033 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.021 0.11 0.26 1 -0.39 22 23
VASP -0.021 0.12 0.24 1 -0.39 23 24
ZYX -0.026 0.12 -10000 0 -0.38 26 26
JUB -0.025 0.12 -10000 0 -0.31 54 54
EGFR(dimer) -0.16 0.2 -10000 0 -0.42 115 115
E-cadherin/beta catenin-gamma catenin 0.035 0.091 -10000 0 -0.32 25 25
mol:PI-3-4-5-P3 -0.007 0.13 -10000 0 -0.3 48 48
PIK3CA 0.032 0.011 -10000 0 -10000 0 0
PI3K -0.007 0.13 -10000 0 -0.31 48 48
FYN -0.025 0.11 -10000 0 -0.4 20 20
mol:Ca2+ -0.024 0.099 -10000 0 -0.28 43 43
JUP 0.034 0.011 -10000 0 -10000 0 0
PIK3R1 -0.019 0.17 -10000 0 -0.54 47 47
mol:DAG -0.025 0.1 -10000 0 -0.29 43 43
CDH1 0.006 0.12 -10000 0 -0.54 22 22
RhoA/GDP -0.14 0.18 0.32 3 -0.38 100 103
establishment of polarity of embryonic epithelium -0.021 0.12 0.24 1 -0.38 23 24
SRC 0.033 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 -0.54 269 269
CASR -0.023 0.099 0.24 2 -0.32 17 19
RhoA/GTP -0.006 0.1 -10000 0 -0.31 17 17
AKT2 -0.022 0.11 -10000 0 -0.37 17 17
actin cable formation -0.021 0.12 0.25 3 -0.38 23 26
apoptosis 0.018 0.12 0.32 47 -0.26 4 51
CTNNA1 0.034 0.007 -10000 0 -10000 0 0
mol:GDP -0.16 0.18 -10000 0 -0.4 102 102
PIP5K1A -0.023 0.11 -10000 0 -0.4 22 22
PLCG1 -0.025 0.1 -10000 0 -0.3 43 43
Rac1/GTP -0.14 0.19 -10000 0 -0.39 114 114
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
Nectin adhesion 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
PDGFRB 0.034 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 68 68
positive regulation of JNK cascade -0.025 0.15 -10000 0 -0.32 86 86
CDC42/GDP -0.019 0.2 0.46 1 -0.43 86 87
Rac1/GDP -0.019 0.2 -10000 0 -0.42 87 87
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
CDC42/GTP -0.023 0.18 -10000 0 -0.39 85 85
nectin-3/I-afadin -0.024 0.17 -10000 0 -0.39 85 85
RAPGEF1 -0.043 0.2 0.47 1 -0.46 80 81
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.22 -10000 0 -0.52 82 82
PDGFB-D/PDGFRB 0.034 0.006 -10000 0 -10000 0 0
TLN1 -0.039 0.12 0.2 3 -0.48 21 24
Rap1/GTP -0.03 0.14 -10000 0 -0.33 77 77
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 85 85
PVR 0.035 0.015 -10000 0 -10000 0 0
Necl-5(dimer) 0.035 0.015 -10000 0 -10000 0 0
mol:GDP -0.045 0.24 0.47 1 -0.52 87 88
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PI3K -0.004 0.18 -10000 0 -0.34 105 105
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 -0.021 0.16 -10000 0 -0.33 84 84
PVRL1 0.031 0.015 -10000 0 -10000 0 0
PVRL3 -0.053 0.21 -10000 0 -0.54 77 77
PVRL2 0.039 0.027 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
CDH1 0.006 0.12 -10000 0 -0.54 22 22
CLDN1 -0.003 0.16 -10000 0 -0.54 41 41
JAM-A/CLDN1 -0.007 0.17 -10000 0 -0.36 81 81
SRC -0.075 0.24 -10000 0 -0.56 85 85
ITGB3 0.035 0.019 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.25 9 9
FARP2 -0.045 0.24 0.48 1 -0.54 79 80
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 79 79
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 79 79
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 -0.025 0.15 -10000 0 -0.32 86 86
alphaV/beta3 Integrin/Talin -0.005 0.13 0.3 1 -0.48 19 20
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 84 84
VAV2 -0.042 0.24 0.46 1 -0.54 75 76
RAP1/GDP -0.015 0.19 -10000 0 -0.4 81 81
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 79 79
nectin-3(dimer)/I-afadin/I-afadin -0.024 0.17 -10000 0 -0.39 85 85
Rac1/GTP -0.022 0.19 -10000 0 -0.4 84 84
PTPRM -0.035 0.14 -10000 0 -0.29 83 83
E-cadherin/beta catenin/alpha catenin 0.052 0.1 -10000 0 -0.29 26 26
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.25 186 186
GNAZ 0.026 0.062 -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 -0.25 186 186
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 -0.54 183 183
Insulin Pathway

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
CBL/APS/CAP -0.16 0.2 -10000 0 -0.32 285 285
TC10/GTP -0.13 0.16 -10000 0 -0.28 274 274
Insulin Receptor/Insulin/IRS1/Shp2 0.04 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 0.19 -10000 0 -0.54 52 52
FOXO3 -0.03 0.16 -10000 0 -0.6 33 33
AKT1 -0.046 0.16 0.33 8 -0.45 22 30
INSR 0.039 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.091 0.073 0.46 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.03 0.051 -10000 0 -0.54 4 4
SORBS1 -0.28 0.29 -10000 0 -0.54 279 279
CRK 0.031 0.01 -10000 0 -10000 0 0
PTPN1 0.019 0.054 0.28 17 -10000 0 17
CAV1 -0.24 0.18 -10000 0 -0.33 368 368
CBL/APS/CAP/Crk-II/C3G -0.13 0.18 -10000 0 -0.3 278 278
Insulin Receptor/Insulin/IRS1/NCK2 0.041 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 93 93
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 -0.41 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 0.017 0.061 -10000 0 -0.56 5 5
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.012 0.15 -10000 0 -0.42 20 20
HRAS/GTP -0.009 0.077 -10000 0 -0.26 37 37
Insulin Receptor 0.039 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.038 0.12 -10000 0 -0.3 42 42
PRKCI 0.01 0.086 -10000 0 -0.5 7 7
Insulin Receptor/Insulin/GRB14/PDK1 -0.045 0.16 -10000 0 -0.32 106 106
SHC1 0.027 0.014 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.057 0.058 -10000 0 -0.48 5 5
PI3K 0.007 0.15 -10000 0 -0.3 93 93
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 0.081 -10000 0 -0.47 9 9
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.01 0.09 -10000 0 -0.28 45 45
F2RL2 0.046 0.065 -10000 0 -0.54 3 3
TRIP10 0.033 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 0.034 0.006 -10000 0 -10000 0 0
RASA1 0.034 0.012 -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 -0.31 279 279
TC10/GDP 0.024 0.019 -10000 0 -0.4 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.069 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 0.012 -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 -0.034 0.19 -10000 0 -0.54 60 60
p62DOK/RasGAP 0.058 0.058 -10000 0 -0.48 5 5
INS 0.039 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.036 0.095 -10000 0 -0.29 59 59
GRB2 0.034 0.018 -10000 0 -10000 0 0
EIF4EBP1 -0.044 0.14 0.31 5 -0.4 21 26
PTPRA 0.038 0.013 -10000 0 -10000 0 0
PIK3CA 0.033 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 0.057 0.024 -10000 0 -10000 0 0
Par3/Par6 0.072 0.058 -10000 0 -0.3 5 5
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.049 0.011 -10000 0 -10000 0 0
Necdin/E2F1 -0.045 0.18 -10000 0 -0.37 117 117
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.003 0.15 -10000 0 -0.31 89 89
NGF (dimer)/p75(NTR)/BEX1 -0.006 0.14 -10000 0 -0.33 75 75
NT-4/5 (dimer)/p75(NTR) -0.04 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 0.014 0.15 -10000 0 -0.34 72 72
FURIN 0.036 0.023 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.001 0.15 -10000 0 -0.34 75 75
LINGO1 0.056 0.052 -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 0.022 -10000 0 -10000 0 0
RTN4R 0.041 0.035 -10000 0 -10000 0 0
neuron apoptosis -0.012 0.16 0.51 2 -0.48 14 16
IRAK1 0.036 0.015 -10000 0 -10000 0 0
SHC1 -0.023 0.1 -10000 0 -0.34 50 50
ARHGDIA 0.033 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 0.094 -10000 0 -0.54 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.078 0.2 -10000 0 -0.37 149 149
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 0.036 -10000 0 -10000 0 0
APP 0.03 0.06 -10000 0 -0.54 5 5
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.033 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.01 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 0.094 -10000 0 -0.25 57 57
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.018 0.14 -10000 0 -0.33 78 78
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 -0.021 0.13 -10000 0 -0.31 74 74
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.012 0.077 -10000 0 -0.21 56 56
p75(NTR)/beta APP -0.025 0.16 -10000 0 -0.38 83 83
BEX1 0.054 0.05 -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 65 65
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.028 0.15 -10000 0 -0.31 70 70
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RAC1/GTP -0.013 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 -0.017 0.15 -10000 0 -0.36 78 78
RHOB 0.032 0.037 -10000 0 -0.54 2 2
RHOA 0.033 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.058 0.036 -10000 0 -10000 0 0
NT3 (dimer) -0.12 0.26 -10000 0 -0.54 134 134
TP53 -0.028 0.13 0.37 8 -0.29 70 78
PRDM4 -0.017 0.13 -10000 0 -0.31 74 74
BDNF (dimer) 0.055 0.17 -10000 0 -0.31 70 70
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
SORT1 0.034 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.14 -10000 0 -0.31 89 89
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0 0.13 -10000 0 -0.31 74 74
RHOC 0.034 0.005 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.029 0.14 0.31 5 -0.33 67 72
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 -0.022 0.13 -10000 0 -0.31 74 74
APH1B 0.032 0.027 -10000 0 -0.54 1 1
APH1A 0.031 0.028 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.017 0.14 -10000 0 -0.34 74 74
PSEN1 0.033 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.049 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.13 0.23 -10000 0 -0.42 183 183
MAPK8 -0.025 0.14 0.3 7 -0.32 69 76
MAPK9 -0.025 0.13 0.28 6 -0.32 64 70
APAF1 0.034 0.003 -10000 0 -10000 0 0
NTF3 -0.12 0.26 -10000 0 -0.54 134 134
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.099 0.24 -10000 0 -0.54 117 117
RAC1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.009 0.14 -10000 0 -0.3 71 71
p75 CTF/Sortilin/TRAF6/NRIF 0.08 0.027 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.018 0.15 -10000 0 -0.35 78 78
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.027 0.14 -10000 0 -0.3 71 71
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.017 0.14 -10000 0 -0.31 75 75
PRKACB 0.035 0.082 -10000 0 -0.54 8 8
proBDNF (dimer)/p75 ECD 0.052 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 0.031 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.16 -10000 0 -0.4 99 99
BAD -0.025 0.15 0.41 8 -0.33 65 73
RIPK2 0.029 0.021 -10000 0 -10000 0 0
NGFR -0.054 0.2 -10000 0 -0.54 75 75
CYCS -0.008 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 0.4 9 -0.33 65 74
BDNF (dimer)/p75(NTR) -0.02 0.16 -10000 0 -0.38 80 80
PI3K -0.03 0.16 -10000 0 -0.34 99 99
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0 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 0.035 0.017 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.04 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 -0.31 74 74
TRAF6 0.034 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 -0.027 0.13 -10000 0 -0.33 74 74
SQSTM1 0.034 0.009 -10000 0 -10000 0 0
NGFRAP1 0.009 0.12 -10000 0 -0.54 22 22
CASP3 -0.023 0.14 0.39 9 -0.31 66 75
E2F1 0.05 0.047 -10000 0 -10000 0 0
CASP9 0.033 0.008 -10000 0 -10000 0 0
IKK complex 0.03 0.085 -10000 0 -0.3 1 1
NGF (dimer)/TRKA 0.022 0.016 -10000 0 -10000 0 0
MMP7 -0.042 0.19 -10000 0 -0.54 64 64
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.012 0.13 -10000 0 -0.3 73 73
MMP3 0.093 0.099 -10000 0 -0.54 5 5
APAF-1/Caspase 9 -0.033 0.1 -10000 0 -0.41 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.011 0.091 -10000 0 -0.26 46 46
epithelial cell differentiation 0.04 0.086 -10000 0 -0.29 26 26
CYFIP2 0.05 0.047 -10000 0 -10000 0 0
ENAH -0.008 0.071 0.28 5 -0.3 2 7
EGFR -0.27 0.29 -10000 0 -0.54 269 269
EPHA2 0.026 0.062 -10000 0 -0.54 6 6
MYO6 0 0.074 -10000 0 -0.28 25 25
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
ABI1/Sra1/Nap1 0.074 0.035 -10000 0 -10000 0 0
AQP5 -0.14 0.24 -10000 0 -0.49 151 151
CTNND1 0.033 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.072 -10000 0 -0.28 25 25
regulation of calcium-dependent cell-cell adhesion -0.024 0.1 -10000 0 -0.29 63 63
EGF -0.15 0.27 -10000 0 -0.54 164 164
NCKAP1 0.034 0.005 -10000 0 -10000 0 0
AQP3 -0.053 0.18 -10000 0 -0.49 64 64
cortical microtubule organization 0.04 0.086 -10000 0 -0.29 26 26
GO:0000145 -0.022 0.064 -10000 0 -0.27 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.089 -10000 0 -0.29 26 26
MLLT4 0.029 0.046 -10000 0 -0.54 3 3
ARF6/GDP -0.03 0.059 -10000 0 -0.27 25 25
ARF6 0.034 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.057 0.059 -10000 0 -0.32 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.002 0.069 -10000 0 -0.42 1 1
PVRL2 0.039 0.027 -10000 0 -10000 0 0
ZYX -0.003 0.073 -10000 0 -0.28 26 26
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 -0.35 357 357
RhoA/GDP 0.04 0.084 -10000 0 -0.28 25 25
actin cytoskeleton organization -0.022 0.067 -10000 0 -0.28 25 25
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
GIT1 0.032 0.011 -10000 0 -10000 0 0
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
DIAPH1 0.057 0.12 -10000 0 -0.56 8 8
Wnt receptor signaling pathway -0.04 0.086 0.29 26 -10000 0 26
RHOA 0.033 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.059 -10000 0 -0.27 25 25
CTNNA1 0.033 0.006 -10000 0 -10000 0 0
VCL -0.022 0.069 -10000 0 -0.28 25 25
EFNA1 0.028 0.016 -10000 0 -10000 0 0
LPP -0.024 0.066 -10000 0 -0.28 25 25
Ephrin A1/EPHA2 0.022 0.084 -10000 0 -0.29 26 26
SEC6/SEC8 -0.007 0.068 -10000 0 -0.27 26 26
MGAT3 -0.024 0.11 -10000 0 -0.29 63 63
HGF/MET 0.004 0.13 -10000 0 -0.29 73 73
HGF 0.035 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.011 0.092 -10000 0 -0.26 46 46
actin cable formation 0.054 0.11 0.36 14 -0.29 1 15
KIAA1543 -0.022 0.065 -10000 0 -0.27 25 25
KIFC3 0 0.07 -10000 0 -0.28 25 25
NCK1 0.034 0.005 -10000 0 -10000 0 0
EXOC3 0.032 0.008 -10000 0 -10000 0 0
ACTN1 -0.002 0.072 -10000 0 -0.28 25 25
NCK1/GIT1 0.046 0.016 -10000 0 -10000 0 0
mol:GDP 0.04 0.086 -10000 0 -0.29 26 26
EXOC4 0.034 0.005 -10000 0 -10000 0 0
STX4 -0.002 0.071 -10000 0 -0.28 25 25
PIP5K1C -0.002 0.072 -10000 0 -0.28 25 25
LIMA1 0.013 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 -0.34 2 15
adherens junction assembly -0.032 0.13 0.3 1 -0.61 14 15
IGF-1R heterotetramer/IGF1 -0.13 0.18 -10000 0 -0.3 250 250
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 -0.022 0.17 -10000 0 -0.54 50 50
PLEKHA7 -0.002 0.072 -10000 0 -0.28 25 25
mol:GTP 0.055 0.058 -10000 0 -0.31 6 6
establishment of epithelial cell apical/basal polarity -0.013 0.087 0.36 5 -0.35 1 6
cortical actin cytoskeleton stabilization -0.011 0.091 -10000 0 -0.26 46 46
regulation of cell-cell adhesion -0.022 0.067 -10000 0 -0.28 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.011 0.092 -10000 0 -0.26 46 46
TCGA08_retinoblastoma

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
CDKN2B 0.035 0.033 -10000 0 -10000 0 0
CDKN2C -0.022 0.15 -10000 0 -0.52 41 41
CDKN2A 0.057 0.055 -10000 0 -10000 0 0
CCND2 -0.007 0.06 0.18 28 -0.19 16 44
RB1 0.005 0.072 0.22 14 -0.2 31 45
CDK4 -0.003 0.073 0.21 35 -0.21 13 48
CDK6 -0.005 0.073 0.21 33 -0.21 17 50
G1/S progression 0.003 0.087 0.21 53 -0.23 16 69
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.036 0.085 -10000 0 -0.41 14 14
HDAC1 0.023 0.028 -10000 0 -10000 0 0
AES 0.033 0.008 -10000 0 -10000 0 0
FBXW11 0.033 0.007 -10000 0 -10000 0 0
DTX1 0.031 0.044 -10000 0 -0.54 3 3
LRP6/FZD1 0.047 0.024 -10000 0 -0.4 1 1
TLE1 0.016 0.098 -10000 0 -0.55 15 15
AP1 -0.22 0.19 -10000 0 -0.34 323 323
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 0.02 0.14 -10000 0 -0.73 9 9
NICD/RBPSUH 0.055 0.092 -10000 0 -0.41 13 13
WIF1 -0.38 0.26 -10000 0 -0.54 370 370
NOTCH1 0.019 0.072 -10000 0 -0.42 12 12
PSENEN 0.035 0.015 -10000 0 -10000 0 0
KREMEN2 0.1 0.076 -10000 0 -10000 0 0
DKK1 0.007 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.01 0.094 -10000 0 -0.43 9 9
APH1B 0.032 0.027 -10000 0 -0.54 1 1
APH1A 0.031 0.028 -10000 0 -10000 0 0
AXIN1 0.016 0.07 -10000 0 -0.6 4 4
CtBP/CBP/TCF1/TLE1/AES 0.001 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 -0.54 344 344
JUN -0.067 0.22 -10000 0 -0.54 89 89
MAP3K7 0.03 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.091 -10000 0 -0.45 9 9
MAPK3 0.032 0.009 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.07 -10000 0 -0.31 3 3
HNF1A 0.034 0.013 -10000 0 -10000 0 0
CTBP1 0.032 0.009 -10000 0 -10000 0 0
MYC -0.051 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 0.056 0.095 -10000 0 -0.41 14 14
apoptosis -0.22 0.19 -10000 0 -0.34 323 323
Delta 1/NOTCHprecursor 0.053 0.092 -10000 0 -0.41 14 14
DLL1 0.032 0.009 -10000 0 -10000 0 0
PPARD 0.024 0.11 -10000 0 -0.8 7 7
Gamma Secretase 0.075 0.054 -10000 0 -0.3 1 1
APC 0.006 0.1 -10000 0 -0.55 12 12
DVL1 -0.039 0.094 -10000 0 -0.38 24 24
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.081 0.13 0.25 50 -0.29 41 91
LRP6 0.033 0.008 -10000 0 -10000 0 0
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
NLK 0.015 0.025 -10000 0 -10000 0 0
CCND1 0.037 0.23 -10000 0 -1.3 12 12
WNT1 0.034 0.005 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.019 0.12 0.34 2 -0.5 11 13
DKK2 0.031 0.054 -10000 0 -0.54 4 4
NOTCH1 precursor/DVL1 -0.015 0.12 -10000 0 -0.65 12 12
GSK3B 0.034 0.008 -10000 0 -10000 0 0
FRAT1 0.034 0.008 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.036 0.087 -10000 0 -0.41 14 14
PPP2R5D -0.002 0.064 -10000 0 -0.38 10 10
MAPK1 0.032 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.2 0.18 -10000 0 -0.32 356 356
RBPJ 0.033 0.008 -10000 0 -10000 0 0
CREBBP 0.033 0.03 -10000 0 -0.55 1 1
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.035 0.11 0.31 7 -0.34 6 13
epithelial cell differentiation 0.087 0.091 -10000 0 -10000 0 0
ITCH 0.047 0.025 -10000 0 -10000 0 0
WWP1 0.05 0.15 0.53 29 -10000 0 29
FYN 0.03 0.037 -10000 0 -0.54 2 2
EGFR -0.27 0.29 -10000 0 -0.54 269 269
PRL 0.033 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis 0.028 0.12 0.37 10 -0.36 6 16
PTPRZ1 -0.36 0.27 -10000 0 -0.54 354 354
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.016 0.1 -10000 0 -0.38 6 6
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.011 0.11 0.27 8 -0.32 35 43
ADAM17 0.047 0.025 -10000 0 -10000 0 0
ErbB4/ErbB4 0.031 0.12 0.4 30 -0.36 4 34
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.036 0.11 0.32 8 -0.33 4 12
NCOR1 0.031 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.004 0.11 -10000 0 -0.39 7 7
GRIN2B -0.017 0.1 -10000 0 -0.37 7 7
ErbB4/ErbB2/betacellulin 0.028 0.097 -10000 0 -0.36 4 4
STAT1 0.059 0.055 -10000 0 -10000 0 0
HBEGF 0.029 0.051 -10000 0 -0.54 4 4
PRLR 0.071 0.064 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.005 0.14 0.3 13 -0.38 42 55
axon guidance 0.12 0.14 0.38 57 -10000 0 57
NEDD4 0.04 0.06 -10000 0 -0.52 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.074 0.047 -10000 0 -10000 0 0
CBFA2T3 -0.023 0.17 -10000 0 -0.54 47 47
ErbB4/ErbB2/HBEGF 0.037 0.086 -10000 0 -0.32 4 4
MAPK3 0.029 0.12 0.37 8 -0.36 6 14
STAT1 (dimer) 0.055 0.11 0.35 11 -0.34 3 14
MAPK1 0.034 0.12 0.39 11 -0.36 6 17
JAK2 0.032 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.003 0.11 -10000 0 -0.3 27 27
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 -0.54 339 339
NRG4 0.034 0.013 -10000 0 -10000 0 0
heart development 0.12 0.14 0.38 57 -10000 0 57
neural crest cell migration 0.003 0.11 -10000 0 -0.3 27 27
ERBB2 0.021 0.028 0.3 1 -0.37 1 2
WWOX/E4ICDs 0.028 0.1 0.31 17 -0.34 3 20
SHC1 0.027 0.014 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.13 0.16 -10000 0 -0.36 22 22
apoptosis -0.037 0.095 0.31 4 -0.31 24 28
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.19 0.17 -10000 0 -0.32 256 256
ErbB4/ErbB2/epiregulin 0.047 0.093 0.32 10 -0.29 4 14
ErbB4/ErbB4/betacellulin/betacellulin 0.022 0.12 0.31 6 -0.35 17 23
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.087 0.12 0.38 9 -0.32 2 11
MDM2 0.029 0.11 0.34 34 -0.34 3 37
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.1 -10000 0 -0.3 37 37
STAT5A 0.11 0.12 0.41 32 -10000 0 32
ErbB4/EGFR/neuregulin 1 beta -0.15 0.18 -10000 0 -0.34 190 190
DLG4 0.031 0.011 -10000 0 -10000 0 0
GRB2/SHC 0.039 0.026 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.024 0.09 0.27 2 -0.31 3 5
STAT5A (dimer) 0.14 0.12 0.4 24 -10000 0 24
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.13 0.12 0.4 30 -0.36 1 31
LRIG1 0.014 0.1 -10000 0 -0.54 17 17
EREG 0.045 0.049 -10000 0 -0.54 1 1
BTC 0.011 0.12 -10000 0 -0.54 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.11 0.13 0.39 53 -10000 0 53
ERBB4 0.031 0.12 0.4 30 -0.36 4 34
STAT5B 0.033 0.01 -10000 0 -10000 0 0
YAP1 -0.002 0.12 0.26 6 -0.38 39 45
GRB2 0.034 0.018 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.038 0.081 -10000 0 -10000 0 0
glial cell differentiation -0.023 0.089 0.31 3 -0.27 2 5
WWOX 0.034 0.03 -10000 0 -10000 0 0
cell proliferation 0.051 0.14 0.38 17 -0.39 8 25
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 -0.25 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.061 0.28 3 -0.24 2 5
AP1 -0.22 0.19 -10000 0 -0.33 344 344
mol:PIP3 -0.15 0.16 -10000 0 -0.29 277 277
AKT1 0.005 0.091 -10000 0 -0.33 7 7
PTK2B -0.015 0.081 -10000 0 -0.18 88 88
RHOA 0.009 0.066 -10000 0 -0.27 18 18
PIK3CB 0.034 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.058 0.19 45 -0.27 1 46
MAGI3 0.04 0.042 -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 -0.015 0.079 0.23 5 -0.24 11 16
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 45 45
ADCY5 -0.047 0.094 -10000 0 -0.22 45 45
ADCY6 -0.047 0.094 -10000 0 -0.22 43 43
ADCY7 -0.037 0.091 -10000 0 -0.27 19 19
ADCY1 -0.046 0.093 -10000 0 -0.22 44 44
ADCY2 -0.05 0.1 -10000 0 -0.24 48 48
ADCY3 -0.046 0.094 -10000 0 -0.22 43 43
ADCY8 -0.041 0.087 -10000 0 -0.23 30 30
ADCY9 -0.043 0.09 -10000 0 -0.23 35 35
GSK3B -0.015 0.079 0.25 4 -0.22 18 22
arachidonic acid secretion -0.054 0.1 -10000 0 -0.24 61 61
GNG2 0.032 0.026 -10000 0 -0.54 1 1
TRIP6 0.023 0.02 -10000 0 -0.39 1 1
GNAO1 0.019 0.021 -10000 0 -0.26 2 2
HRAS 0.034 0.013 -10000 0 -10000 0 0
NFKBIA 0.027 0.061 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 0.05 0.11 -10000 0 -0.85 7 7
JUN -0.067 0.22 -10000 0 -0.54 89 89
LPA/LPA2/NHERF2 0.024 0.017 -10000 0 -0.11 3 3
TIAM1 0.031 0.12 -10000 0 -1 7 7
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.026 0.056 0.2 45 -10000 0 45
PLCB3 0.036 0.05 0.19 42 -10000 0 42
FOS -0.35 0.27 -10000 0 -0.54 344 344
positive regulation of mitosis -0.054 0.1 -10000 0 -0.24 61 61
LPA/LPA1-2-3 0.007 0.02 -10000 0 -0.18 5 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
stress fiber formation 0.016 0.059 -10000 0 -0.27 7 7
GNAZ 0.015 0.044 -10000 0 -0.28 10 10
EGFR/PI3K-beta/Gab1 -0.15 0.17 -10000 0 -0.3 277 277
positive regulation of dendritic cell cytokine production 0.007 0.019 -10000 0 -0.18 5 5
LPA/LPA2/MAGI-3 0.029 0.03 -10000 0 -0.2 3 3
ARHGEF1 0.037 0.055 -10000 0 -0.22 2 2
GNAI2 0.02 0.025 0.15 2 -0.21 5 7
GNAI3 0.02 0.023 0.15 2 -0.22 4 6
GNAI1 -0.11 0.17 -10000 0 -0.34 184 184
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 -0.31 249 249
HBEGF 0.066 0.077 -10000 0 -0.4 4 4
mol:DAG 0.026 0.056 0.2 45 -10000 0 45
cAMP biosynthetic process -0.056 0.1 0.24 1 -0.25 39 40
NFKB1 0.034 0.005 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
GNB1 0.034 0.012 -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 0.075 2 -0.15 5 7
IL8 -0.19 0.22 0.34 14 -0.38 264 278
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 -0.54 269 269
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 -0.23 2 2
PI3K-beta -0.01 0.089 -10000 0 -0.36 9 9
cell migration 0.027 0.044 -10000 0 -0.25 7 7
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 61 61
RAC1 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.094 0.074 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
PRKCD 0.024 0.059 0.2 15 -0.26 1 16
Gi(beta/gamma) -0.051 0.11 -10000 0 -0.26 55 55
mol:LPA 0.003 0.016 0.075 2 -0.15 5 7
TRIP6/p130 Cas/FAK1/Paxillin 0.03 0.052 -10000 0 -0.24 3 3
MAPKKK cascade -0.054 0.1 -10000 0 -0.24 61 61
contractile ring contraction involved in cytokinesis 0.008 0.068 -10000 0 -0.26 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.021 0.039 0.1 1 -0.26 5 6
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 -0.015 0.08 0.23 5 -0.25 11 16
GNA11 0.015 0.009 -10000 0 -0.087 2 2
Rac1/GTP 0.051 0.11 -10000 0 -0.91 7 7
MMP2 0.016 0.053 0.27 2 -0.47 5 7
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.005 0.13 -10000 0 -0.39 50 50
CRKL -0.002 0.11 0.37 1 -0.39 17 18
mol:PIP3 0.009 0.064 0.49 7 -10000 0 7
AKT1 0.021 0.08 0.39 11 -10000 0 11
PTK2B 0.027 0.014 -10000 0 -10000 0 0
RAPGEF1 -0.003 0.11 0.35 1 -0.4 13 14
RANBP10 0.03 0.012 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.023 0.12 -10000 0 -0.34 50 50
MAP3K5 -0.013 0.13 0.37 1 -0.41 24 25
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.12 -10000 0 -0.32 51 51
AP1 -0.29 0.24 -10000 0 -0.44 346 346
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 -0.77 367 367
STAT3 (dimer) -0.007 0.11 -10000 0 -0.42 16 16
GAB1/CRKL/SHP2/PI3K 0.01 0.14 -10000 0 -0.44 16 16
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.014 0.11 0.36 1 -0.37 17 18
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 0.026 0.067 -10000 0 -0.54 7 7
ELK1 -0.019 0.084 0.26 15 -0.21 8 23
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.006 0.064 -10000 0 -0.25 6 6
PAK1 0.046 0.099 0.42 14 -10000 0 14
HGF/MET/RANBP10 0.021 0.12 -10000 0 -0.34 50 50
HRAS -0.032 0.2 -10000 0 -0.58 57 57
DOCK1 -0.004 0.11 0.43 2 -0.4 14 16
GAB1 -0.003 0.12 -10000 0 -0.38 22 22
CRK -0.003 0.11 0.37 1 -0.36 22 23
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.18 -10000 0 -0.53 55 55
JUN -0.067 0.22 -10000 0 -0.54 89 89
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.013 0.087 -10000 0 -0.27 51 51
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
cell morphogenesis -0.017 0.15 0.41 6 -0.44 18 24
GRB2/SHC 0.02 0.081 -10000 0 -0.25 31 31
FOS -0.36 0.27 -10000 0 -0.54 344 344
GLMN 0.004 0.004 -10000 0 -10000 0 0
cell motility -0.019 0.084 0.26 15 -0.21 8 23
HGF/MET/MUC20 0.008 0.12 -10000 0 -0.34 50 50
cell migration 0.019 0.08 -10000 0 -0.24 31 31
GRB2 0.034 0.018 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
MET/RANBP10 0.001 0.13 -10000 0 -0.39 51 51
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.012 0.097 -10000 0 -0.38 14 14
MET/MUC20 -0.017 0.13 -10000 0 -0.39 52 52
RAP1B 0.003 0.11 0.32 2 -0.4 10 12
RAP1A -0.004 0.1 0.51 1 -0.4 10 11
HGF/MET/RANBP9 0.027 0.12 -10000 0 -0.34 48 48
RAF1 -0.025 0.19 -10000 0 -0.55 57 57
STAT3 -0.007 0.11 -10000 0 -0.42 16 16
cell proliferation 0.025 0.15 0.35 9 -0.39 31 40
RPS6KB1 0.001 0.061 -10000 0 -0.33 9 9
MAPK3 -0.037 0.081 0.62 3 -10000 0 3
MAPK1 -0.004 0.17 0.65 29 -10000 0 29
RANBP9 0.034 0.009 -10000 0 -10000 0 0
MAPK8 -0.004 0.13 0.45 1 -0.38 23 24
SRC -0.006 0.096 -10000 0 -0.36 14 14
PI3K -0.01 0.13 -10000 0 -0.28 84 84
MET/Glomulin -0.013 0.11 -10000 0 -0.35 50 50
SOS1 0.034 0.004 -10000 0 -10000 0 0
MAP2K1 -0.022 0.18 0.48 1 -0.52 55 56
MET -0.022 0.17 -10000 0 -0.54 50 50
MAP4K1 0.002 0.12 0.39 1 -0.4 20 21
PTK2 0.027 0.014 -10000 0 -10000 0 0
MAP2K2 -0.022 0.18 0.48 1 -0.52 56 57
BAD 0.018 0.074 0.35 11 -10000 0 11
MAP2K4 -0.013 0.12 0.35 1 -0.38 24 25
SHP2/GRB2/SOS1/GAB1 0.02 0.14 -10000 0 -0.36 52 52
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 0.035 0.01 -10000 0 -10000 0 0
RASA1 0.034 0.012 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
PTPRJ 0.035 0.017 -10000 0 -10000 0 0
NCK/PLCgamma1 0.026 0.093 -10000 0 -0.24 48 48
PDPK1 0.024 0.087 0.47 8 -10000 0 8
HGF/MET/SHIP 0.008 0.12 -10000 0 -0.34 50 50
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.028 0.081 -10000 0 -0.43 10 10
Crk/p130 Cas/Paxillin -0.082 0.14 -10000 0 -0.38 73 73
JUN -0.002 0.15 0.26 6 -0.35 38 44
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 0.055 0.14 0.24 1 -0.31 61 62
RHOA 0.033 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.076 0.15 -10000 0 -0.27 60 60
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 0.057 0.14 0.25 8 -0.29 42 50
BCAR1 0.029 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.015 0.2 -10000 0 -0.38 93 93
lamellipodium assembly -0.044 0.16 -10000 0 -0.34 78 78
RET51/GFRalpha1/GDNF/SHC 0.091 0.16 -10000 0 -0.3 45 45
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.044 0.13 -10000 0 -0.31 46 46
RET9/GFRalpha1/GDNF/Shank3 0.049 0.14 -10000 0 -0.31 62 62
MAPK3 0.042 0.13 0.27 9 -0.28 46 55
DOK1 0.036 0.016 0.18 6 -10000 0 6
DOK6 0.032 0.049 -10000 0 -0.54 3 3
PXN 0.034 0.003 -10000 0 -10000 0 0
neurite development 0.043 0.12 0.33 1 -0.33 2 3
DOK5 0.012 0.11 -10000 0 -0.54 18 18
GFRA1 0.028 0.23 -10000 0 -0.54 65 65
MAPK8 0.053 0.12 0.27 4 -0.26 47 51
HRAS/GTP 0.092 0.16 0.3 4 -0.3 56 60
tube development 0.055 0.14 0.31 13 -0.3 58 71
MAPK1 0.044 0.13 0.28 9 -0.28 46 55
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.02 0.11 -10000 0 -0.26 59 59
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
PDLIM7 0.034 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.11 0.17 0.35 2 -0.28 58 60
SHC1 0.027 0.014 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.09 0.17 -10000 0 -0.3 60 60
RET51/GFRalpha1/GDNF/Dok5 0.087 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 0.042 0.12 -10000 0 -0.28 33 33
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.018 0.097 -10000 0 -0.25 41 41
RET51/GFRalpha1/GDNF/Grb7 0.099 0.16 -10000 0 -0.3 45 45
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.073 -10000 0 -10000 0 0
DOK4 0.03 0.012 -10000 0 -10000 0 0
JNK cascade -0.001 0.15 0.26 6 -0.34 38 44
RET9/GFRalpha1/GDNF/FRS2 0.05 0.15 0.24 1 -0.31 63 64
SHANK3 0.032 0.009 -10000 0 -10000 0 0
RASA1 0.034 0.012 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.019 0.099 -10000 0 -0.25 41 41
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.054 0.13 0.26 7 -0.26 46 53
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.06 0.13 0.25 4 -0.27 47 51
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.047 0.11 0.25 6 -0.26 33 39
PI3K -0.039 0.26 0.31 8 -0.53 78 86
SOS1 0.034 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.058 0.14 -10000 0 -0.3 58 58
GRB10 0.03 0.051 -10000 0 -0.54 4 4
activation of MAPKK activity 0.056 0.12 0.24 13 -0.24 44 57
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 -0.034 0.19 -10000 0 -0.54 60 60
IRS2 -0.1 0.24 -10000 0 -0.54 117 117
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.046 0.12 0.25 6 -0.25 33 39
RET51/GFRalpha1/GDNF/PKC alpha 0.098 0.17 -10000 0 -0.3 57 57
GRB2 0.034 0.018 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GDNF 0.034 0.009 0.18 1 -10000 0 1
RAC1 0.034 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.071 0.23 -10000 0 -0.38 87 87
Rac1/GTP -0.032 0.2 0.25 3 -0.42 76 79
RET9/GFRalpha1/GDNF 0.038 0.15 -10000 0 -0.33 66 66
GFRalpha1/GDNF 0.039 0.17 -10000 0 -0.39 66 66
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 -0.29 13 13
NFATC4 -0.028 0.08 0.28 3 -0.25 16 19
ERBB2IP 0.034 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.033 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.036 0.087 -10000 0 -0.3 29 29
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 27 29
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.098 -10000 0 -0.3 25 25
AKT1 0.007 0.016 0.14 6 -10000 0 6
BAD -0.005 0.014 -10000 0 -10000 0 0
MAPK10 -0.022 0.07 0.24 5 -0.26 7 12
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.037 0.093 -10000 0 -0.32 29 29
RAF1 -0.038 0.096 -10000 0 -0.33 7 7
ErbB2/ErbB3/neuregulin 2 -0.18 0.17 -10000 0 -0.33 272 272
STAT3 0.01 0.16 -10000 0 -0.84 18 18
cell migration -0.014 0.071 0.26 7 -0.26 3 10
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.26 0.28 -10000 0 -0.67 116 116
FOS -0.33 0.26 -10000 0 -0.5 365 365
NRAS 0.034 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.087 -10000 0 -0.3 29 29
MAPK3 -0.16 0.21 -10000 0 -0.52 86 86
MAPK1 -0.18 0.24 -10000 0 -0.56 105 105
JAK2 -0.033 0.089 0.26 2 -0.29 27 29
NF2 0.003 0.069 -10000 0 -0.68 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.08 -10000 0 -0.27 26 26
NRG1 -0.021 0.16 -10000 0 -0.55 43 43
GRB2/SOS1 0.047 0.019 -10000 0 -10000 0 0
MAPK8 -0.038 0.1 -10000 0 -0.28 37 37
MAPK9 -0.02 0.064 0.26 3 -10000 0 3
ERBB2 -0.022 0.013 -10000 0 -10000 0 0
ERBB3 0.036 0.025 -10000 0 -10000 0 0
SHC1 0.026 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.02 0.027 -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 27 27
ErbB2/ErbB2/HSP90 (dimer) -0.008 0.023 -10000 0 -10000 0 0
CHRNA1 -0.12 0.17 -10000 0 -0.4 67 67
myelination -0.021 0.089 0.33 6 -0.24 13 19
PPP3CB -0.033 0.086 0.25 2 -0.27 26 28
KRAS 0.033 0.018 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.035 0.1 -10000 0 -0.25 22 22
NRG2 -0.35 0.27 -10000 0 -0.54 339 339
mol:GDP 0 0.08 -10000 0 -0.27 27 27
SOS1 0.033 0.004 -10000 0 -10000 0 0
MAP2K2 -0.054 0.1 -10000 0 -0.35 11 11
SRC 0.033 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 27 29
MAP2K1 -0.17 0.21 -10000 0 -0.6 51 51
heart morphogenesis -0.036 0.087 -10000 0 -0.3 29 29
RAS family/GDP 0.029 0.11 -10000 0 -0.29 6 6
GRB2 0.033 0.018 -10000 0 -10000 0 0
PRKACA 0.005 0.082 -10000 0 -0.68 7 7
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 -0.14 6 6
nervous system development -0.036 0.087 -10000 0 -0.3 29 29
CDC42 0.033 0.007 -10000 0 -10000 0 0
IL27-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 0.042 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 -0.01 0.22 0.7 24 -0.53 8 32
IL27/IL27R/JAK1 0.032 0.28 0.65 17 -1 19 36
TBX21 0.024 0.26 0.52 43 -0.59 39 82
IL12B 0.042 0.027 -10000 0 -10000 0 0
IL12A 0.005 0.061 0.15 3 -0.4 11 14
IL6ST 0.034 0.08 0.24 1 -0.54 8 9
IL27RA/JAK1 0.003 0.24 0.53 3 -1.2 18 21
IL27 -0.019 0.18 0.33 1 -0.54 51 52
TYK2 0.043 0.026 -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 -0.01 0.22 0.7 24 -0.53 8 32
T cell proliferation during immune response -0.01 0.22 0.7 24 -0.53 8 32
MAPKKK cascade 0.01 0.22 0.53 8 -0.7 24 32
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT2 0.034 0.004 -10000 0 -10000 0 0
STAT1 0.061 0.057 0.2 6 -10000 0 6
IL12RB1 0.036 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.05 0.25 0.55 48 -0.63 23 71
IL27/IL27R/JAK2/TYK2 0.009 0.22 0.53 8 -0.71 24 32
positive regulation of T cell mediated cytotoxicity 0.01 0.22 0.53 8 -0.7 24 32
STAT1 (dimer) 0.037 0.33 0.8 23 -1 22 45
JAK2 0.039 0.023 0.24 1 -10000 0 1
JAK1 0.036 0.013 -10000 0 -10000 0 0
STAT2 (dimer) 0.025 0.21 0.5 6 -0.68 23 29
T cell proliferation -0.18 0.25 0.5 5 -0.59 77 82
IL12/IL12R/TYK2/JAK2 0.065 0.19 0.53 2 -0.77 15 17
IL17A -0.19 0.14 -10000 0 -0.78 2 2
mast cell activation -0.01 0.22 0.7 24 -0.53 8 32
IFNG 0.033 0.066 0.14 102 -0.1 11 113
T cell differentiation 0 0.009 0.02 27 -0.024 20 47
STAT3 (dimer) 0.023 0.21 0.51 5 -0.69 22 27
STAT5A (dimer) 0.023 0.21 0.51 5 -0.67 24 29
STAT4 (dimer) 0.021 0.21 0.5 6 -0.68 24 30
STAT4 0.027 0.069 -10000 0 -0.54 7 7
T cell activation -0.005 0.028 0.12 17 -0.12 9 26
IL27R/JAK2/TYK2 0.052 0.25 0.55 3 -1.1 18 21
GATA3 -0.013 0.37 0.66 17 -1.3 33 50
IL18 0.019 0.036 0.14 41 -10000 0 41
positive regulation of mast cell cytokine production 0.024 0.2 0.5 5 -0.67 22 27
IL27/EBI3 0.015 0.14 0.34 3 -0.39 50 53
IL27RA -0.016 0.25 0.52 5 -1.3 18 23
IL6 -0.37 0.26 -10000 0 -0.54 365 365
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
monocyte differentiation 0.002 0.003 -10000 0 -10000 0 0
IL2 -0.009 0.12 0.47 18 -1.2 1 19
IL1B 0.009 0.044 0.14 10 -0.4 5 15
EBI3 0.041 0.026 0.25 1 -10000 0 1
TNF 0.013 0.02 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.033 0.008 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.028 0.095 -10000 0 -0.27 17 17
NT3 (dimer)/TRKC -0.082 0.21 -10000 0 -0.4 150 150
NT3 (dimer)/TRKB -0.25 0.29 -10000 0 -0.48 280 280
SHC/Grb2/SOS1/GAB1/PI3K 0.002 0.073 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
BDNF 0.038 0.047 -10000 0 -0.54 2 2
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DYNLT1 0.032 0.009 -10000 0 -10000 0 0
NTRK1 0.03 0.022 -10000 0 -10000 0 0
NTRK2 -0.23 0.29 -10000 0 -0.54 237 237
NTRK3 0.015 0.1 -10000 0 -0.54 16 16
NT-4/5 (dimer)/TRKB -0.17 0.23 -10000 0 -0.41 223 223
neuron apoptosis 0.12 0.21 0.46 102 -10000 0 102
SHC 2-3/Grb2 -0.13 0.23 -10000 0 -0.51 101 101
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 -0.14 0.24 -10000 0 -0.56 105 105
SHC3 -0.12 0.21 -10000 0 -0.52 80 80
STAT3 (dimer) 0.054 0.077 -10000 0 -0.36 10 10
NT3 (dimer)/TRKA -0.084 0.2 -10000 0 -0.38 134 134
RIN/GDP 0.006 0.11 0.27 4 -0.28 17 21
GIPC1 0.034 0.011 -10000 0 -10000 0 0
KRAS 0.034 0.018 -10000 0 -10000 0 0
DNAJA3 -0.054 0.13 -10000 0 -0.34 71 71
RIN/GTP 0.024 0.019 -10000 0 -0.4 1 1
CCND1 0.015 0.12 -10000 0 -0.78 10 10
MAGED1 0.044 0.036 -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 0.034 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.04 0.027 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.032 0.067 -10000 0 -0.4 9 9
ELMO1 0.034 0.005 -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 0.044 -10000 0 -0.54 3 3
GAB2 0.03 0.012 -10000 0 -10000 0 0
RIT2 0.032 0.026 -10000 0 -0.54 1 1
RIT1 0.028 0.014 -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 6 -0.39 24 30
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.025 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.005 0.097 0.29 1 -0.28 16 17
TIAM1 0.035 0.012 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
BDNF (dimer)/TRKB -0.12 0.2 -10000 0 -0.34 234 234
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) -0.12 0.26 -10000 0 -0.54 134 134
RAP1/GDP 0.002 0.09 -10000 0 -0.24 17 17
KIDINS220/CRKL 0.033 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 0.076 0.039 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.026 0.067 -10000 0 -0.3 7 7
RAP1B 0.033 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.17 0.22 -10000 0 -0.35 271 271
ABL1 0.034 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
Rap1/GTP -0.041 0.12 -10000 0 -0.43 23 23
STAT3 0.054 0.077 -10000 0 -0.36 10 10
axon guidance -0.17 0.2 -10000 0 -0.34 271 271
MAPK3 0.048 0.067 0.28 4 -10000 0 4
MAPK1 0.052 0.069 0.28 5 -10000 0 5
CDC42/GDP 0.008 0.11 0.28 7 -0.28 17 24
NTF3 -0.12 0.26 -10000 0 -0.54 134 134
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.038 0.022 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.4 44 44
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 -0.35 74 74
SOS1 0.034 0.004 -10000 0 -10000 0 0
MCF2L -0.083 0.17 -10000 0 -0.35 140 140
RGS19 0.034 0.022 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.099 0.36 1 -0.43 5 6
Rac1/GDP 0.007 0.11 0.27 5 -0.28 17 22
NGF (dimer)/TRKA/GRIT 0.02 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.025 0.22 0.42 1 -0.73 28 29
NGF (dimer)/TRKA/NEDD4-2 0.03 0.058 -10000 0 -0.34 9 9
MAP2K1 0.065 0.088 0.36 14 -10000 0 14
NGFR -0.054 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 0.085 -10000 0 -0.26 40 40
FRS2 family/SHP2/GRB2/SOS1 0.087 0.044 -10000 0 -0.3 1 1
NRAS 0.036 0.016 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
PRKCI 0.035 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 0.034 0.012 -10000 0 -10000 0 0
TRKA/c-Abl 0.042 0.024 -10000 0 -10000 0 0
SQSTM1 0.034 0.009 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.099 0.2 -10000 0 -0.31 232 232
NGF (dimer)/TRKA/p62/Atypical PKCs 0.049 0.03 -10000 0 -10000 0 0
MATK 0.038 0.028 -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 14 14
NGF (dimer)/TRKA -0.059 0.14 -10000 0 -0.36 80 80
Rac1/GTP -0.05 0.098 -10000 0 -0.29 39 39
FRS2 family/SHP2/CRK family 0.082 0.046 -10000 0 -0.3 1 1
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.034 0.008 -10000 0 -10000 0 0
CCL5 0.029 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 79 -0.34 8 87
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 0.071 0.14 0.3 23 -0.34 9 32
MAPK3 0.071 0.13 0.28 29 -0.33 7 36
HGF/MET 0.006 0.13 -10000 0 -0.4 50 50
TGFB1/TGF beta receptor Type II 0.034 0.008 -10000 0 -10000 0 0
BSG 0.034 0.015 -10000 0 -10000 0 0
keratinocyte migration 0.069 0.14 0.29 17 -0.34 9 26
Syndecan-1/RANTES 0.076 0.15 0.3 31 -0.37 11 42
Syndecan-1/CD147 0.093 0.15 0.32 22 -0.34 8 30
Syndecan-1/Syntenin/PIP2 0.066 0.13 0.28 23 -0.32 9 32
LAMA5 0.032 0.012 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.064 0.13 0.28 23 -0.32 9 32
MMP7 -0.042 0.19 -10000 0 -0.54 64 64
HGF 0.035 0.01 -10000 0 -10000 0 0
Syndecan-1/CASK 0.058 0.13 0.25 24 -0.32 11 35
Syndecan-1/HGF/MET 0.063 0.18 0.31 19 -0.38 32 51
regulation of cell adhesion 0.061 0.12 0.3 11 -0.33 6 17
HPSE 0.045 0.04 -10000 0 -10000 0 0
positive regulation of cell migration 0.087 0.14 0.27 79 -0.34 8 87
SDC1 0.087 0.13 0.26 93 -0.32 4 97
Syndecan-1/Collagen 0.087 0.14 0.27 79 -0.34 8 87
PPIB 0.034 0.009 -10000 0 -10000 0 0
MET -0.022 0.17 -10000 0 -0.54 50 50
PRKACA 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.094 0.074 -10000 0 -10000 0 0
MAPK1 0.071 0.13 0.28 29 -0.32 7 36
homophilic cell adhesion 0.085 0.14 0.27 79 -0.34 8 87
MMP1 0.11 0.077 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.035 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 -0.54 269 269
AKT -0.018 0.12 0.37 5 -0.26 38 43
FOXO3 0.032 0.01 -10000 0 -10000 0 0
AKT1 0.035 0.017 -10000 0 -10000 0 0
FOXO1 -0.023 0.17 -10000 0 -0.54 48 48
AKT3 0.028 0.019 -10000 0 -10000 0 0
FOXO4 0.034 0.002 -10000 0 -10000 0 0
MET -0.022 0.17 -10000 0 -0.54 50 50
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PIK3CB 0.033 0.006 -10000 0 -10000 0 0
NRAS 0.036 0.016 -10000 0 -10000 0 0
PIK3CG 0.037 0.022 -10000 0 -10000 0 0
PIK3R3 0.042 0.034 -10000 0 -10000 0 0
PIK3R2 0.035 0.017 -10000 0 -10000 0 0
NF1 0.032 0.009 -10000 0 -10000 0 0
RAS -0.077 0.14 0.24 1 -0.33 86 87
ERBB2 0.028 0.029 -10000 0 -0.54 1 1
proliferation/survival/translation -0.016 0.098 0.3 26 -0.27 2 28
PI3K -0.068 0.16 0.29 11 -0.31 103 114
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
KRAS 0.034 0.018 -10000 0 -10000 0 0
FOXO 0.034 0.081 0.32 7 -0.17 10 17
AKT2 0.034 0.006 -10000 0 -10000 0 0
PTEN 0.026 0.067 -10000 0 -0.54 7 7
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL 0.018 0.18 -10000 0 -0.75 3 3
PCK1 -0.74 0.54 -10000 0 -1 387 387
HNF4A 0.033 0.2 0.71 2 -0.75 3 5
KCNJ11 0.038 0.24 0.75 3 -0.76 3 6
AKT1 0.012 0.15 -10000 0 -0.46 5 5
response to starvation 0.005 0.002 -10000 0 -10000 0 0
DLK1 0.028 0.22 0.88 1 -0.81 3 4
NKX2-1 0.034 0.12 0.64 1 -10000 0 1
ACADM 0.015 0.21 -10000 0 -0.86 8 8
TAT -0.058 0.2 -10000 0 -0.72 16 16
CEBPB 0.034 0.028 -10000 0 -0.54 1 1
CEBPA 0.035 0.045 -10000 0 -0.54 3 3
TTR -0.033 0.26 0.59 1 -0.64 48 49
PKLR 0.035 0.19 0.6 1 -0.79 2 3
APOA1 0.022 0.22 0.73 1 -0.88 3 4
CPT1C 0.028 0.2 0.71 1 -0.76 3 4
ALAS1 0.031 0.14 -10000 0 -10000 0 0
TFRC -0.017 0.2 0.68 3 -0.55 1 4
FOXF1 0.025 0.021 -10000 0 -10000 0 0
NF1 0.038 0.01 -10000 0 -10000 0 0
HNF1A (dimer) 0.05 0.022 -10000 0 -10000 0 0
CPT1A 0.025 0.21 0.72 3 -0.7 3 6
HMGCS1 0.023 0.2 0.75 2 -0.76 3 5
NR3C1 0 0.16 -10000 0 -0.51 43 43
CPT1B 0.018 0.19 -10000 0 -0.75 3 3
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.015 -10000 0 -10000 0 0
GCK 0.023 0.19 -10000 0 -0.76 3 3
CREB1 -0.18 0.14 -10000 0 -0.26 371 371
IGFBP1 0.015 0.14 -10000 0 -0.82 2 2
PDX1 0.043 0.16 -10000 0 -1.1 2 2
UCP2 0.026 0.2 0.66 2 -0.7 3 5
ALDOB 0.023 0.22 -10000 0 -0.81 3 3
AFP -0.052 0.14 0.39 1 -0.4 7 8
BDH1 0.025 0.19 0.67 2 -0.76 3 5
HADH 0.018 0.23 -10000 0 -0.93 5 5
F2 0.038 0.22 -10000 0 -0.82 3 3
HNF1A 0.05 0.022 -10000 0 -10000 0 0
G6PC -0.098 0.12 -10000 0 -10000 0 0
SLC2A2 0.047 0.16 -10000 0 -0.84 2 2
INS 0.022 0.015 0.25 1 -10000 0 1
FOXA1 -0.003 0.23 0.38 3 -0.54 72 75
FOXA3 -0.12 0.14 -10000 0 -0.27 118 118
FOXA2 0.03 0.27 -10000 0 -0.92 3 3
ABCC8 -0.065 0.42 0.9 1 -0.93 86 87
ALB -0.054 0.15 0.39 1 -0.4 40 41
Regulation of nuclear SMAD2/3 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
EP300 0.035 0.016 -10000 0 -10000 0 0
HSPA8 0.029 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.073 0.19 0.33 1 -0.4 109 110
AKT1 0.038 0.02 -10000 0 -10000 0 0
GSC -0.095 0.4 -10000 0 -1.3 48 48
NKX2-5 0.045 0.05 -10000 0 -10000 0 0
muscle cell differentiation 0 0.12 0.48 16 -10000 0 16
SMAD2-3/SMAD4/SP1 0.053 0.12 -10000 0 -0.31 13 13
SMAD4 -0.028 0.084 -10000 0 -0.27 24 24
CBFB 0.03 0.014 -10000 0 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.16 0.2 -10000 0 -0.34 275 275
SMAD3/SMAD4/VDR 0.052 0.095 -10000 0 -0.35 6 6
MYC -0.006 0.12 -10000 0 -0.55 25 25
CDKN2B -0.049 0.2 -10000 0 -0.77 18 18
AP1 -0.26 0.29 -10000 0 -0.64 136 136
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.11 -10000 0 -0.39 19 19
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.009 0.11 0.26 1 -0.35 25 26
SP3 0.035 0.008 -10000 0 -10000 0 0
CREB1 0.034 0.006 -10000 0 -10000 0 0
FOXH1 0.018 0.041 -10000 0 -0.16 6 6
SMAD3/SMAD4/GR -0.045 0.14 -10000 0 -0.39 51 51
GATA3 0.038 0.16 -10000 0 -0.53 33 33
SKI/SIN3/HDAC complex/NCoR1 0.017 0.083 -10000 0 -0.38 15 15
MEF2C/TIF2 0.008 0.15 0.34 1 -0.53 25 26
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 0.022 -10000 0 -10000 0 0
RBBP4 0.033 0.006 -10000 0 -10000 0 0
RUNX2 0.036 0.019 -10000 0 -10000 0 0
RUNX3 -0.006 0.15 -10000 0 -0.54 36 36
RUNX1 0.018 0.098 -10000 0 -0.54 15 15
CTBP1 0.033 0.008 -10000 0 -10000 0 0
NR3C1 -0.019 0.16 -10000 0 -0.55 40 40
VDR 0.032 0.037 -10000 0 -0.54 2 2
CDKN1A 0.004 0.11 -10000 0 -1.1 3 3
KAT2B 0.001 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.026 0.11 -10000 0 -0.3 42 42
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 -0.27 15 15
SMAD3/SMAD4/ATF3 -0.09 0.2 -10000 0 -0.41 133 133
SAP30 0.033 0.009 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.062 0.04 -10000 0 -10000 0 0
JUN -0.26 0.28 -10000 0 -0.66 127 127
SMAD3/SMAD4/IRF7 0.021 0.094 -10000 0 -0.28 10 10
TFE3 0.03 0.046 -10000 0 -0.19 6 6
COL1A2 0.075 0.13 0.31 60 -0.71 5 65
mesenchymal cell differentiation -0.005 0.093 0.28 10 -10000 0 10
DLX1 0.043 0.036 -10000 0 -10000 0 0
TCF3 0.035 0.017 -10000 0 -10000 0 0
FOS -0.37 0.28 -10000 0 -0.56 346 346
SMAD3/SMAD4/Max -0.018 0.089 -10000 0 -0.27 15 15
Cbp/p300/SNIP1 0.06 0.033 -10000 0 -0.32 1 1
ZBTB17 0.028 0.021 -10000 0 -10000 0 0
LAMC1 -0.038 0.15 -10000 0 -0.6 27 27
TGIF2/HDAC complex/SMAD3/SMAD4 0.005 0.091 -10000 0 -0.26 15 15
IRF7 0.039 0.024 0.22 1 -10000 0 1
ESR1 -0.068 0.25 0.23 3 -0.55 106 109
HNF4A 0.033 0.008 -10000 0 -10000 0 0
MEF2C 0.015 0.17 0.42 9 -0.55 28 37
SMAD2-3/SMAD4 0.009 0.11 -10000 0 -0.29 27 27
Cbp/p300/Src-1 0.062 0.039 -10000 0 -0.32 2 2
IGHV3OR16-13 -0.007 0.07 -10000 0 -0.45 10 10
TGIF2/HDAC complex 0.033 0.01 -10000 0 -10000 0 0
CREBBP 0.032 0.028 -10000 0 -0.52 1 1
SKIL 0.045 0.042 -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 0.019 0.13 -10000 0 -0.38 31 31
MSG1/HSC70 -0.21 0.22 -10000 0 -0.4 297 297
SMAD2 0.02 0.053 -10000 0 -0.18 5 5
SMAD3 -0.015 0.063 -10000 0 -0.21 7 7
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.07 -10000 0 -0.29 8 8
SMAD2/SMAD2/SMAD4 0.01 0.053 0.22 6 -0.22 5 11
NCOR1 0.031 0.011 -10000 0 -10000 0 0
NCOA2 0.028 0.015 -10000 0 -10000 0 0
NCOA1 0.033 0.026 -10000 0 -0.54 1 1
MYOD/E2A 0.049 0.035 -10000 0 -0.4 2 2
SMAD2-3/SMAD4/SP1/MIZ-1 0.074 0.12 -10000 0 -0.32 8 8
IFNB1 -0.012 0.072 0.33 2 -0.3 1 3
SMAD3/SMAD4/MEF2C 0.022 0.18 0.41 1 -0.56 29 30
CITED1 -0.3 0.29 -10000 0 -0.54 296 296
SMAD2-3/SMAD4/ARC105 0.025 0.11 -10000 0 -0.28 19 19
RBL1 0.04 0.032 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.001 0.11 -10000 0 -0.4 18 18
RUNX1-3/PEBPB2 0.02 0.13 -10000 0 -0.35 49 49
SMAD7 -0.18 0.22 -10000 0 -0.53 82 82
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 -0.006 0.12 0.4 1 -0.37 28 29
PIASy/HDAC complex 0.026 0.028 -10000 0 -10000 0 0
PIAS3 0.034 0.009 -10000 0 -10000 0 0
CDK2 0.04 0.023 0.21 2 -10000 0 2
IL5 -0.002 0.12 0.4 1 -0.36 32 33
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 -0.54 128 128
SMAD3/SMAD4/SP1 0.039 0.1 -10000 0 -0.3 11 11
FOXG1 0.042 0.037 -10000 0 -10000 0 0
FOXO3 0.021 0.02 -10000 0 -10000 0 0
FOXO1 -0.019 0.12 -10000 0 -0.39 48 48
FOXO4 0.022 0.02 -10000 0 -10000 0 0
heart looping 0.015 0.17 0.42 9 -0.55 28 37
CEBPB 0.031 0.029 -10000 0 -0.54 1 1
SMAD3/SMAD4/DLX1 0.013 0.094 -10000 0 -0.26 12 12
MYOD1 0.033 0.041 -10000 0 -0.54 2 2
SMAD3/SMAD4/HNF4 0.006 0.091 -10000 0 -0.26 15 15
SMAD3/SMAD4/GATA3 0.027 0.15 -10000 0 -0.41 33 33
SnoN/SIN3/HDAC complex/NCoR1 0.045 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.006 0.15 -10000 0 -0.36 50 50
SMAD3/SMAD4/SP1-3 0.061 0.11 -10000 0 -0.34 4 4
MED15 0.033 0.008 -10000 0 -10000 0 0
SP1 0.047 0.024 -10000 0 -10000 0 0
SIN3B 0.035 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 -0.33 34 34
ITGB5 -0.003 0.084 0.33 1 -0.41 4 5
TGIF/SIN3/HDAC complex/CtBP 0.024 0.07 -10000 0 -0.33 12 12
SMAD3/SMAD4/AR -0.044 0.16 -10000 0 -0.37 82 82
AR -0.04 0.19 -10000 0 -0.54 66 66
negative regulation of cell growth -0.022 0.12 -10000 0 -0.36 29 29
SMAD3/SMAD4/MYOD 0.004 0.096 -10000 0 -0.3 12 12
E2F5 0.035 0.036 -10000 0 -10000 0 0
E2F4 0.03 0.012 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.05 0.11 -10000 0 -0.34 13 13
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.11 -10000 0 -0.35 25 25
TFDP1 0.033 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.25 0.3 -10000 0 -0.66 130 130
SMAD3/SMAD4/RUNX2 0.006 0.093 -10000 0 -0.29 10 10
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 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
Syndecan-2/Fibronectin 0.071 0.094 0.23 3 -0.32 16 19
EPHB2 0.043 0.037 -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 -0.058 0.17 -10000 0 -0.32 136 136
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 0.008 -10000 0 -10000 0 0
BAX 0 0.063 0.49 2 -10000 0 2
EPB41 0.033 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.015 0.059 -10000 0 -0.3 16 16
LAMA3 -0.15 0.27 -10000 0 -0.54 161 161
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 -0.54 318 318
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 -0.36 19 19
dendrite morphogenesis 0.022 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 0.034 0.006 -10000 0 -10000 0 0
MAPK3 0.042 0.094 0.25 6 -0.3 16 22
MAPK1 0.047 0.097 0.2 101 -0.3 16 117
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 0.067 0.41 2 -0.33 17 19
Syndecan-2/alpha2/beta1 Integrin 0.035 0.091 -10000 0 -0.33 23 23
Syndecan-2/Kininogen 0.017 0.065 -10000 0 -0.33 16 16
ITGB1 0.033 0.006 -10000 0 -10000 0 0
SRC 0.042 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 0.065 -10000 0 -0.33 16 16
actin cytoskeleton reorganization 0.07 0.094 0.23 3 -0.32 16 19
Syndecan-2/Caveolin-2/Ras -0.15 0.18 -10000 0 -0.32 237 237
Syndecan-2/Laminin alpha3 -0.082 0.17 -10000 0 -0.35 132 132
Syndecan-2/RasGAP 0.042 0.066 -10000 0 -0.28 15 15
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
PRKCD 0.035 0.017 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 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 0.034 0.012 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.081 -10000 0 -0.36 19 19
Syndecan-2/Synbindin 0.015 0.065 -10000 0 -0.33 16 16
TGFB1 0.034 0.008 -10000 0 -10000 0 0
CASP3 0.042 0.095 0.2 92 -0.3 16 108
FN1 0.13 0.068 -10000 0 -10000 0 0
Syndecan-2/IL8 0.024 0.074 0.23 1 -0.34 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 0.065 -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 0.016 0.06 -10000 0 -0.3 16 16
Syndecan-2/Ezrin 0.015 0.059 -10000 0 -0.3 16 16
PRKACA 0.043 0.096 0.2 99 -0.3 16 115
angiogenesis 0.024 0.073 0.23 1 -0.33 16 17
MMP2 0.028 0.039 -10000 0 -0.54 2 2
IL8 0.048 0.053 -10000 0 -0.54 1 1
calcineurin-NFAT signaling pathway 0.016 0.065 -10000 0 -0.33 16 16
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.021 0.077 -10000 0 -0.28 5 5
alphaM/beta2 Integrin/GPIbA -0.016 0.079 0.27 3 -10000 0 3
alphaM/beta2 Integrin/proMMP-9 0.042 0.098 0.26 15 -10000 0 15
PLAUR 0.068 0.062 -10000 0 -10000 0 0
HMGB1 -0.03 0.045 -10000 0 -0.23 2 2
alphaM/beta2 Integrin/Talin -0.02 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 -0.37 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.094 0.074 -10000 0 -10000 0 0
CYR61 -0.13 0.26 -10000 0 -0.54 143 143
TLN1 0.033 0.006 -10000 0 -10000 0 0
Rap1/GTP 0.06 0.087 -10000 0 -0.34 8 8
RHOA 0.033 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.1 0.24 -10000 0 -0.54 117 117
MYH2 0.064 0.094 0.3 4 -0.5 4 8
MST1R 0.043 0.038 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.013 0.067 -10000 0 -10000 0 0
APOB 0.034 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.028 0.039 -10000 0 -0.54 2 2
JAM3 -0.008 0.14 -10000 0 -0.54 34 34
GP1BA 0.036 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.033 0.099 -10000 0 -0.36 21 21
alphaM/beta2 Integrin 0.048 0.083 0.24 3 -0.35 9 12
JAM3 homodimer -0.008 0.14 -10000 0 -0.54 34 34
ICAM2 0.021 0.076 -10000 0 -0.54 9 9
ICAM1 0.039 0.029 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor 0.045 0.087 0.24 3 -0.34 11 14
cell adhesion -0.016 0.078 0.27 3 -10000 0 3
NFKB1 -0.22 0.19 0.4 1 -0.36 301 302
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 -0.34 74 74
IL6 -0.53 0.36 0.38 1 -0.74 375 376
ITGB2 -0.022 0.063 0.2 2 -10000 0 2
elevation of cytosolic calcium ion concentration 0.032 0.11 0.31 8 -10000 0 8
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.2 -10000 0 -0.42 122 122
JAM2 -0.12 0.25 -10000 0 -0.54 132 132
alphaM/beta2 Integrin/ICAM1 0.008 0.092 0.3 1 -10000 0 1
alphaM/beta2 Integrin/uPA/Plg 0.01 0.091 -10000 0 -0.36 1 1
RhoA/GTP 0.043 0.1 -10000 0 -0.4 13 13
positive regulation of phagocytosis 0.036 0.083 0.28 3 -0.33 4 7
Ron/MSP 0.056 0.028 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.033 0.11 0.32 8 -10000 0 8
alphaM/beta2 Integrin/uPAR 0.01 0.095 0.26 12 -10000 0 12
PLAU 0.057 0.053 -10000 0 -10000 0 0
PLAT -0.066 0.21 -10000 0 -0.54 84 84
actin filament polymerization 0.065 0.097 0.31 9 -0.44 5 14
MST1 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.011 0.071 -10000 0 -10000 0 0
TNF -0.21 0.18 0.41 3 -0.6 7 10
RAP1B 0.033 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.003 0.085 0.26 1 -10000 0 1
fibrinolysis 0.009 0.089 -10000 0 -0.36 1 1
HCK 0.036 0.022 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation 0.045 0.087 0.24 3 -0.34 11 14
VTN 0.032 0.011 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.11 0.18 -10000 0 -0.35 151 151
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 0.24 15 -0.36 2 17
FN1 0.13 0.068 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.017 0.075 0.26 1 -10000 0 1
MPO 0.031 0.016 -10000 0 -10000 0 0
KNG1 0.033 0.007 -10000 0 -10000 0 0
RAP1/GDP 0.044 0.012 -10000 0 -10000 0 0
ROCK1 0.063 0.11 0.28 8 -0.4 11 19
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.031 0.027 -10000 0 -0.54 1 1
CTGF 0.011 0.11 -10000 0 -0.54 19 19
alphaM/beta2 Integrin/Hck -0.017 0.076 0.27 5 -10000 0 5
ITGAM -0.028 0.044 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.073 0.16 -10000 0 -0.36 99 99
HP 0.029 0.012 -10000 0 -10000 0 0
leukocyte adhesion -0.17 0.2 -10000 0 -0.44 135 135
SELP -0.1 0.24 -10000 0 -0.54 117 117
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.089 0.16 0.34 70 -0.38 13 83
FYN 0.061 0.16 0.41 25 -0.41 17 42
LAT/GRAP2/SLP76 0.071 0.16 0.46 22 -0.41 11 33
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 0.059 0.16 0.37 47 -0.31 29 76
B2M 0.037 0.011 -10000 0 -10000 0 0
IKBKG 0.034 0.071 0.19 51 -0.12 2 53
MAP3K8 -0.04 0.19 -10000 0 -0.54 65 65
mol:Ca2+ -0.011 0.017 -10000 0 -0.089 12 12
integrin-mediated signaling pathway 0.037 0.023 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.052 0.18 0.5 22 -0.41 28 50
TRPV6 0.013 0.22 1.3 10 -0.54 17 27
CD28 0.028 0.084 -10000 0 -0.55 10 10
SHC1 0.072 0.18 0.34 74 -0.45 16 90
receptor internalization 0.024 0.19 0.36 25 -0.39 65 90
PRF1 0.037 0.16 0.54 10 -0.74 7 17
KRAS 0.034 0.018 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
COT/AKT1 0.036 0.17 0.34 44 -0.3 39 83
LAT 0.055 0.17 0.42 27 -0.42 19 46
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D 0.04 0.036 0.22 3 -10000 0 3
CD3E 0.034 0.016 0.22 1 -10000 0 1
CD3G 0.038 0.073 0.2 11 -0.54 5 16
RASGRP2 0.009 0.049 0.17 10 -0.16 28 38
RASGRP1 0.064 0.16 0.45 28 -0.33 15 43
HLA-A 0.041 0.025 0.21 4 -10000 0 4
RASSF5 0.03 0.023 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.038 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.067 0.098 0.25 59 -0.13 2 61
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.01 0.048 -10000 0 -0.18 16 16
PRKCA 0.041 0.1 0.33 25 -0.22 6 31
GRAP2 0.034 0.019 -10000 0 -10000 0 0
mol:IP3 0.002 0.091 0.29 10 -0.33 10 20
EntrezGene:6957 0.003 0.006 0.042 3 -10000 0 3
TCR/CD3/MHC I/CD8 0.024 0.13 0.32 20 -0.3 48 68
ORAI1 -0.02 0.17 -10000 0 -1.1 10 10
CSK 0.045 0.16 0.41 19 -0.43 17 36
B7 family/CD28 0.082 0.17 0.48 23 -0.44 13 36
CHUK 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.041 0.17 0.4 22 -0.39 35 57
PTPN6 0.044 0.16 0.38 24 -0.42 17 41
VAV1 0.043 0.16 0.46 17 -0.44 17 34
Monovalent TCR/CD3 0.023 0.1 0.28 21 -0.37 21 42
CBL 0.03 0.011 -10000 0 -10000 0 0
LCK 0.062 0.16 0.42 24 -0.41 14 38
PAG1 0.061 0.17 0.39 29 -0.45 14 43
RAP1A 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.04 0.17 0.38 24 -0.42 24 48
CD80 0.045 0.038 -10000 0 -10000 0 0
CD86 0.036 0.013 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 0.01 0.067 -10000 0 -0.21 16 16
HRAS 0.034 0.013 -10000 0 -10000 0 0
GO:0035030 0.042 0.14 0.38 26 -0.39 13 39
CD8A 0.003 0.006 0.044 4 -10000 0 4
CD8B 0.041 0.026 -10000 0 -10000 0 0
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDK1/PKC theta 0.07 0.19 0.42 56 -0.39 18 74
CSK/PAG1 0.064 0.16 0.39 28 -0.45 12 40
SOS1 0.034 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.057 0.024 -10000 0 -10000 0 0
GRAP2/SLP76 0.065 0.17 0.47 18 -0.42 16 34
STIM1 0.004 0.1 1.2 3 -10000 0 3
RAS family/GTP 0.076 0.11 0.28 49 -0.18 10 59
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.021 0.19 0.36 25 -0.41 65 90
mol:DAG -0.016 0.068 0.13 2 -0.28 12 14
RAP1A/GDP 0.036 0.048 0.13 51 -10000 0 51
PLCG1 0.032 0.008 -10000 0 -10000 0 0
CD247 0.022 0.11 0.21 9 -0.55 15 24
cytotoxic T cell degranulation 0.038 0.16 0.53 10 -0.67 8 18
RAP1A/GTP 0.002 0.016 -10000 0 -0.06 28 28
mol:PI-3-4-5-P3 0.054 0.17 0.48 22 -0.35 28 50
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.023 0.12 0.33 9 -0.41 10 19
NRAS 0.036 0.016 -10000 0 -10000 0 0
ZAP70 0.038 0.024 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.045 0.13 0.33 8 -0.4 11 19
MALT1 0.033 0.01 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
CD8 heterodimer 0.033 0.022 0.19 5 -10000 0 5
CARD11 0.038 0.027 -10000 0 -10000 0 0
PRKCB -0.013 0.051 0.16 4 -0.2 13 17
PRKCE 0.045 0.11 0.33 27 -0.22 8 35
PRKCQ 0.059 0.18 0.48 28 -0.4 24 52
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 0.059 0.15 0.34 54 -0.27 29 83
IKK complex 0.056 0.093 0.23 70 -10000 0 70
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 0.028 0.14 0.28 50 -0.25 29 79
PDPK1 0.063 0.16 0.39 52 -0.3 25 77
TCR/CD3/MHC I/CD8/Fyn 0.013 0.17 0.4 13 -0.54 18 31
Canonical Wnt signaling 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
HDAC1 0.027 0.043 0.26 5 -10000 0 5
AES 0.026 0.036 0.22 4 -10000 0 4
FBXW11 0.033 0.007 -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 0.026 -10000 0 -0.54 1 1
DKK2 0.031 0.054 -10000 0 -0.54 4 4
TLE1 0.01 0.1 0.24 4 -0.55 15 19
MACF1 0.034 0.006 -10000 0 -10000 0 0
CTNNB1 0.15 0.11 0.34 31 -0.41 3 34
WIF1 -0.38 0.26 -10000 0 -0.54 370 370
beta catenin/RanBP3 0.041 0.15 0.51 38 -0.43 2 40
KREMEN2 0.1 0.076 -10000 0 -10000 0 0
DKK1 0.007 0.18 -10000 0 -0.54 44 44
beta catenin/beta TrCP1 0.16 0.1 0.35 25 -0.38 3 28
FZD1 0.034 0.026 -10000 0 -0.54 1 1
AXIN2 0.029 0.29 0.65 48 -1.1 15 63
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 0.07 0.086 -10000 0 -0.54 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.091 0.15 0.36 7 -0.57 14 21
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 -0.43 2 3
HNF1A 0.027 0.041 0.25 6 -10000 0 6
CTBP1 0.025 0.038 0.24 4 -10000 0 4
MYC 0.096 0.44 0.76 43 -1.3 29 72
RANBP3 0.033 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.1 0.07 -10000 0 -0.31 3 3
NKD1 0.031 0.021 -10000 0 -10000 0 0
TCF4 0.019 0.076 0.23 6 -0.54 7 13
TCF3 0.027 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 0.001 0.21 0.55 32 -0.56 12 44
LEF1 0.054 0.068 0.27 8 -10000 0 8
DVL1 0.08 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 0.082 0.13 0.26 50 -0.29 41 91
LRP6 0.033 0.008 -10000 0 -10000 0 0
CSNK1A1 0.027 0.042 0.26 5 -10000 0 5
NLK 0.036 0.031 -10000 0 -10000 0 0
CCND1 0.12 0.38 0.84 66 -1.3 13 79
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 0.035 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 0.23 337 -0.3 1 338
CREBBP 0.023 0.044 0.25 3 -0.55 1 4
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.006 -10000 0 -10000 0 0
mol:S1P 0.001 0.003 0.031 6 -10000 0 6
S1P1/S1P/Gi -0.091 0.16 -10000 0 -0.28 187 187
GNAO1 0.031 0.013 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.041 0.016 -10000 0 -10000 0 0
AKT1 -0.011 0.11 -10000 0 -0.5 17 17
AKT3 -0.015 0.12 -10000 0 -0.58 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.034 0.006 -10000 0 -10000 0 0
GNAI2 0.035 0.011 -10000 0 -10000 0 0
GNAI3 0.035 0.007 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.002 0.004 0.036 6 -10000 0 6
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.07 0.14 0.24 2 -0.34 58 60
MAPK3 -0.062 0.13 0.23 1 -0.33 48 49
MAPK1 -0.068 0.13 0.23 1 -0.33 55 56
JAK2 -0.062 0.15 0.26 4 -0.34 64 68
CXCR4 -0.063 0.14 0.25 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 -0.066 0.13 0.32 2 -0.32 55 57
S1P/S1P3/Gi -0.071 0.14 0.24 2 -0.34 58 60
RAC1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.059 0.14 -10000 0 -0.31 58 58
VEGFA 0.052 0.047 0.22 1 -10000 0 1
S1P/S1P2/Gi -0.074 0.14 -10000 0 -0.25 186 186
VEGFR1 homodimer/VEGFA homodimer 0.062 0.039 0.27 1 -10000 0 1
RHOA 0.033 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.026 0.038 -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 0.068 -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 -0.32 58 58
Coregulation of Androgen receptor activity

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
NRIP1 0.029 0.064 -10000 0 -0.54 6 6
SVIL 0.022 0.084 -10000 0 -0.54 11 11
ZNF318 0.03 0.008 -10000 0 -10000 0 0
JMJD2C 0.007 0.01 0.12 4 -10000 0 4
T-DHT/AR/Ubc9 -0.036 0.14 -10000 0 -0.3 85 85
CARM1 0.035 0.014 -10000 0 -10000 0 0
PRDX1 0.035 0.015 -10000 0 -10000 0 0
PELP1 0.031 0.01 -10000 0 -10000 0 0
CTNNB1 0.03 0.052 -10000 0 -0.54 4 4
AKT1 0.034 0.018 -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 0.036 0.008 -10000 0 -10000 0 0
GSN -0.11 0.25 -10000 0 -0.54 132 132
NCOA2 0.028 0.015 -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 -0.2 171 171
FHL2 -0.11 0.32 -10000 0 -0.96 60 60
RANBP9 0.035 0.009 -10000 0 -10000 0 0
JMJD1A -0.027 0.061 -10000 0 -0.14 122 122
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 0.15 -10000 0 -0.36 76 76
XRCC6 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.057 0.17 -10000 0 -0.25 199 199
CTDSP1 0.034 0.006 -10000 0 -10000 0 0
CTDSP2 0.031 0.008 -10000 0 -10000 0 0
BRCA1 0.037 0.022 -10000 0 -10000 0 0
TCF4 0.024 0.067 -10000 0 -0.55 7 7
CDKN2A 0.051 0.054 -10000 0 -10000 0 0
SRF 0.02 0.058 -10000 0 -10000 0 0
NKX3-1 -0.072 0.11 -10000 0 -0.22 174 174
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 -0.31 85 85
AR -0.069 0.2 0.18 1 -0.47 82 83
UBA3 0 0.001 -10000 0 -10000 0 0
PATZ1 0.031 0.01 -10000 0 -10000 0 0
PAWR 0.034 0.03 -10000 0 -0.54 1 1
PRKDC 0.031 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 78 78
RPS6KA3 0.034 0.037 -10000 0 -0.54 2 2
T-DHT/AR/ARA70 -0.039 0.14 -10000 0 -0.32 82 82
LATS2 0.02 0.076 -10000 0 -0.54 9 9
T-DHT/AR/PRX1 -0.034 0.13 -10000 0 -0.29 83 83
Cyclin D3/CDK11 p58 0.025 0.004 -10000 0 -10000 0 0
VAV3 0.03 0.12 -10000 0 -0.54 19 19
KLK2 -0.018 0.069 -10000 0 -0.42 1 1
CASP8 0.033 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.019 0.13 -10000 0 -0.32 54 54
TMPRSS2 -0.23 0.42 -10000 0 -0.97 122 122
CCND1 0.024 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 -0.071 141 142
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 -0.31 93 93
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 0.038 0.026 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.013 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.1 -10000 0 -0.36 22 22
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 0.26 1 -0.4 3 4
IL1A 0.036 0.016 -10000 0 -10000 0 0
IL1B -0.017 0.12 -10000 0 -0.42 41 41
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 -0.031 0.18 -10000 0 -0.54 58 58
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.031 0.13 -10000 0 -0.34 61 61
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 0.29 1 -0.35 1 2
JUN -0.051 0.1 -10000 0 -0.27 83 83
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.026 0.2 -10000 0 -0.37 112 112
IL1 alpha/IL1R1/IL1RAP/MYD88 0.039 0.13 -10000 0 -0.32 58 58
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.052 0.13 -10000 0 -0.3 57 57
IL1 beta fragment/IL1R1/IL1RAP -0.024 0.16 -10000 0 -0.35 91 91
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 0.014 0.15 -10000 0 -0.39 58 58
IRAK4 0.034 0.005 -10000 0 -10000 0 0
PRKCI 0.035 0.017 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.4 44 44
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.022 0.14 -10000 0 -0.32 66 66
CHUK 0.034 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.024 0.16 -10000 0 -0.35 91 91
IL1 beta/IL1R2 0.007 0.12 0.23 1 -0.36 44 45
IRAK/TRAF6/TAK1/TAB1/TAB2 0.046 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.035 0.18 -10000 0 -0.35 108 108
IRAK3 0.035 0.033 -10000 0 -0.54 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.008 0.16 -10000 0 -0.32 90 90
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.1 -10000 0 -0.27 56 56
IL1 alpha/IL1R1/IL1RAP 0.022 0.13 -10000 0 -0.34 58 58
RELA 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.034 0.009 -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 -0.023 0.12 -10000 0 -0.29 83 83
CASP1 -0.013 0.15 -10000 0 -0.54 38 38
IL1RN/IL1R2 0.067 0.056 0.26 6 -0.4 3 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.006 0.16 -10000 0 -0.34 91 91
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.13 -10000 0 -0.34 60 60
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
IL1RN 0.054 0.05 -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
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.039 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 0.09 -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 -0.032 0.13 -10000 0 -0.27 101 101
RXRs/NUR77 0.07 0.093 -10000 0 -0.3 18 18
RXRs/PPAR -0.15 0.14 -10000 0 -0.4 43 43
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 0.015 0.14 -10000 0 -0.3 74 74
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 0.006 0.13 -10000 0 -0.29 75 75
RARG 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 0.063 0.17 0.56 52 -10000 0 52
RARs/THRs/DNA/SMRT -0.031 0.13 -10000 0 -0.27 101 101
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 0.07 -10000 0 -0.3 4 4
NR1H4 0.035 0.009 0.18 2 -10000 0 2
RXRs/LXRs/DNA 0.1 0.088 -10000 0 -0.28 5 5
NR1H2 0.043 0.016 -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 0.007 0.12 -10000 0 -0.54 24 24
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 0.055 -10000 0 -0.54 4 4
RXR alpha/CCPG 0.052 0.02 -10000 0 -10000 0 0
RXRA 0.042 0.015 -10000 0 -10000 0 0
RXRB 0.044 0.017 -10000 0 -10000 0 0
THRB 0.028 0.057 -10000 0 -0.54 5 5
PPARG -0.38 0.26 -10000 0 -0.54 369 369
PPARD 0.034 0.01 -10000 0 -10000 0 0
TNF 0.082 0.09 -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 -0.057 0.21 -10000 0 -0.54 80 80
RXRs/NUR77/BCL2 -0.028 0.12 -10000 0 -0.26 84 84
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 0.004 0.16 -10000 0 -0.32 99 99
RXRs/FXR 0.084 0.065 -10000 0 -0.31 4 4
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.034 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.048 0.13 0.24 4 -0.3 95 99
FRAP1 -0.014 0.11 0.34 1 -0.5 18 19
AKT1 -0.041 0.12 0.25 5 -0.29 69 74
INSR 0.034 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.044 0.011 -10000 0 -10000 0 0
mol:GTP -0.004 0.12 0.27 3 -0.36 12 15
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.057 -10000 0 -0.23 7 7
TSC2 0.031 0.01 -10000 0 -10000 0 0
RHEB/GDP -0.013 0.094 -10000 0 -0.26 32 32
TSC1 0.034 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.019 0.13 -10000 0 -0.33 72 72
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.004 0.072 -10000 0 -0.27 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.034 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.009 0.1 0.3 4 -0.34 20 24
MAP3K5 -0.019 0.097 0.2 5 -0.29 51 56
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
apoptosis -0.019 0.097 0.2 5 -0.29 51 56
mol:LY294002 0 0.001 0.001 2 -0.002 61 63
EIF4B -0.008 0.096 0.28 5 -0.32 15 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.016 0.098 0.25 2 -0.3 14 16
eIF4E/eIF4G1/eIF4A1 -0.002 0.069 -10000 0 -0.32 14 14
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.026 0.15 -10000 0 -0.31 103 103
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.077 0.25 12 -0.21 11 23
FKBP1A 0.034 0.012 -10000 0 -10000 0 0
RHEB/GTP 0.005 0.1 0.26 2 -0.34 10 12
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 85 92
EIF4E 0.034 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.04 0.21 -10000 0 -0.57 61 61
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.049 -10000 0 -0.25 2 2
TSC1/TSC2 -0.003 0.12 0.29 3 -0.39 12 15
tumor necrosis factor receptor activity 0 0.001 0.002 61 -0.001 2 63
RPS6 0.032 0.026 -10000 0 -0.54 1 1
PPP5C 0.036 0.017 -10000 0 -10000 0 0
EIF4G1 0.033 0.007 -10000 0 -10000 0 0
IRS1 -0.041 0.13 -10000 0 -0.35 73 73
INS 0.033 0.007 -10000 0 -10000 0 0
PTEN 0.025 0.067 -10000 0 -0.54 7 7
PDK2 -0.046 0.12 0.22 9 -0.29 75 84
EIF4EBP1 -0.033 0.25 -10000 0 -1 29 29
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PPP2R5D -0.012 0.1 0.35 3 -0.44 18 21
peptide biosynthetic process 0.019 0.016 -10000 0 -10000 0 0
RHEB 0.034 0.009 -10000 0 -10000 0 0
EIF4A1 0.031 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.005 15 -0.003 6 21
EEF2 0.02 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.016 0.24 -10000 0 -0.97 29 29
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 -0.54 269 269
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 0.028 -9999 0 -10000 0 0
NCAN 0.039 0.028 -9999 0 -10000 0 0
long-term memory 0.041 0.096 -9999 0 -0.45 13 13
Syndecan-3/IL8 0.049 0.11 -9999 0 -0.47 16 16
PSEN1 0.033 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.04 0.021 -9999 0 -10000 0 0
FYN 0.03 0.037 -9999 0 -0.54 2 2
limb bud formation -0.001 0.089 -9999 0 -0.48 16 16
MC4R 0.034 0.013 -9999 0 -10000 0 0
SRC 0.033 0.008 -9999 0 -10000 0 0
PTN -0.37 0.27 -9999 0 -0.54 355 355
FGFR/FGF/Syndecan-3 -0.001 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 0.048 0.053 -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
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.007 0.23 -10000 0 -0.9 24 24
NCK1/PAK1/Dok-R -0.034 0.093 -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 0.034 0.013 -10000 0 -10000 0 0
NF kappa B/RelA 0.043 0.23 -10000 0 -0.94 23 23
FN1 0.13 0.068 -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 0.19 -10000 0 -0.54 52 52
ELK1 0.005 0.21 -10000 0 -0.94 23 23
GRB7 0.029 0.013 -10000 0 -10000 0 0
PAK1 0.043 0.046 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.096 0.25 -10000 0 -0.96 23 23
CDKN1A -0.003 0.19 -10000 0 -0.67 20 20
ITGA5 0.034 0.008 -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 0.016 0.18 -10000 0 -0.65 24 24
PLG -0.004 0.23 -10000 0 -1 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.002 0.21 -10000 0 -0.84 24 24
GRB2 0.034 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
ANGPT2 -0.075 0.23 -10000 0 -0.62 43 43
BMX -0.16 0.28 -10000 0 -1.3 23 23
ANGPT1 -0.012 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 -0.002 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 -0.54 380 380
STAT5A (dimer) -0.002 0.23 -10000 0 -0.85 21 21
mol:L-citrulline 0.016 0.18 -10000 0 -0.65 24 24
AGTR1 -0.18 0.3 -10000 0 -0.54 207 207
MAPK14 -0.003 0.26 -10000 0 -1 26 26
Tie2/SHP2 0.001 0.21 -10000 0 -1 15 15
TEK -0.004 0.22 -10000 0 -1.1 15 15
RPS6KB1 0.021 0.23 -10000 0 -0.86 24 24
Angiotensin II/AT1 -0.13 0.22 -10000 0 -0.39 209 209
Tie2/Ang1/GRB2 0.011 0.24 -10000 0 -1.1 23 23
MAPK3 0.005 0.22 -10000 0 -0.93 23 23
MAPK1 -0.004 0.21 -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 0.23 -10000 0 -1 23 23
PI3K -0.005 0.26 -10000 0 -1 24 24
FES -0.01 0.26 -10000 0 -1.1 26 26
Crk/Dok-R 0.017 0.24 -10000 0 -1 23 23
Tie2/Ang1/ABIN2 0.013 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 0.25 -10000 0 -1 21 21
Tie2/Ang1 0.001 0.25 -10000 0 -1.1 23 23
FOXO1 0.006 0.22 -10000 0 -0.82 25 25
ELF1 0.035 0.027 -10000 0 -10000 0 0
ELF2 0.002 0.23 -10000 0 -1 23 23
mol:Choline -0.002 0.22 -10000 0 -0.99 23 23
cell migration -0.015 0.053 -10000 0 -0.23 24 24
FYN -0.018 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 0.038 0.054 0.26 1 -0.25 13 14
MAPKKK cascade -0.002 0.22 -10000 0 -0.99 23 23
RASA1 0.034 0.012 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.003 0.24 -10000 0 -1 23 23
NCK1 0.034 0.005 -10000 0 -10000 0 0
vasculogenesis 0.019 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 0.016 0.18 -10000 0 -0.65 24 24
Rac1/GTP 0.014 0.21 -10000 0 -0.8 24 24
MMP2 -0.003 0.24 -10000 0 -1 23 23
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.011 0.096 0.34 10 -0.31 9 19
TBX21 -0.13 0.37 0.74 5 -1.3 36 41
B2M 0.038 0.013 -10000 0 -10000 0 0
TYK2 0.017 0.036 -10000 0 -10000 0 0
IL12RB1 0.017 0.036 -10000 0 -10000 0 0
GADD45B -0.071 0.28 0.7 2 -0.87 29 31
IL12RB2 0.03 0.076 0.26 6 -0.55 1 7
GADD45G -0.062 0.26 0.7 3 -0.75 31 34
natural killer cell activation -0.008 0.022 -10000 0 -10000 0 0
RELB 0.036 0.02 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL18 0.045 0.046 0.22 8 -10000 0 8
IL2RA 0.041 0.035 -10000 0 -10000 0 0
IFNG 0.063 0.066 -10000 0 -0.54 1 1
STAT3 (dimer) -0.062 0.24 0.57 10 -0.61 42 52
HLA-DRB5 -0.008 0.032 -10000 0 -10000 0 0
FASLG -0.061 0.26 0.73 7 -0.82 16 23
NF kappa B2 p52/RelB -0.083 0.25 0.54 5 -0.59 62 67
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 0.21 1 -10000 0 1
CD3G 0.004 0.081 0.2 12 -0.56 5 17
IL12Rbeta2/JAK2 0.028 0.075 0.3 7 -0.41 1 8
CCL3 -0.087 0.25 0.71 2 -0.8 19 21
CCL4 -0.087 0.25 0.71 2 -0.8 19 21
HLA-A 0.043 0.026 0.2 6 -10000 0 6
IL18/IL18R 0.058 0.14 0.37 16 -0.36 42 58
NOS2 -0.086 0.26 0.6 9 -0.59 67 76
IL12/IL12R/TYK2/JAK2/SPHK2 0.008 0.099 0.34 9 -0.32 9 18
IL1R1 -0.17 0.43 0.71 2 -1.2 63 65
IL4 0.038 0.03 -10000 0 -10000 0 0
JAK2 0.016 0.037 0.25 1 -10000 0 1
EntrezGene:6957 -0.011 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.003 0.15 0.34 21 -0.46 13 34
RAB7A -0.045 0.24 0.64 4 -0.71 25 29
lysosomal transport -0.042 0.24 0.64 4 -0.67 25 29
FOS -0.83 0.6 0.57 1 -1.2 367 368
STAT4 (dimer) -0.034 0.27 0.62 10 -0.68 39 49
STAT5A (dimer) -0.061 0.26 0.58 8 -0.61 54 62
GZMA -0.093 0.25 0.57 7 -0.59 63 70
GZMB -0.092 0.26 0.71 6 -0.85 19 25
HLX 0.025 0.038 -10000 0 -0.54 2 2
LCK -0.086 0.27 0.69 9 -0.63 62 71
TCR/CD3/MHC II/CD4 -0.12 0.16 0.28 5 -0.43 63 68
IL2/IL2R 0.088 0.056 0.37 4 -0.32 1 5
MAPK14 -0.06 0.28 0.63 8 -0.77 39 47
CCR5 -0.068 0.28 0.72 9 -0.77 35 44
IL1B 0.014 0.071 0.26 1 -0.55 5 6
STAT6 -0.039 0.18 0.39 7 -0.66 27 34
STAT4 0.027 0.069 -10000 0 -0.54 7 7
STAT3 0.033 0.007 -10000 0 -10000 0 0
STAT1 0.059 0.055 -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 0.048 0.25 2 -10000 0 2
CD8A 0.005 0.009 -10000 0 -10000 0 0
CD8B 0.042 0.027 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.011 0.096 0.3 9 -0.33 10 19
IL2RB 0.035 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.26 0.61 10 -0.63 39 49
IL2RG 0.043 0.035 -10000 0 -10000 0 0
IL12 0.007 0.089 0.29 3 -0.41 11 14
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
CD247 -0.003 0.11 0.21 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 0.006 0.093 0.24 1 -0.56 11 12
IL12/IL12R/TYK2/JAK2 -0.1 0.27 0.68 8 -0.66 63 71
MAP2K3 -0.071 0.29 0.62 8 -0.75 50 58
RIPK2 0.029 0.021 -10000 0 -10000 0 0
MAP2K6 -0.063 0.27 0.63 8 -0.74 39 47
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.012 0.034 -10000 0 -10000 0 0
IL18RAP -0.009 0.16 0.21 3 -0.55 42 45
IL12Rbeta1/TYK2 0.029 0.047 0.25 1 -10000 0 1
EOMES 0.042 0.1 -10000 0 -0.56 5 5
STAT1 (dimer) -0.013 0.26 0.67 15 -0.61 36 51
T cell proliferation -0.031 0.22 0.54 9 -0.55 40 49
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.037 0.031 -10000 0 -0.56 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.23 0.52 2 -0.62 38 40
ATF2 -0.057 0.26 0.6 7 -0.71 39 46
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.099 0.077 0.32 5 -0.29 4 9
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.1 0.36 19 -10000 0 19
alphaV/beta3 Integrin/Osteopontin/Src 0.099 0.072 0.26 2 -0.39 4 6
AP1 -0.14 0.22 0.49 1 -0.46 90 91
ILK 0.077 0.073 0.36 2 -0.3 4 6
bone resorption 0.059 0.071 -10000 0 -10000 0 0
PTK2B 0.027 0.014 -10000 0 -10000 0 0
PYK2/p130Cas 0.1 0.09 0.33 1 -0.28 4 5
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 0.047 0.031 -10000 0 -0.4 2 2
alphaV/beta3 Integrin/Osteopontin 0.12 0.078 0.32 3 -0.33 4 7
MAP3K1 0.079 0.078 0.3 11 -0.3 5 16
JUN -0.066 0.22 -10000 0 -0.54 89 89
MAPK3 0.079 0.096 0.35 18 -0.28 3 21
MAPK1 0.078 0.093 0.3 27 -0.28 4 31
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.064 0.077 0.3 9 -0.29 6 15
ITGB3 0.041 0.021 0.2 3 -10000 0 3
NFKBIA 0.077 0.099 0.32 34 -10000 0 34
FOS -0.35 0.27 -10000 0 -0.54 344 344
CD44 0.033 0.028 -10000 0 -0.54 1 1
CHUK 0.034 0.005 -10000 0 -10000 0 0
PLAU 0.084 0.15 0.48 14 -0.53 1 15
NF kappa B1 p50/RelA 0.14 0.1 0.42 16 -10000 0 16
BCAR1 0.029 0.013 -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 0.08 0.075 0.31 9 -0.3 4 13
VAV3 0.063 0.096 0.3 15 -0.29 11 26
MAP3K14 0.087 0.083 0.3 13 -0.3 4 17
ROCK2 0.033 0.026 -10000 0 -0.54 1 1
SPP1 0.096 0.088 -10000 0 -0.54 3 3
RAC1 0.034 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.072 0.088 0.28 10 -0.27 10 20
MMP2 -0.13 0.17 0.47 1 -0.41 73 74
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.021 0.12 -10000 0 -0.4 46 46
MAP4K4 0.003 0.084 -10000 0 -0.3 19 19
BAG4 0.028 0.016 -10000 0 -10000 0 0
PKC zeta/ceramide -0.013 0.067 0.14 30 -0.27 9 39
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 0.008 0.075 0.72 5 -10000 0 5
BAD -0.013 0.07 0.17 6 -0.28 8 14
SMPD1 0.018 0.064 0.23 7 -0.25 10 17
RB1 -0.013 0.068 0.16 2 -0.28 8 10
FADD/Caspase 8 0.031 0.12 0.29 10 -0.42 8 18
MAP2K4 -0.014 0.071 0.18 2 -0.35 6 8
NSMAF 0.028 0.028 -10000 0 -0.54 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.074 0.31 3 -0.35 4 7
EGF -0.15 0.27 -10000 0 -0.54 164 164
mol:ceramide -0.012 0.074 0.16 35 -0.28 9 44
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 -0.024 0.12 -10000 0 -0.41 47 47
ASAH1 0.027 0.042 -10000 0 -0.54 2 2
negative regulation of cell cycle -0.014 0.068 0.16 2 -0.28 8 10
cell proliferation -0.11 0.14 -10000 0 -0.3 86 86
BID -0.014 0.19 -10000 0 -0.66 36 36
MAP3K1 -0.011 0.073 0.17 5 -0.28 10 15
EIF2A -0.005 0.073 0.25 10 -0.25 5 15
TRADD 0.03 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 0.078 0.27 5 -0.36 4 9
Cathepsin D/ceramide 0.011 0.08 0.18 3 -0.25 9 12
FADD 0.028 0.1 0.28 2 -0.3 16 18
KSR1 -0.006 0.073 0.21 6 -0.3 6 12
MAPK8 -0.008 0.07 -10000 0 -0.27 10 10
PRKRA -0.012 0.071 0.16 6 -0.27 9 15
PDGFA -0.019 0.16 -10000 0 -0.54 46 46
TRAF2 0.035 0.012 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.54 252 252
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.012 0.074 0.16 35 -0.28 9 44
CTSD 0.046 0.043 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.049 0.01 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.11 0.15 -10000 0 -0.32 85 85
PRKCD 0.035 0.017 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.024 0.12 -10000 0 -0.41 47 47
RelA/NF kappa B1 0.049 0.01 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.034 0.03 -10000 0 -0.54 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.007 0.091 -10000 0 -0.32 20 20
TNFR1A/BAG4/TNF-alpha 0.053 0.035 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.021 0.12 -10000 0 -0.4 46 46
MAP2K1 -0.008 0.072 0.29 4 -0.34 4 8
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
CYCS 0.027 0.082 0.19 57 -0.25 6 63
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 -0.008 0.07 0.21 7 -0.3 5 12
TNF-alpha/TNFR1A/FAN 0.057 0.036 -10000 0 -0.33 1 1
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.022 0.093 -10000 0 -0.41 16 16
MAP2K2 -0.007 0.073 0.29 4 -0.33 4 8
SMPD3 -0.002 0.12 0.24 3 -0.3 57 60
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 0.23 191 -0.22 3 194
NF kappa B1/RelA/I kappa B alpha 0.075 0.031 -10000 0 -0.3 1 1
AIFM1 0.026 0.082 0.19 58 -0.24 7 65
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.037 0.1 0.48 2 -0.67 4 6
oxygen homeostasis 0.026 0.03 0.21 2 -10000 0 2
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 0.45 19 -0.32 5 24
EPO 0.22 0.25 0.68 59 -0.46 3 62
FIH (dimer) 0.056 0.031 0.24 2 -10000 0 2
APEX1 0.058 0.038 0.24 2 -10000 0 2
SERPINE1 0.26 0.25 0.72 45 -0.5 4 49
FLT1 -0.016 0.17 -10000 0 -0.66 23 23
ADORA2A 0.26 0.25 0.67 74 -0.48 4 78
germ cell development 0.25 0.23 0.69 38 -0.49 3 41
SLC11A2 0.26 0.24 0.71 41 -0.5 4 45
BHLHE40 0.18 0.23 0.68 36 -0.49 4 40
HIF1AN 0.056 0.031 0.24 2 -10000 0 2
HIF2A/ARNT/SIRT1 0.17 0.19 0.55 39 -0.36 5 44
ETS1 0.041 0.034 -10000 0 -0.54 1 1
CITED2 0.005 0.15 -10000 0 -0.88 11 11
KDR -0.006 0.15 -10000 0 -0.67 16 16
PGK1 0.26 0.24 0.71 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 0.77 23 -0.56 4 27
EPAS1 0.16 0.18 0.49 57 -0.32 10 67
SP1 0.047 0.029 -10000 0 -10000 0 0
ABCG2 0.24 0.26 0.7 39 -0.62 10 49
EFNA1 0.18 0.22 0.66 20 -0.5 4 24
FXN 0.25 0.24 0.67 48 -0.48 3 51
POU5F1 0.25 0.24 0.7 38 -0.51 3 41
neuron apoptosis -0.22 0.26 0.55 4 -0.75 26 30
EP300 0.032 0.009 -10000 0 -10000 0 0
EGLN3 0.08 0.074 0.27 17 -0.54 1 18
EGLN2 0.059 0.035 0.25 1 -10000 0 1
EGLN1 0.045 0.034 0.26 1 -10000 0 1
VHL/Elongin B/Elongin C 0.053 0.033 -10000 0 -10000 0 0
VHL 0.036 0.018 -10000 0 -10000 0 0
ARNT 0.045 0.038 0.21 1 -10000 0 1
SLC2A1 0.25 0.24 0.68 56 -0.48 4 60
TWIST1 0.21 0.29 0.68 44 -0.54 32 76
ELK1 0.04 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.14 0.18 0.55 21 -0.36 5 26
VEGFA 0.26 0.25 0.72 45 -0.5 4 49
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Thromboxane A2 receptor signaling

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
TGM2 0.046 0.042 0.19 1 -10000 0 1
GNB1/GNG2 -0.019 0.054 -10000 0 -0.18 46 46
AKT1 0.059 0.13 0.4 19 -0.32 7 26
EGF -0.15 0.27 -10000 0 -0.54 164 164
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.029 0.053 0.26 2 -10000 0 2
mol:Ca2+ 0.06 0.16 0.49 16 -0.3 35 51
LYN 0.026 0.052 0.26 3 -10000 0 3
RhoA/GTP 0.025 0.067 0.19 15 -0.14 3 18
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK 0.058 0.17 0.55 13 -0.34 43 56
GNG2 0.033 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 0.012 0.12 -10000 0 -0.56 17 17
G beta5/gamma2 -0.014 0.075 -10000 0 -0.24 45 45
PRKCH 0.053 0.18 0.62 9 -0.36 44 53
DNM1 0.034 0.008 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.015 0.029 -10000 0 -0.53 1 1
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
PTGDR 0.03 0.06 0.18 8 -0.54 5 13
G12 family/GTP 0.004 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 -0.042 0.13 0.38 14 -0.46 9 23
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 0.059 0.18 0.64 9 -0.37 40 49
cell morphogenesis 0.044 0.012 -10000 0 -10000 0 0
PLCB2 0.051 0.22 0.71 8 -0.5 45 53
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.03 0.055 0.25 4 -10000 0 4
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.029 0.056 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 0.64 9 -0.37 45 54
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 0.23 0.73 8 -0.51 46 54
LCK 0.038 0.061 0.25 6 -10000 0 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.044 0.042 -10000 0 -0.23 5 5
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.098 -10000 0 -0.4 21 21
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.04 0.042 -10000 0 -0.23 5 5
MAPK14 0.052 0.13 0.41 19 -0.24 13 32
TGM2/GTP 0.056 0.2 0.68 9 -0.41 36 45
MAPK11 0.05 0.13 0.42 19 -0.24 14 33
ARHGEF1 0.046 0.11 0.35 17 -0.2 8 25
GNAI2 0.033 0.01 -10000 0 -10000 0 0
JNK cascade 0.059 0.19 0.63 10 -0.38 45 55
RAB11/GDP 0.031 0.01 -10000 0 -10000 0 0
ICAM1 0.058 0.15 0.47 18 -0.28 40 58
cAMP biosynthetic process 0.054 0.17 0.61 9 -0.35 36 45
Gq family/GTP/EBP50 0.033 0.048 0.16 2 -0.22 6 8
actin cytoskeleton reorganization 0.044 0.012 -10000 0 -10000 0 0
SRC 0.027 0.053 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 -0.064 0.11 0.26 3 -0.28 46 49
VCAM1 0.053 0.16 0.48 16 -0.31 45 61
TP beta/Gq family/GDP/G beta5/gamma2 0.012 0.12 -10000 0 -0.56 17 17
platelet activation 0.063 0.16 0.55 13 -0.32 17 30
PGI2/IP 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.031 -10000 0 -0.27 5 5
Gq family/GDP/G beta5/gamma2 0.015 0.11 -10000 0 -0.49 17 17
TXA2/TP beta/beta Arrestin2 -0.004 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 0.66 9 -0.42 45 54
EGFR -0.27 0.29 -10000 0 -0.54 269 269
TXA2/TP alpha 0.058 0.21 0.71 8 -0.47 37 45
Gq family/GTP 0.009 0.052 0.22 1 -0.21 19 20
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 0.13 6 -0.4 5 11
SLC9A3R1 0.059 0.058 -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 -0.35 1 1
NOS3 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.064 0.18 0.59 11 -0.35 40 51
PRKCB 0.053 0.17 0.61 9 -0.35 46 55
PRKCE 0.055 0.17 0.6 10 -0.36 44 54
PRKCD 0.054 0.18 0.6 10 -0.38 46 56
PRKCG 0.056 0.18 0.61 10 -0.38 45 55
muscle contraction 0.055 0.22 0.72 8 -0.48 45 53
PRKCZ 0.057 0.17 0.5 16 -0.34 45 61
ARR3 0.035 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.044 0.049 -10000 0 -0.25 5 5
PRKCQ 0.06 0.18 0.59 12 -0.35 45 57
MAPKKK cascade 0.054 0.2 0.69 8 -0.44 42 50
SELE 0.049 0.18 0.48 17 -0.38 48 65
TP beta/GNAI2/GDP/G beta/gamma 0.062 0.049 0.29 1 -0.35 1 2
ROCK1 0.034 0.006 -10000 0 -10000 0 0
GNA14 0.043 0.068 -10000 0 -0.54 4 4
chemotaxis 0.05 0.25 0.76 8 -0.59 49 57
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
Reelin signaling pathway

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
CDK5R1/CDK5 0.049 0.023 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 65 65
CRKL 0.033 0.008 -10000 0 -10000 0 0
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.54 2 2
ITGA3 0.03 0.028 -10000 0 -0.54 1 1
RELN/VLDLR/Fyn -0.011 0.16 -10000 0 -0.36 82 82
MAPK8IP1/MKK7/MAP3K11/JNK1 0.078 0.047 -10000 0 -10000 0 0
AKT1 -0.056 0.14 -10000 0 -0.52 24 24
MAP2K7 0.034 0.005 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
DAB1 0.034 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.07 0.084 -10000 0 -0.29 20 20
LRPAP1/LRP8 0.073 0.047 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.075 0.088 -10000 0 -0.28 22 22
DAB1/alpha3/beta1 Integrin 0.018 0.13 -10000 0 -0.3 58 58
long-term memory 0.081 0.11 -10000 0 -0.33 20 20
DAB1/LIS1 0.034 0.15 -10000 0 -0.31 64 64
DAB1/CRLK/C3G 0.019 0.14 -10000 0 -0.3 64 64
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
DAB1/NCK2 0.039 0.15 -10000 0 -0.31 64 64
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 -0.02 0.17 -10000 0 -0.54 47 47
RELN/LRP8/Fyn 0.066 0.095 -10000 0 -0.32 22 22
GRIN2A/RELN/LRP8/DAB1/Fyn 0.084 0.095 -10000 0 -0.3 14 14
MAPK8 0.033 0.026 -10000 0 -0.54 1 1
RELN/VLDLR/DAB1 -0.005 0.15 -10000 0 -0.33 80 80
ITGB1 0.033 0.006 -10000 0 -10000 0 0
MAP1B -0.037 0.16 0.28 8 -0.34 88 96
RELN/LRP8 0.07 0.091 -10000 0 -0.32 20 20
GRIN2B/RELN/LRP8/DAB1/Fyn 0.08 0.11 -10000 0 -0.33 23 23
PI3K 0.005 0.13 -10000 0 -0.4 44 44
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.043 0.027 -10000 0 -0.4 1 1
RAP1A -0.029 0.12 0.35 3 -0.48 5 8
PAFAH1B1 0.032 0.01 -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 -0.55 1 4
neuron adhesion -0.012 0.13 0.38 5 -0.46 4 9
LRP8 0.072 0.064 -10000 0 -10000 0 0
GSK3B -0.051 0.14 -10000 0 -0.5 24 24
RELN/VLDLR/DAB1/Fyn 0.005 0.15 -10000 0 -0.31 82 82
MAP3K11 0.034 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.055 0.16 -10000 0 -0.31 114 114
CDK5 0.037 0.023 -10000 0 -10000 0 0
MAPT 0.014 0.12 0.79 10 -0.5 3 13
neuron migration -0.027 0.15 0.38 4 -0.4 27 31
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.048 0.068 -10000 0 -0.55 1 1
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 80 80
TCGA08_p53

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
CDKN2A 0.027 0.046 -10000 0 -10000 0 0
TP53 -0.002 0.055 -10000 0 -0.19 37 37
Senescence -0.006 0.06 -10000 0 -0.19 47 47
Apoptosis -0.006 0.06 -10000 0 -0.19 47 47
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.009 0.068 0.3 19 -10000 0 19
MDM4 0.028 0.017 -10000 0 -10000 0 0
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 -0.23 243 243
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.032 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 0.03 0.037 -10000 0 -0.54 2 2
MAP3K12 0.034 0.004 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.04 0.093 -10000 0 -0.31 40 40
PRKG1 0.034 0.005 -10000 0 -10000 0 0
DUSP8 0.033 0.007 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.012 0.12 -10000 0 -0.32 33 33
apoptosis -0.039 0.089 -10000 0 -0.3 39 39
RAL/GTP 0.045 0.01 -10000 0 -10000 0 0
LYN 0.03 0.015 0.18 2 -10000 0 2
DUSP1 -0.2 0.28 -10000 0 -0.54 208 208
PAK1 0.043 0.046 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.071 0.036 -10000 0 -10000 0 0
TRAF6 0.034 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 0.012 -10000 0 -10000 0 0
MAPK11 0.001 0.13 0.35 3 -0.37 32 35
BLK 0.039 0.044 -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 0.016 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.13 0.39 2 -0.34 38 40
positive regulation of innate immune response 0.001 0.16 0.47 2 -0.41 36 38
LCK 0.048 0.044 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.014 0.15 0.58 1 -0.4 33 34
p38alpha-beta/MKP5 0.009 0.15 0.58 1 -0.41 32 33
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 76 76
CDC42 0.033 0.007 -10000 0 -10000 0 0
RALB 0.034 0.005 -10000 0 -10000 0 0
RALA 0.034 0.006 -10000 0 -10000 0 0
PAK3 -0.32 0.28 -10000 0 -0.54 310 310
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 0.002 0.18 -10000 0 -0.89 7 7
RAD9A 0.031 0.01 -10000 0 -10000 0 0
AP1 -0.31 0.27 -10000 0 -0.48 344 344
IFNAR2 0.038 0.012 -10000 0 -10000 0 0
AKT1 -0.004 0.12 -10000 0 -0.38 13 13
ER alpha/Oestrogen -0.041 0.19 -10000 0 -0.39 110 110
NFX1/SIN3/HDAC complex 0.035 0.074 -10000 0 -0.34 12 12
EGF -0.15 0.27 -10000 0 -0.54 164 164
SMG5 0.029 0.016 -10000 0 -10000 0 0
SMG6 0.031 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.056 0.025 -10000 0 -10000 0 0
TERT/c-Abl 0.01 0.17 -10000 0 -0.82 7 7
SAP18 0.033 0.01 -10000 0 -10000 0 0
MRN complex 0.048 0.033 -10000 0 -10000 0 0
WT1 0.087 0.07 -10000 0 -10000 0 0
WRN 0.028 0.015 -10000 0 -10000 0 0
SP1 0.041 0.016 -10000 0 -10000 0 0
SP3 0.036 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.013 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.028 0.16 -10000 0 -0.73 7 7
Mad/Max 0.055 0.018 -10000 0 -10000 0 0
TERT -0.006 0.18 -10000 0 -0.94 7 7
CCND1 0.034 0.26 0.58 6 -1.1 12 18
MAX 0.035 0.01 -10000 0 -10000 0 0
RBBP7 0.038 0.022 -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 0.035 0.009 -10000 0 -10000 0 0
TRF2/PARP2 0.042 0.029 -10000 0 -0.39 1 1
UBE3A 0.035 0.009 -10000 0 -10000 0 0
JUN -0.066 0.22 -10000 0 -0.54 89 89
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.029 0.012 -10000 0 -10000 0 0
FOS -0.35 0.27 -10000 0 -0.54 344 344
IFN-gamma/IRF1 0.082 0.083 0.29 3 -0.32 10 13
PARP2 0.034 0.006 -10000 0 -10000 0 0
BLM 0.073 0.066 -10000 0 -10000 0 0
Telomerase 0.006 0.093 -10000 0 -0.72 4 4
IRF1 0.045 0.048 -10000 0 -0.18 7 7
ESR1 -0.057 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 -0.37 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.043 0.068 -10000 0 -0.38 5 5
HDAC1 0.035 0.006 -10000 0 -10000 0 0
HDAC2 0.039 0.021 -10000 0 -10000 0 0
ATM 0.017 0.021 0.21 1 -10000 0 1
SMAD3 0.009 0.017 -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 0.025 0.18 -10000 0 -0.76 10 10
NR2F2 0.007 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 0.033 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
HNRNPC 0.034 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 0.016 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
mol:Oestrogen 0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.31 0.26 -10000 0 -0.46 354 354
MYC -0.002 0.12 -10000 0 -0.54 25 25
IL2 0.04 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 0.056 -10000 0 -0.39 1 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.023 0.18 -10000 0 -0.83 7 7
SP1/HDAC2 0.061 0.032 -10000 0 -10000 0 0
PINX1 0.027 0.014 -10000 0 -10000 0 0
Telomerase/EST1A 0.022 0.16 -10000 0 -0.73 7 7
Smad3/Myc 0.005 0.081 -10000 0 -0.34 25 25
911 complex 0.061 0.026 0.25 1 -10000 0 1
IFNG 0.065 0.073 -10000 0 -0.22 9 9
Telomerase/PinX1 0.011 0.16 -10000 0 -0.77 6 6
Telomerase/AKT1/mTOR/p70S6K 0.022 0.12 -10000 0 -0.54 12 12
SIN3B 0.036 0.014 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.028 0.16 -10000 0 -0.76 6 6
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 0.028 0.16 -10000 0 -0.73 7 7
E2F1 0.054 0.048 -10000 0 -10000 0 0
ZNFX1 0.033 0.017 -10000 0 -10000 0 0
PIF1 0.039 0.028 0.18 19 -10000 0 19
NCL 0.034 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 0.12 0.3 2 -0.63 4 6
Syndecan-4/Syndesmos 0.13 0.12 0.4 4 -0.72 4 8
positive regulation of JNK cascade 0.062 0.18 0.41 1 -0.66 6 7
Syndecan-4/ADAM12 0.15 0.13 0.42 4 -0.76 4 8
CCL5 0.029 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 0.008 -10000 0 -10000 0 0
SDCBP 0.028 0.028 -10000 0 -0.54 1 1
PLG 0.012 0.041 -10000 0 -0.54 1 1
ADAM12 0.057 0.061 -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 0.42 1 -0.72 6 7
Syndecan-4/Laminin alpha3 0.054 0.16 0.42 2 -0.75 5 7
MDK 0.044 0.037 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.062 0.17 0.39 2 -0.72 5 7
Syndecan-4/Midkine 0.14 0.12 0.4 4 -0.7 4 8
FZD7 -0.13 0.26 -10000 0 -0.54 145 145
Syndecan-4/FGFR1/FGF -0.066 0.16 0.4 1 -0.58 10 11
THBS1 0.038 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 0.062 0.18 0.41 1 -0.66 6 7
Syndecan-4/TACI 0.13 0.12 0.42 2 -0.76 4 6
CXCR4 0.044 0.037 -10000 0 -10000 0 0
cell adhesion 0.091 0.071 0.27 51 -10000 0 51
Syndecan-4/Dynamin 0.14 0.12 0.4 2 -0.76 4 6
Syndecan-4/TSP1 0.14 0.12 0.44 3 -0.76 4 7
Syndecan-4/GIPC 0.14 0.12 0.42 3 -0.76 4 7
Syndecan-4/RANTES 0.13 0.13 0.41 1 -0.76 4 5
ITGB1 0.033 0.006 -10000 0 -10000 0 0
LAMA1 0.033 0.01 -10000 0 -10000 0 0
LAMA3 -0.15 0.27 -10000 0 -0.54 161 161
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.03 0.22 0.7 49 -10000 0 49
Syndecan-4/alpha-Actinin 0.14 0.12 0.42 1 -0.76 4 5
TFPI -0.19 0.28 -10000 0 -0.54 198 198
F2 0.039 0.02 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.049 0.012 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.044 0.15 0.41 1 -0.76 4 5
ACTN1 0.033 0.007 -10000 0 -10000 0 0
TNC 0.037 0.036 -10000 0 -0.54 1 1
Syndecan-4/CXCL12 0.056 0.19 0.42 1 -0.7 7 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 -0.54 152 152
TNFRSF13B 0.032 0.014 -10000 0 -10000 0 0
FGF2 -0.39 0.25 -10000 0 -0.54 380 380
FGFR1 0.018 0.076 -10000 0 -0.54 9 9
Syndecan-4/PI-4-5-P2 0.096 0.12 -10000 0 -0.76 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.076 -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 0.41 1 -0.76 4 5
MMP9 0.094 0.078 -10000 0 -10000 0 0
Rac1/GTP 0.092 0.072 0.27 51 -10000 0 51
cytoskeleton organization 0.13 0.12 0.4 4 -0.69 4 8
GIPC1 0.034 0.011 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.036 0.19 0.4 3 -0.8 5 8
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 0.024 -10000 0 -10000 0 0
HDAC7 -0.052 0.12 -10000 0 -0.33 43 43
JUN -0.067 0.22 -10000 0 -0.54 89 89
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 48 48
T-DHT/AR -0.027 0.14 -10000 0 -0.35 43 43
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 0.029 0.015 -10000 0 -10000 0 0
CEBPA 0.03 0.044 -10000 0 -0.54 3 3
EHMT2 0.035 0.004 -10000 0 -10000 0 0
cell proliferation 0.037 0.15 0.43 13 -0.46 3 16
NR0B1 -0.094 0.25 -10000 0 -0.54 120 120
EGR1 -0.43 0.23 -10000 0 -0.54 414 414
RXRs/9cRA 0.051 0.043 -10000 0 -0.31 4 4
AR/RACK1/Src 0.003 0.1 0.34 5 -0.34 7 12
AR/GR -0.04 0.14 -10000 0 -0.29 96 96
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
PKN1 0.034 0.01 -10000 0 -10000 0 0
RCHY1 0.029 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 -0.012 0.16 -10000 0 -0.54 40 40
KLK3 -0.042 0.097 0.45 1 -10000 0 1
APPBP2 0.018 0.027 -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 -0.34 13 13
TMPRSS2 -0.22 0.45 -10000 0 -1 123 123
RXRG 0.024 0.053 -10000 0 -0.54 4 4
mol:9cRA 0 0 0.003 4 -10000 0 4
RXRA 0.034 0.006 -10000 0 -10000 0 0
RXRB 0.034 0.005 -10000 0 -10000 0 0
CARM1 0.035 0.014 -10000 0 -10000 0 0
NR2C2 0.035 0.014 -10000 0 -10000 0 0
KLK2 0.013 0.078 0.38 1 -10000 0 1
AR -0.025 0.1 -10000 0 -0.26 70 70
SENP1 0.034 0.004 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
MDM2 0.032 0.011 -10000 0 -10000 0 0
SRY -0.001 0.002 -10000 0 -0.025 4 4
GATA2 0.042 0.033 -10000 0 -10000 0 0
MYST2 0 0.001 -10000 0 -0.006 4 4
HOXB13 0.078 0.07 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0 0.1 0.35 6 -0.34 8 14
positive regulation of transcription 0.042 0.033 -10000 0 -10000 0 0
DNAJA1 0.019 0.03 -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 -0.019 0.17 -10000 0 -0.54 50 50
T-DHT/AR/TIF2 0.017 0.079 0.38 2 -0.3 5 7
T-DHT/AR/Hsp90 -0.011 0.098 0.36 2 -0.36 11 13
GSK3B 0.033 0.01 -10000 0 -10000 0 0
NR2C1 0.033 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 0.17 0.36 2 -0.34 112 114
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
SMARCE1 0.033 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.006 0.029 0.36 1 -0.34 1 2
SNTA1 0.032 0.026 -10000 0 -0.54 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.011 0.058 0.33 6 -0.34 1 7
MAPK12 0.008 0.086 0.21 40 -0.28 24 64
CCND1 0.009 0.083 0.21 2 -0.5 10 12
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 40 -0.27 24 64
MAP2K6 0.015 0.098 0.25 45 -0.3 25 70
MAPT 0.013 0.067 0.27 8 -0.26 10 18
MAPK13 0.017 0.027 -10000 0 -0.4 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.062 -10000 0 -0.33 17 17
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.03 0.027 -10000 0 -0.54 1 1
GNB1/GNG2 0.024 0.15 -10000 0 -0.44 27 27
mol:DAG 0.005 0.13 -10000 0 -0.41 25 25
PLCG1 0.004 0.13 -10000 0 -0.43 25 25
YES1 -0.003 0.13 0.25 1 -0.48 24 25
FZD3 0.014 0.091 -10000 0 -0.54 13 13
FZD6 0.007 0.11 -10000 0 -0.54 18 18
G protein 0.035 0.15 0.35 4 -0.45 21 25
MAP3K7 -0.006 0.11 0.25 1 -0.38 20 21
mol:Ca2+ 0.005 0.12 -10000 0 -0.4 25 25
mol:IP3 0.005 0.13 -10000 0 -0.41 25 25
NLK 0.004 0.13 -10000 0 -0.81 12 12
GNB1 0.034 0.011 -10000 0 -10000 0 0
CAMK2A -0.001 0.12 0.26 1 -0.4 21 22
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.016 0.13 -10000 0 -0.48 25 25
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
GNAS -0.006 0.13 0.25 1 -0.45 24 25
GO:0007205 -0.001 0.12 0.26 1 -0.42 24 25
WNT6 0.033 0.04 -10000 0 -0.54 2 2
WNT4 0.04 0.033 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.016 0.14 -10000 0 -0.46 20 20
GNG2 0.032 0.026 -10000 0 -0.54 1 1
WNT5A 0.01 0.13 -10000 0 -0.54 25 25
WNT11 0.024 0.079 -10000 0 -0.54 9 9
CDC42 -0.004 0.13 -10000 0 -0.46 22 22
Cellular roles of Anthrax toxin

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
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 25 25
MAP2K2 0.004 0.097 -10000 0 -0.57 14 14
MAP2K1 -0.005 0.01 -10000 0 -10000 0 0
MAP2K7 -0.005 0.01 -10000 0 -10000 0 0
MAP2K6 -0.01 0.042 0.086 1 -0.3 10 11
CYAA -0.011 0.043 -10000 0 -0.29 11 11
MAP2K4 -0.005 0.012 -10000 0 -0.18 1 1
IL1B -0.013 0.05 0.24 1 -0.22 16 17
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 0.075 -10000 0 -0.4 16 16
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 0.086 113 -0.29 143 256
PA/Cellular Receptors 0.038 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 0.007 0.049 0.18 37 -10000 0 37
TNF 0.038 0.023 -10000 0 -10000 0 0
VCAM1 0.012 0.086 -10000 0 -0.35 25 25
platelet activation 0.002 0.075 -10000 0 -0.4 16 16
MAPKKK cascade -0.003 0.03 0.12 3 -0.14 6 9
IL18 -0.001 0.04 0.14 1 -0.18 9 10
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.073 11 11
LEF -0.002 0.01 -10000 0 -0.073 11 11
CASP1 -0.006 0.033 -10000 0 -0.11 35 35
mol:cAMP 0.002 0.075 -10000 0 -0.41 16 16
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
IL2 signaling events mediated by PI3K

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
BCL2L1 0.02 0.091 -10000 0 -10000 0 0
UGCG 0.029 0.11 -10000 0 -0.64 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT 0 0.18 0.33 1 -0.44 31 32
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.03 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 -10000 0 -0.51 39 39
FRAP1 -0.036 0.24 -10000 0 -0.6 40 40
FOXO3 0.005 0.18 0.39 2 -0.62 18 20
AKT1 0.002 0.2 0.38 1 -0.57 28 29
GAB2 0.027 0.014 -10000 0 -10000 0 0
SMPD1 0.009 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 -0.028 0.097 -10000 0 -0.34 44 44
CALM1 0.033 0.006 -10000 0 -10000 0 0
cell proliferation 0.049 0.12 0.42 1 -0.53 7 8
EIF3A 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.004 0.13 -10000 0 -0.4 44 44
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 -0.021 0.17 -10000 0 -0.54 47 47
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 0.54 1 -0.94 30 31
MYB -0.047 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 14 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.035 0.13 -10000 0 -0.71 9 9
mol:PI-3-4-5-P3 0.03 0.13 0.32 1 -0.37 14 15
Rac1/GDP -0.011 0.096 -10000 0 -0.31 44 44
T cell proliferation 0.028 0.12 0.31 1 -0.35 14 15
SHC1 0.025 0.016 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.028 0.094 25 -0.068 41 66
PRKCZ 0.027 0.12 0.31 1 -0.36 14 15
NF kappa B1 p50/RelA -0.008 0.22 -10000 0 -0.52 38 38
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.021 0.097 -10000 0 -0.39 8 8
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL2RA 0.039 0.035 -10000 0 -10000 0 0
IL2RB 0.035 0.023 -10000 0 -10000 0 0
TERT 0.032 0.028 -10000 0 -0.54 1 1
E2F1 0.013 0.14 0.34 1 -0.4 46 47
SOS1 0.032 0.009 -10000 0 -10000 0 0
RPS6 0.032 0.026 -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 0.037 -10000 0 -10000 0 0
actin cytoskeleton organization 0.028 0.12 0.31 1 -0.35 14 15
GRB2 0.032 0.02 0.18 1 -10000 0 1
IL2 0.032 0.029 -10000 0 -0.54 1 1
PIK3CA 0.032 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.1 -10000 0 -0.29 44 44
LCK 0.047 0.045 -10000 0 -10000 0 0
BCL2 -0.12 0.38 0.52 1 -0.84 103 104
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.038 0.15 -10000 0 -0.43 44 44
KLHL20 0.042 0.12 0.31 41 -0.28 10 51
CYFIP2 0.05 0.047 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.12 0.34 4 -0.3 25 29
ENAH -0.033 0.14 -10000 0 -0.43 37 37
AP1M1 0.034 0.006 -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 0.029 0.052 -10000 0 -0.54 4 4
CDC42/GTP 0.009 0.076 -10000 0 -0.28 3 3
ABI1/Sra1/Nap1 -0.016 0.04 -10000 0 -0.18 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.049 0.095 -10000 0 -0.31 26 26
RAPGEF1 -0.031 0.14 0.34 1 -0.4 38 39
CTNND1 0.033 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.032 0.16 -10000 0 -0.44 51 51
CRK -0.028 0.14 0.35 1 -0.42 43 44
E-cadherin/gamma catenin/alpha catenin 0.037 0.089 -10000 0 -0.34 21 21
alphaE/beta7 Integrin 0.046 0.016 -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 -0.041 0.16 -10000 0 -0.43 50 50
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.061 -10000 0 -0.21 10 10
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 -0.022 0.081 -10000 0 -0.28 7 7
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 0.095 -10000 0 -0.4 21 21
TIAM1 0.035 0.012 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.046 0.089 -10000 0 -0.29 26 26
AKT1 -0.007 0.057 -10000 0 -0.2 1 1
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
CDH1 0.006 0.12 -10000 0 -0.54 22 22
RhoA/GDP 0 0.12 0.33 4 -0.35 6 10
actin cytoskeleton organization 0.037 0.094 0.26 43 -0.2 10 53
CDC42/GDP 0 0.12 0.31 6 -0.3 25 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 0.096 -10000 0 -0.31 26 26
E-cadherin/Ca2+/beta catenin/alpha catenin 0.032 0.082 -10000 0 -0.29 26 26
mol:GDP -0.019 0.12 0.33 4 -0.35 25 29
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 5 8
RAC1/GTP/IQGAP1 0.044 0.012 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.049 0.012 -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 0.016 0.068 0.2 26 -0.23 11 37
NME1 0.031 0.011 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.037 0.16 -10000 0 -0.44 47 47
regulation of cell-cell adhesion -0.001 0.061 -10000 0 -0.24 3 3
WASF2 0.02 0.044 0.12 32 -0.13 1 33
Rap1/GTP 0.012 0.087 0.27 2 -0.31 3 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.059 0.092 -10000 0 -0.3 21 21
CCND1 0.017 0.08 0.25 20 -0.28 11 31
VAV2 -0.02 0.19 0.41 1 -0.67 16 17
RAP1/GDP 0.009 0.1 0.31 3 -0.35 4 7
adherens junction assembly -0.035 0.16 -10000 0 -0.42 48 48
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 0.18 1 -10000 0 1
regulation of heterotypic cell-cell adhesion 0.044 0.089 -10000 0 -0.29 24 24
E-cadherin/beta catenin -0.007 0.089 -10000 0 -0.34 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.039 0.16 -10000 0 -0.43 49 49
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.14 0.28 59 -0.44 15 74
E-cadherin/beta catenin/alpha catenin 0.036 0.096 -10000 0 -0.34 26 26
ITGAE 0.031 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.033 0.17 -10000 0 -0.45 51 51
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.035 0.074 0.32 1 -0.34 8 9
ACTA1 0.007 0.083 0.24 3 -0.32 5 8
NUMA1 0.027 0.082 0.29 2 -0.38 8 10
SPTAN1 0.02 0.068 0.3 5 -0.48 1 6
LIMK1 0.033 0.074 0.28 12 -0.48 1 13
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BIRC2 0.03 0.011 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
CASP10 -0.003 0.04 0.24 8 -0.35 1 9
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 -10000 0 -0.001 37 37
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 -0.055 0.14 0.35 1 -0.29 90 91
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 0.011 0.095 -10000 0 -0.39 22 22
TRADD 0.03 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 0.008 0.15 -10000 0 -0.68 20 20
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.024 0.074 0.29 2 -0.36 4 6
APAF1 0.034 0.003 -10000 0 -10000 0 0
CASP6 0.023 0.14 -10000 0 -0.85 11 11
TRAF2 0.035 0.012 -10000 0 -10000 0 0
ICAD/CAD 0.017 0.062 0.28 2 -0.47 1 3
CASP7 0.016 0.082 0.26 26 -0.29 5 31
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 -0.33 3 20
actin filament polymerization 0.016 0.13 0.27 61 -0.29 10 71
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.023 0.046 0.21 8 -0.2 5 13
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 0.085 0.24 6 -0.3 17 23
JNK cascade -0.011 0.095 0.39 22 -10000 0 22
CASP3 0.024 0.07 0.31 3 -0.37 2 5
LMNB2 0.018 0.13 0.35 2 -0.51 21 23
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CASP4 0.025 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 0.041 0.097 -10000 0 -0.64 8 8
stress fiber formation 0.02 0.068 0.29 4 -0.37 2 6
GZMB 0.022 0.046 0.29 7 -0.4 2 9
CASP1 -0.017 0.12 -10000 0 -0.4 41 41
LMNB1 0.042 0.13 0.35 3 -0.57 13 16
APP 0.007 0.15 -10000 0 -0.69 20 20
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
response to stress 0 0 0.001 17 -0.001 27 44
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM 0.015 0.11 0.31 2 -0.44 10 12
LMNA 0.022 0.082 0.34 2 -0.38 8 10
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.088 -10000 0 -0.3 22 22
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 -0.017 0.13 0.3 10 -0.28 61 71
GAS2 -0.16 0.15 0.3 5 -0.28 247 252
positive regulation of apoptosis 0.035 0.12 0.38 2 -0.48 17 19
PRF1 0.037 0.022 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
GNB1/GNG2 0.048 0.088 -10000 0 -0.34 23 23
forebrain development -0.043 0.2 -10000 0 -0.58 46 46
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 -0.44 11 12
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 0.032 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
XPO1 0.036 0.006 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.19 -10000 0 -0.66 26 26
SAP30 0.033 0.009 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 -10000 0 -0.54 22 22
MIM/GLI2A 0.033 0.029 0.31 1 -10000 0 1
IFT88 0.031 0.027 -10000 0 -0.54 1 1
GNAI3 0.034 0.006 -10000 0 -10000 0 0
GLI2 0.016 0.084 -10000 0 -0.37 14 14
GLI3 0.017 0.11 0.3 1 -0.43 14 15
CSNK1D 0.032 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.009 -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 -0.36 74 74
SIN3B 0.035 0.014 -10000 0 -10000 0 0
SIN3A 0.033 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.025 0.11 -10000 0 -0.45 15 15
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 -0.043 0.2 -10000 0 -0.58 46 46
SPOP 0.031 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 -0.043 0.2 -10000 0 -0.58 46 46
SUFU 0.019 0.049 -10000 0 -0.38 1 1
LGALS3 -0.03 0.18 -10000 0 -0.54 56 56
catabolic process 0.037 0.13 0.32 1 -0.57 13 14
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 -0.59 46 46
RAB23 0.035 0.014 -10000 0 -10000 0 0
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
IFT172 0.033 0.026 -10000 0 -0.54 1 1
RBBP7 0.037 0.022 -10000 0 -10000 0 0
Su(fu)/Galectin3 -0.009 0.13 -10000 0 -0.33 59 59
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 -0.083 0.17 -10000 0 -0.4 70 70
PTCH1 -0.038 0.18 -10000 0 -0.71 16 16
MIM/GLI1 -0.024 0.18 -10000 0 -0.66 23 23
CREBBP 0.002 0.12 -10000 0 -0.36 49 49
Su(fu)/SIN3/HDAC complex 0.015 0.1 -10000 0 -0.47 15 15
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.028 0.016 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.047 0.14 -10000 0 -0.45 16 16
NEF 0.011 0.022 -10000 0 -10000 0 0
NFKBIA 0.029 0.037 -10000 0 -0.35 1 1
BIRC3 0.008 0.14 0.38 1 -0.49 26 27
CYCS 0.033 0.13 0.27 17 -0.44 14 31
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CD247 0.029 0.11 0.23 17 -0.55 15 32
MAP2K7 0.038 0.19 0.34 3 -0.69 19 22
protein ubiquitination 0.014 0.11 0.37 2 -0.38 16 18
CRADD 0.034 0.005 -10000 0 -10000 0 0
DAXX 0.034 0.008 -10000 0 -10000 0 0
FAS -0.003 0.14 -10000 0 -0.54 33 33
BID 0.032 0.13 0.25 9 -0.45 16 25
NF-kappa-B/RelA/I kappa B alpha 0.06 0.087 -10000 0 -0.3 16 16
TRADD 0.03 0.012 -10000 0 -10000 0 0
MAP3K5 0.003 0.13 -10000 0 -0.54 26 26
CFLAR 0.033 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 0.087 -10000 0 -0.31 16 16
MAPK8 0.037 0.17 0.4 4 -0.63 19 23
APAF1 0.034 0.003 -10000 0 -10000 0 0
TRAF1 0.035 0.015 -10000 0 -10000 0 0
TRAF2 0.035 0.012 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.036 0.14 0.26 8 -0.44 19 27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.14 0.27 1 -0.48 18 19
CHUK 0.012 0.12 0.38 2 -0.42 16 18
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.12 -10000 0 -0.33 41 41
TCRz/NEF 0.031 0.093 0.24 17 -0.41 15 32
TNF 0.038 0.023 -10000 0 -10000 0 0
FASLG 0.036 0.11 0.31 43 -0.37 15 58
NFKB1 0.03 0.035 -10000 0 -0.17 1 1
TNFR1A/BAG4/TNF-alpha 0.053 0.035 -10000 0 -10000 0 0
CASP6 0.053 0.15 -10000 0 -0.54 16 16
CASP7 0.019 0.19 0.4 16 -0.48 40 56
RELA 0.03 0.034 -10000 0 -0.17 1 1
CASP2 0.033 0.006 -10000 0 -10000 0 0
CASP3 0.016 0.19 0.4 15 -0.47 43 58
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 0.008 -10000 0 -10000 0 0
MAP3K14 0.015 0.13 0.36 1 -0.46 17 18
APAF-1/Caspase 9 0.02 0.13 -10000 0 -0.38 26 26
BCL2 -0.007 0.18 0.45 6 -0.55 23 29
Signaling events mediated by PRL

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
CCNE1 0.058 0.056 -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 0.1 -10000 0 -0.53 17 17
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 0.042 0.048 -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 -0.39 413 413
CDK2/Cyclin E1 -0.042 0.11 -10000 0 -0.47 16 16
MAPK3 0.015 0.018 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.051 0.017 -10000 0 -10000 0 0
MAPK1 0.015 0.019 -10000 0 -10000 0 0
PTP4A1 -0.22 0.13 -10000 0 -10000 0 0
PTP4A3 0.03 0.025 -10000 0 -10000 0 0
PTP4A2 0.036 0.021 -10000 0 -10000 0 0
ITGB1 0.015 0.019 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
RAC1 -0.058 0.079 -10000 0 -0.49 8 8
Rab GGTase beta/Rab GGTase alpha 0.049 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 -0.53 9 9
RHOA -0.064 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 -0.28 2 2
ROCK1 -0.082 0.095 0.27 1 -0.4 22 23
RABGGTB 0.034 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 0.011 0.18 2 -10000 0 2
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.034 0.094 -9999 0 -0.34 25 25
E-cadherin/beta catenin 0.018 0.1 -9999 0 -0.4 26 26
CTNNB1 0.029 0.052 -9999 0 -0.54 4 4
JUP 0.033 0.01 -9999 0 -10000 0 0
CDH1 0.006 0.12 -9999 0 -0.54 22 22
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.016 0.13 -9999 0 -0.48 25 25
FZD6 0.007 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 0.091 -9999 0 -0.54 13 13
WNT5A 0.01 0.13 -9999 0 -0.54 25 25
WNT11 0.024 0.079 -9999 0 -0.54 9 9
BCR signaling 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
JUN 0.016 0.15 0.36 6 -0.39 16 22
IKBKB 0.05 0.092 0.35 8 -0.35 2 10
AKT1 0.062 0.12 0.31 47 -0.25 2 49
IKBKG 0.056 0.077 0.33 8 -0.28 3 11
CALM1 0.031 0.086 0.27 9 -0.35 9 18
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
MAP3K1 0.068 0.14 0.42 5 -0.49 12 17
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.031 0.091 0.28 8 -0.34 12 20
DOK1 0.036 0.016 0.18 6 -10000 0 6
AP-1 -0.073 0.11 0.32 1 -0.24 62 63
LYN 0.03 0.015 0.18 2 -10000 0 2
BLNK 0.039 0.026 0.18 17 -10000 0 17
SHC1 0.027 0.014 -10000 0 -10000 0 0
BCR complex 0.041 0.07 0.26 3 -0.4 10 13
CD22 0.015 0.088 0.3 4 -0.45 11 15
CAMK2G 0.029 0.084 0.26 11 -0.37 6 17
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.023 0.044 -10000 0 -0.28 6 6
GO:0007205 0.032 0.092 0.28 8 -0.34 12 20
SYK 0.038 0.026 -10000 0 -10000 0 0
ELK1 0.033 0.09 0.28 8 -0.34 10 18
NFATC1 0.064 0.11 0.3 14 -0.41 8 22
B-cell antigen/BCR complex 0.041 0.07 0.26 3 -0.4 10 13
PAG1/CSK 0.043 0.028 0.26 1 -10000 0 1
NFKBIB 0.043 0.053 0.21 9 -0.13 9 18
HRAS 0.044 0.095 0.26 19 -0.34 9 28
NFKBIA 0.043 0.052 0.2 10 -0.13 8 18
NF-kappa-B/RelA/I kappa B beta 0.047 0.048 0.2 10 -10000 0 10
RasGAP/Csk 0.064 0.079 0.35 2 -0.39 6 8
mol:GDP 0.032 0.089 0.28 8 -0.32 12 20
PTEN 0.026 0.067 -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 0.048 0.2 10 -10000 0 10
GRB2 0.034 0.018 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.049 0.15 0.38 9 -0.48 14 23
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.03 0.09 0.29 7 -0.35 11 18
CSK 0.034 0.011 -10000 0 -10000 0 0
FOS -0.15 0.14 0.27 1 -0.36 60 61
CHUK 0.053 0.084 0.33 8 -0.34 5 13
IBTK 0.033 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.054 0.091 0.3 4 -0.36 6 10
PTPN6 0.031 0.1 0.29 10 -0.55 6 16
RELA 0.034 0.005 -10000 0 -10000 0 0
BCL2A1 0.042 0.044 0.2 9 -10000 0 9
VAV2 0.045 0.11 0.32 3 -0.57 6 9
ubiquitin-dependent protein catabolic process 0.046 0.052 0.21 9 -0.12 13 22
BTK 0.017 0.09 -10000 0 -0.96 4 4
CD19 0.022 0.092 0.3 4 -0.43 11 15
MAP4K1 0.037 0.021 -10000 0 -10000 0 0
CD72 0.062 0.059 -10000 0 -10000 0 0
PAG1 0.031 0.025 -10000 0 -10000 0 0
MAPK14 0.065 0.13 0.4 8 -0.42 12 20
SH3BP5 0.018 0.094 -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 0.28 10 -0.44 7 17
RAF1 0.042 0.09 0.26 14 -0.33 8 22
RasGAP/p62DOK/SHIP 0.054 0.071 0.3 1 -0.37 6 7
CD79A 0.042 0.034 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.071 0.11 0.32 1 -0.24 58 59
RASA1 0.034 0.012 -10000 0 -10000 0 0
MAPK3 0.048 0.092 0.28 19 -0.34 4 23
MAPK1 0.038 0.083 0.3 6 -0.34 4 10
CD72/SHP1 0.093 0.12 0.37 19 -0.52 6 25
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.065 0.13 0.38 9 -0.42 12 21
actin cytoskeleton organization 0.071 0.11 0.32 18 -0.49 6 24
NF-kappa-B/RelA 0.093 0.088 0.36 9 -0.22 2 11
Calcineurin 0.042 0.091 0.28 1 -0.34 8 9
PI3K -0.002 0.074 -10000 0 -0.4 7 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.032 0.095 0.3 9 -0.42 10 19
SOS1 0.034 0.004 -10000 0 -10000 0 0
Bam32/HPK1 0.065 0.16 -10000 0 -0.64 15 15
DAPP1 0.031 0.16 -10000 0 -0.71 16 16
cytokine secretion 0.063 0.11 0.29 17 -0.38 8 25
mol:DAG 0.03 0.09 0.29 7 -0.35 11 18
PLCG2 0.021 0.073 -10000 0 -0.54 8 8
MAP2K1 0.039 0.087 0.26 10 -0.37 4 14
B-cell antigen/BCR complex/FcgammaRIIB 0.046 0.074 0.35 1 -0.43 7 8
mol:PI-3-4-5-P3 0.031 0.1 0.3 22 -0.3 6 28
ETS1 0.026 0.081 0.26 12 -0.34 7 19
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.075 0.079 0.43 1 -0.3 9 10
B-cell antigen/BCR complex/LYN 0.016 0.084 -10000 0 -0.47 11 11
MALT1 0.033 0.009 -10000 0 -10000 0 0
TRAF6 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.063 0.11 0.32 16 -0.52 6 22
B-cell antigen/BCR complex/LYN/SYK 0.043 0.099 0.35 4 -0.53 6 10
CARD11 0.034 0.094 0.29 12 -0.34 10 22
FCGR2B 0.026 0.039 -10000 0 -0.54 2 2
PPP3CA 0.03 0.051 -10000 0 -0.54 4 4
BCL10 0.033 0.007 -10000 0 -10000 0 0
IKK complex 0.045 0.059 0.18 32 -0.14 1 33
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDPK1 0.038 0.096 0.27 34 -0.22 4 38
PPP3CB 0.034 0.004 -10000 0 -10000 0 0
PPP3CC 0.024 0.046 -10000 0 -0.54 3 3
POU2F2 0.036 0.039 0.24 5 -10000 0 5
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.087 0.075 0.31 1 -0.28 5 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.033 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.099 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 -0.004 0.097 0.17 1 -0.28 36 37
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 0.075 0.089 0.3 28 -0.27 5 33
AKT1 0.018 0.11 0.32 10 -0.32 17 27
MAP2K1 0.026 0.074 0.26 10 -0.26 5 15
MAP3K11 0.043 0.07 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 0.046 0.09 -10000 0 -0.44 7 7
Rap1/GTP 0.018 0.035 -10000 0 -10000 0 0
CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.095 0.075 -10000 0 -0.3 5 5
CEBPB 0.057 0.14 0.4 9 -0.59 5 14
STAT3 0.033 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.092 0.1 -10000 0 -0.75 4 4
STAT1 0.059 0.093 0.29 33 -0.27 5 38
CALM1 0.033 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.061 0.064 -10000 0 -0.55 1 1
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.075 0.09 0.31 27 -0.26 5 32
CEBPB/PTGES2/Cbp/p300 0.039 0.085 0.29 3 -0.37 5 8
mol:Ca2+ 0.082 0.072 0.3 1 -0.28 5 6
MAPK3 0.042 0.12 -10000 0 -0.63 9 9
STAT1 (dimer) 0.02 0.15 0.32 3 -0.43 25 28
MAPK1 0.01 0.2 0.39 1 -0.7 33 34
JAK2 0.035 0.016 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
JAK1 0.036 0.013 -10000 0 -10000 0 0
CAMK2D 0.03 0.052 -10000 0 -0.54 4 4
DAPK1 0.058 0.11 0.41 12 -0.35 4 16
SMAD7 0.022 0.071 0.23 7 -0.19 3 10
CBL/CRKL/C3G 0.069 0.069 0.33 3 -0.26 3 6
PI3K 0.048 0.12 -10000 0 -0.31 33 33
IFNG 0.061 0.064 -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 0.034 0.006 -10000 0 -10000 0 0
CAMK2B 0.039 0.069 -10000 0 -0.54 5 5
FRAP1 0.002 0.1 0.29 11 -0.3 16 27
PRKCD 0.018 0.11 0.32 11 -0.32 14 25
RAP1B 0.033 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.004 0.097 0.17 1 -0.28 36 37
PTPN2 0.033 0.007 -10000 0 -10000 0 0
EP300 0.033 0.009 -10000 0 -10000 0 0
IRF1 0.066 0.12 0.4 35 -10000 0 35
STAT1 (dimer)/PIASy 0.072 0.091 0.31 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 4 7
CASP1 0.005 0.11 0.25 11 -0.27 57 68
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 0.031 0.1 -10000 0 -0.3 33 33
RAP1/GDP 0.051 0.052 -10000 0 -10000 0 0
CBL 0.041 0.068 0.31 4 -0.27 5 9
MAP3K1 0.045 0.071 0.3 5 -0.27 6 11
PIAS1 0.033 0.007 -10000 0 -10000 0 0
PIAS4 0.034 0.016 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.004 0.097 0.17 1 -0.28 36 37
PTPN11 0.044 0.072 0.27 10 -0.28 5 15
CREBBP 0.031 0.028 -10000 0 -0.54 1 1
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.016 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.041 0.028 -10000 0 -10000 0 0
CDKN1B 0.018 0.071 0.31 3 -0.35 7 10
CDKN1A 0.02 0.067 0.28 2 -0.34 9 11
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.031 0.019 -10000 0 -10000 0 0
FOXO3 0.023 0.063 0.28 1 -0.36 6 7
AKT1 0.022 0.064 -10000 0 -0.36 9 9
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 0.019 0.062 -10000 0 -0.34 9 9
AKT1/ASK1 0.033 0.096 -10000 0 -0.35 9 9
BAD/YWHAZ 0.051 0.032 -10000 0 -10000 0 0
RICTOR 0.033 0.006 -10000 0 -10000 0 0
RAF1 0.034 0.006 -10000 0 -10000 0 0
JNK cascade -0.032 0.093 0.34 9 -10000 0 9
TSC1 0.021 0.057 -10000 0 -0.36 6 6
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
AKT1/RAF1 0.055 0.077 0.3 2 -0.34 9 11
EP300 0.032 0.009 -10000 0 -10000 0 0
mol:GDP 0.022 0.063 -10000 0 -0.35 9 9
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.027 0.08 0.28 22 -0.34 9 31
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
TBC1D4 0.002 0.048 0.25 2 -0.32 10 12
MAP3K5 0.003 0.13 -10000 0 -0.54 26 26
MAPKAP1 0.034 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.041 0.079 0.28 9 -0.26 3 12
YWHAH 0.033 0.014 -10000 0 -10000 0 0
AKT1S1 0.023 0.068 -10000 0 -0.34 9 9
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 0.084 0.32 4 -0.33 8 12
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 0.033 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.062 -10000 0 -0.36 5 5
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.054 -10000 0 -0.33 9 9
CHUK 0.02 0.061 -10000 0 -0.34 8 8
BAD/BCL-XL 0.056 0.074 0.3 2 -0.38 4 6
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 0.043 0.11 0.37 4 -0.4 12 16
PDPK1 0.031 0.01 -10000 0 -10000 0 0
MDM2 0.024 0.071 0.28 4 -0.34 9 13
MAPKKK cascade -0.055 0.076 0.34 9 -0.3 2 11
MDM2/Cbp/p300 0.06 0.082 0.36 2 -0.4 3 5
TSC1/TSC2 0.025 0.08 0.27 23 -0.33 9 32
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.078 0.35 2 -0.35 4 6
glucose import -0.15 0.15 0.21 1 -0.31 237 238
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.055 0.19 1 -0.3 4 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 0.21 1 -0.31 237 238
GSK3A 0.021 0.065 -10000 0 -0.34 9 9
FOXO1 -0.006 0.096 -10000 0 -0.43 9 9
GSK3B 0.021 0.062 0.28 1 -0.34 8 9
SFN 0.032 0.04 -10000 0 -0.54 2 2
G1/S transition of mitotic cell cycle 0.031 0.076 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 0.009 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.004 0.13 0.28 1 -0.46 21 22
BAG4 0.028 0.016 -10000 0 -10000 0 0
BAD 0.007 0.047 0.18 3 -0.18 8 11
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BAX 0.007 0.052 0.26 3 -0.19 4 7
EnzymeConsortium:3.1.4.12 0.003 0.032 0.09 4 -0.097 21 25
IKBKB 0.012 0.13 0.35 1 -0.45 15 16
MAP2K2 0.011 0.059 0.23 10 -0.24 1 11
MAP2K1 0.011 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 0.031 0.14 0.33 7 -0.44 20 27
MAP2K4 0.007 0.052 0.19 3 -0.23 6 9
protein ubiquitination 0.002 0.13 0.36 3 -0.44 20 23
EnzymeConsortium:2.7.1.37 0.01 0.063 0.24 10 -0.24 2 12
response to UV 0 0.001 0.003 12 -0.002 1 13
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 0.05 0.15 4 -0.15 20 24
I-kappa-B-alpha/RELA/p50/ubiquitin 0.043 0.014 -10000 0 -0.14 1 1
MADD 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.054 0.2 2 -0.21 10 12
TRADD 0.03 0.012 -10000 0 -10000 0 0
RELA/p50 0.034 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.06 0.23 11 -0.24 1 12
MAPK1 0.01 0.068 0.23 11 -0.24 4 15
p50/RELA/I-kappa-B-alpha 0.048 0.016 -10000 0 -0.17 1 1
FADD 0.026 0.14 0.3 8 -0.46 18 26
KSR1 0.011 0.057 0.2 14 -0.18 8 22
MAPK8 0.004 0.056 0.23 6 -0.23 6 12
TRAF2 0.035 0.012 -10000 0 -10000 0 0
response to radiation 0 0 0.003 2 -10000 0 2
CHUK -0.007 0.12 -10000 0 -0.44 21 21
TNF R/SODD 0.038 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.025 0.07 0.19 21 -0.18 7 28
IKBKG -0.007 0.13 0.45 1 -0.44 21 22
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.003 0.14 -10000 0 -0.45 25 25
RELA 0.034 0.005 -10000 0 -10000 0 0
RIPK1 0.034 0.006 -10000 0 -10000 0 0
AIFM1 0.024 0.069 0.19 19 -0.18 8 27
TNF/TNF R/SODD 0.053 0.035 -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 0.018 0.13 -10000 0 -0.65 16 16
NSMAF 0.015 0.14 0.28 5 -0.45 19 24
response to hydrogen peroxide 0 0.001 0.003 12 -0.002 1 13
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
PLK2 and PLK4 events

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
PLK2 0.016 0.1 -9999 0 -0.54 17 17
PLK4 0.055 0.052 -9999 0 -10000 0 0
regulation of centriole replication 0.023 0.086 -9999 0 -0.38 16 16
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0.14 -10000 0 -10000 0 0
CRKL 0.015 0.067 0.3 3 -10000 0 3
mol:DAG 0.025 0.074 -10000 0 -10000 0 0
HRAS 0.051 0.089 0.32 13 -10000 0 13
MAPK8 0.047 0.075 0.26 15 -0.32 1 16
RAP1A 0.016 0.067 0.29 4 -10000 0 4
GAB1 0.017 0.066 0.29 3 -10000 0 3
MAPK14 0.048 0.073 0.26 15 -10000 0 15
EPO 0.046 0.052 0.18 1 -10000 0 1
PLCG1 0.025 0.074 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.028 0.024 -10000 0 -10000 0 0
RAPGEF1 0.034 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.053 0.079 -10000 0 -0.35 11 11
GAB1/SHC/GRB2/SOS1 0.043 0.064 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.053 0.047 -10000 0 -10000 0 0
IRS2 -0.052 0.14 0.25 1 -0.32 90 91
STAT1 0.042 0.12 -10000 0 -0.36 2 2
STAT5B 0.029 0.099 -10000 0 -10000 0 0
cell proliferation 0.025 0.08 0.21 60 -0.3 1 61
GAB1/SHIP/PIK3R1/SHP2/SHC 0.002 0.086 -10000 0 -0.26 22 22
TEC 0.016 0.067 0.29 4 -10000 0 4
SOCS3 0.018 0.087 -10000 0 -0.54 12 12
STAT1 (dimer) 0.042 0.11 -10000 0 -0.35 2 2
JAK2 0.031 0.018 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
EPO/EPOR (dimer)/JAK2 0.068 0.091 -10000 0 -10000 0 0
EPO/EPOR 0.053 0.047 -10000 0 -10000 0 0
LYN 0.022 0.026 -10000 0 -10000 0 0
TEC/VAV2 0.033 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 0.055 0.058 -10000 0 -10000 0 0
mol:IP3 0.025 0.074 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.069 0.15 -10000 0 -0.31 122 122
SH2B3 0.033 0.016 -10000 0 -10000 0 0
NFKB1 0.048 0.073 0.26 14 -10000 0 14
EPO/EPOR (dimer)/JAK2/SOCS3 0.024 0.055 -10000 0 -0.27 10 10
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 0.041 0.065 -10000 0 -10000 0 0
SOS1 0.034 0.004 -10000 0 -10000 0 0
PLCG2 0.021 0.073 -10000 0 -0.54 8 8
CRKL/CBL/C3G 0.039 0.077 0.3 3 -10000 0 3
VAV2 0.018 0.068 0.3 4 -10000 0 4
CBL 0.014 0.066 0.29 4 -10000 0 4
SHC/Grb2/SOS1 0.03 0.059 -10000 0 -10000 0 0
STAT5A 0.028 0.1 -10000 0 -0.28 4 4
GRB2 0.034 0.018 -10000 0 -10000 0 0
STAT5 (dimer) 0.025 0.15 -10000 0 -0.37 16 16
LYN/PLCgamma2 0.029 0.061 0.25 1 -0.38 9 10
PTPN11 0.034 0.004 -10000 0 -10000 0 0
BTK 0.02 0.071 0.29 4 -10000 0 4
BCL2 -0.091 0.36 -10000 0 -0.82 98 98
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.034 0.005 -10000 0 -10000 0 0
SPHK1 0.033 0.06 -10000 0 -0.54 4 4
GNAI2 0.033 0.01 -10000 0 -10000 0 0
mol:S1P 0.02 0.034 0.2 2 -0.26 4 6
GNAO1 0.03 0.012 -10000 0 -10000 0 0
mol:Sphinganine-1-P 0.018 0.045 -10000 0 -0.4 4 4
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.053 0.04 -10000 0 -0.21 2 2
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.045 0.017 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.011 0.031 -10000 0 -0.22 5 5
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
S1P/S1P5/G12 0.042 0.04 -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 0.026 0.062 -10000 0 -0.54 6 6
GNA14 0.043 0.068 -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
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.033 0.006 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 65 65
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
NUDC 0.033 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.07 0.091 -10000 0 -0.32 20 20
CaM/Ca2+ 0.025 0.005 -10000 0 -10000 0 0
KATNA1 0.032 0.009 -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 0.034 0.006 -10000 0 -10000 0 0
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
PLA2G7 0.043 0.098 -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 0.073 0.047 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.035 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 -0.008 0.16 -10000 0 -0.36 80 80
YWHAE 0.031 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.041 0.078 0.38 2 -0.32 2 4
MAP1B -0.021 0.089 -10000 0 -0.29 49 49
RAC1 0.016 0.007 -10000 0 -10000 0 0
p35/CDK5 0.035 0.073 0.27 3 -0.28 13 16
RELN 0.012 0.11 -10000 0 -0.54 20 20
PAFAH/LIS1 0.04 0.067 -10000 0 -0.34 10 10
LIS1/CLIP170 0.034 0.014 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.032 0.069 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.008 0.13 -10000 0 -0.3 54 54
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.025 0.073 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 0.082 0.069 -10000 0 -10000 0 0
PAFAH1B2 0.03 0.012 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.005 0.075 -10000 0 -0.36 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.048 0.087 0.36 3 -0.31 2 5
LRP8 0.072 0.064 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.035 0.082 0.38 2 -0.32 2 4
P39/CDK5 0.036 0.072 0.27 2 -0.28 13 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.014 -10000 0 -10000 0 0
CDK5 0.006 0.076 0.28 2 -0.3 13 15
PPP2R5D 0.034 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 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.002 0.15 -10000 0 -0.32 80 80
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 80 80
CDC42 0.016 0.007 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.003 0.098 -10000 0 -10000 0 0
PLK1 0.13 0.22 0.69 9 -0.86 4 13
CDKN1B 0.099 0.18 0.59 4 -0.45 14 18
FOXO3 0.11 0.23 0.57 20 -0.62 16 36
KAT2B 0.02 0.031 0.087 36 -0.063 6 42
FOXO1/SIRT1 0.006 0.1 -10000 0 -0.33 9 9
CAT 0.055 0.36 0.79 4 -1.1 39 43
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
AKT1 0.053 0.046 0.22 1 -10000 0 1
FOXO1 0.001 0.11 -10000 0 -0.35 10 10
MAPK10 0.024 0.06 0.24 3 -0.29 10 13
mol:GTP 0 0.004 -10000 0 -10000 0 0
FOXO4 0.044 0.12 0.43 3 -0.4 6 9
response to oxidative stress 0.023 0.033 0.092 36 -0.063 8 44
FOXO3A/SIRT1 0.085 0.2 0.48 11 -0.6 15 26
XPO1 0.034 0.005 -10000 0 -10000 0 0
EP300 0.035 0.01 -10000 0 -10000 0 0
BCL2L11 0.057 0.082 -10000 0 -0.82 3 3
FOXO1/SKP2 0.016 0.1 -10000 0 -0.32 7 7
mol:GDP 0.023 0.033 0.092 36 -0.063 8 44
RAN 0.034 0.005 -10000 0 -10000 0 0
GADD45A 0.082 0.21 -10000 0 -0.8 15 15
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.036 0.15 -10000 0 -0.55 19 19
MST1 0.047 0.042 -10000 0 -10000 0 0
CSNK1D 0.032 0.008 -10000 0 -10000 0 0
CSNK1E 0.032 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.024 0.14 -10000 0 -0.46 28 28
YWHAB 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.029 0.042 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 0.095 0.2 0.56 9 -0.56 11 20
RBL2 0.035 0.32 0.58 1 -0.8 44 45
RAL/GDP 0.057 0.036 -10000 0 -10000 0 0
CHUK 0.048 0.043 -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 0.042 -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 0.61 21 -0.67 8 29
FOXO1-3a-4/beta catenin 0.096 0.22 0.58 8 -0.41 26 34
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.1 -10000 0 -0.32 7 7
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
SGK1 0.02 0.031 0.087 36 -0.063 6 42
CSNK1G3 0.033 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.02 -10000 0 -10000 0 0
ZFAND5 0.044 0.11 0.44 2 -10000 0 2
SFN 0.032 0.04 -10000 0 -0.54 2 2
CDK2 0.039 0.021 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.054 0.13 -10000 0 -0.48 15 15
CREBBP 0.032 0.028 -10000 0 -0.54 1 1
FBXO32 0.12 0.35 0.72 13 -1.1 26 39
BCL6 0.018 0.4 -10000 0 -1.1 55 55
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 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
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 0.084 0.36 2 -0.43 1 3
VEGFR2 homodimer/Frs2 0.022 0.087 -10000 0 -0.33 27 27
CAV1 -0.38 0.26 -10000 0 -0.54 365 365
CALM1 0.033 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.049 0.092 -10000 0 -0.3 22 22
endothelial cell proliferation 0.051 0.13 0.39 10 -0.44 8 18
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 -0.45 1 1
RP11-342D11.1 0.002 0.087 -10000 0 -0.54 4 4
CDH5 0.03 0.012 -10000 0 -10000 0 0
VEGFA homodimer 0.07 0.059 -10000 0 -0.31 2 2
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 0.006 0.12 -10000 0 -0.54 24 24
HRAS/GDP 0.031 0.08 -10000 0 -0.41 4 4
SH2D2A 0.043 0.048 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.056 0.12 -10000 0 -0.48 11 11
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.049 0.095 -10000 0 -0.47 1 1
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 0.034 0.018 -10000 0 -10000 0 0
PAK1 0.043 0.046 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.067 0.1 -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 0.066 0.091 -10000 0 -0.44 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.033 0.006 -10000 0 -10000 0 0
Nck/Pak 0.053 0.037 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.044 0.095 -10000 0 -0.31 25 25
mol:GDP 0.043 0.09 -10000 0 -0.43 4 4
mol:NADP 0.031 0.11 0.59 1 -0.44 12 13
eNOS/Hsp90 0.046 0.11 0.57 1 -0.43 10 11
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.02 0.092 0.37 1 -0.5 4 5
HIF1A/ARNT 0.037 0.042 -10000 0 -0.4 3 3
SHB 0.035 0.018 -10000 0 -10000 0 0
VEGFA 0.051 0.048 -10000 0 -10000 0 0
VEGFC 0.021 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 -0.45 1 1
PTPN6 0.033 0.015 -10000 0 -10000 0 0
EPAS1 0.01 0.13 -10000 0 -0.54 29 29
mol:L-citrulline 0.031 0.11 0.59 1 -0.44 12 13
ITGAV 0.033 0.028 -10000 0 -0.54 1 1
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.063 0.093 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.049 0.11 -10000 0 -0.47 7 7
VEGFR2/3 heterodimer 0.022 0.087 -10000 0 -0.34 28 28
VEGFB 0.033 0.007 -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 0.093 0.34 2 -0.45 4 6
VEGFA145/NRP2 0.06 0.038 0.26 1 -10000 0 1
VEGFR1/2 heterodimer 0.021 0.087 -10000 0 -0.34 28 28
KDR 0.003 0.096 -10000 0 -0.39 28 28
VEGFA165/NRP1/VEGFR2 homodimer 0.053 0.1 -10000 0 -0.54 4 4
SRC 0.033 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 0.051 0.092 -10000 0 -0.31 24 24
FES 0.018 0.095 -10000 0 -0.56 4 4
GAB1 0.041 0.1 -10000 0 -0.4 6 6
VEGFR2 homodimer/VEGFA homodimer/Src 0.05 0.089 -10000 0 -0.31 21 21
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
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 0.16 -10000 0 -0.45 41 41
VEGFR2 homodimer/VEGFA homodimer/Yes 0.048 0.093 -10000 0 -0.31 24 24
PI3K/GAB1 0.03 0.14 0.39 2 -0.45 13 15
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.075 0.096 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.031 0.1 -10000 0 -0.32 37 37
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
CDC42 0.019 0.097 0.37 1 -0.56 4 5
actin cytoskeleton reorganization 0.048 0.094 -10000 0 -0.46 1 1
PTK2 0.023 0.091 -10000 0 -0.44 3 3
EDG1 0.002 0.087 -10000 0 -0.54 4 4
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 0.002 0.086 -10000 0 -0.53 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.046 0.12 -10000 0 -0.63 7 7
PLCG1 0.02 0.092 0.37 1 -0.51 4 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.068 0.094 0.37 1 -0.45 1 2
IQGAP1 0.033 0.008 -10000 0 -10000 0 0
YES1 0.032 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 0.049 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 0.03 0.037 -10000 0 -0.54 2 2
VEGFB/NRP1 0.022 0.089 -10000 0 -0.52 4 4
mol:NO 0.031 0.11 0.59 1 -0.44 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 0.038 0.11 -10000 0 -0.63 7 7
VHL 0.036 0.018 -10000 0 -10000 0 0
ITGB3 0.035 0.019 -10000 0 -10000 0 0
NOS3 0.03 0.12 0.6 1 -0.49 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 0.084 0.36 1 -0.48 4 5
VCL 0.034 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.026 0.094 -10000 0 -0.54 4 4
VEGFR1/2 heterodimer/VEGFA homodimer 0.047 0.093 -10000 0 -0.31 24 24
VEGFA165/NRP2 0.06 0.038 0.26 1 -10000 0 1
MAPKKK cascade 0.063 0.12 0.39 7 -0.56 5 12
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFC homodimer 0.021 0.084 -10000 0 -0.54 11 11
NCK1 0.034 0.005 -10000 0 -10000 0 0
ROCK1 0.034 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 -0.56 4 4
PDPK1 0.004 0.098 -10000 0 -0.42 8 8
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.079 0.055 0.4 6 -10000 0 6
MAP4K1 0.037 0.021 -10000 0 -10000 0 0
MAP3K8 -0.04 0.19 -10000 0 -0.54 65 65
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.035 0.012 -10000 0 -10000 0 0
CRKL 0.033 0.008 -10000 0 -10000 0 0
MAP3K1 0.031 0.059 0.3 3 -0.3 4 7
JUN -0.04 0.13 -10000 0 -0.36 38 38
MAP3K7 0.029 0.053 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 0.025 -10000 0 -10000 0 0
LCP2 0.036 0.023 -10000 0 -10000 0 0
MAPK8 0.011 0.08 -10000 0 -0.58 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.037 0.061 0.3 3 -0.29 4 7
LAT/GRAP2/SLP76/HPK1/HIP-55 0.089 0.06 0.39 6 -10000 0 6
VEGFR1 specific signals

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
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 0.042 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.042 0.044 -10000 0 -0.3 3 3
CaM/Ca2+ 0.037 0.041 -10000 0 -10000 0 0
HIF1A 0.039 0.055 -10000 0 -0.54 4 4
GAB1 0.033 0.027 -10000 0 -0.54 1 1
AKT1 -0.008 0.099 -10000 0 -0.36 4 4
PLCG1 0.019 0.042 -10000 0 -10000 0 0
NOS3 0.019 0.087 -10000 0 -0.49 6 6
CBL 0.03 0.011 -10000 0 -10000 0 0
mol:NO 0.02 0.093 -10000 0 -0.48 7 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 0.062 0.051 -10000 0 -0.31 3 3
CALM1 0.033 0.006 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
eNOS/Hsp90 0.036 0.095 -10000 0 -0.46 7 7
endothelial cell proliferation 0.027 0.07 0.4 2 -10000 0 2
mol:Ca2+ 0.019 0.041 -10000 0 -10000 0 0
MAPK3 -0.006 0.035 -10000 0 -10000 0 0
MAPK1 -0.006 0.037 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
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 -0.54 365 365
VEGFA homodimer 0.05 0.047 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.047 0.049 -10000 0 -0.34 3 3
platelet activating factor biosynthetic process 0.019 0.073 0.34 2 -10000 0 2
PI3K 0.037 0.11 -10000 0 -0.56 1 1
PRKCA -0.004 0.04 0.26 1 -10000 0 1
PRKCB -0.002 0.039 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.038 0.039 -10000 0 -0.34 4 4
VEGFA 0.05 0.047 -10000 0 -10000 0 0
VEGFB 0.033 0.007 -10000 0 -10000 0 0
mol:IP3 0.019 0.042 -10000 0 -10000 0 0
RASA1 0.02 0.043 -10000 0 -10000 0 0
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer 0.021 0.043 -10000 0 -0.39 4 4
VEGFB homodimer 0.033 0.007 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.16 0.16 -10000 0 -0.48 26 26
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.035 0.11 -10000 0 -0.55 1 1
mol:L-citrulline 0.02 0.093 -10000 0 -0.48 7 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.075 0.059 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.061 0.05 -10000 0 -0.31 3 3
CD2AP 0.034 0.009 -10000 0 -10000 0 0
PI3K/GAB1 0.047 0.12 -10000 0 -0.54 1 1
PDPK1 -0.001 0.095 -10000 0 -0.36 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.062 0.049 -10000 0 -0.31 3 3
mol:NADP 0.02 0.093 -10000 0 -0.48 7 7
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.072 0.057 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.038 0.04 -10000 0 -0.34 4 4
Signaling events mediated by HDAC Class III

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
EP300 0.032 0.009 -10000 0 -10000 0 0
HDAC4 0.033 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.008 -10000 0 -10000 0 0
CDKN1A -0.01 0.043 -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 48 48
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 0.03 0.043 -10000 0 -0.54 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0.03 -10000 0 -0.4 2 2
PPARGC1A -0.023 0.17 -10000 0 -0.54 51 51
FHL2 -0.026 0.18 -10000 0 -0.54 55 55
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.044 0.016 -10000 0 -10000 0 0
HIST2H4A -0.005 0.008 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.022 0.032 -10000 0 -0.21 2 2
SIRT1 0.03 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.053 0.029 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.052 0.053 -10000 0 -0.23 3 3
apoptosis -0.061 0.022 -10000 0 -10000 0 0
SIRT1/PGC1A 0.004 0.12 -10000 0 -0.33 53 53
p53/SIRT1 0.037 0.024 0.42 1 -10000 0 1
SIRT1/FOXO4 0.032 0.045 -10000 0 -0.23 3 3
FOXO1/FHL2/SIRT1 -0.02 0.16 -10000 0 -0.34 91 91
HIST1H1E 0.039 0.043 -10000 0 -0.28 1 1
SIRT1/p300 0.044 0.016 -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 0.023 -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 0.04 0.038 -10000 0 -0.33 3 3
ACSS2 0.014 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.019 0.026 -10000 0 -0.34 2 2
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 0.023 0.085 -10000 0 -0.38 20 20
MAP2K4 0.015 0.085 -10000 0 -0.4 12 12
IKBKB 0.029 0.013 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.028 0.018 -10000 0 -10000 0 0
SMPD1 0.004 0.057 -10000 0 -0.27 18 18
IKBKG 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.014 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.022 0.086 -10000 0 -0.4 19 19
TRAIL/TRAILR3 0.023 0.086 -10000 0 -0.38 20 20
TRAIL/TRAILR1 0.023 0.085 -10000 0 -0.37 21 21
TRAIL/TRAILR4 0.023 0.085 -10000 0 -0.38 20 20
TRAIL/TRAILR1/DAP3/GTP 0.031 0.066 -10000 0 -0.31 13 13
IKK complex 0.024 0.074 -10000 0 -0.42 5 5
RIPK1 0.033 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.01 -10000 0 -10000 0 0
MAPK3 0 0.078 -10000 0 -0.4 19 19
MAP3K1 0.015 0.1 -10000 0 -0.46 14 14
TRAILR4 (trimer) 0.027 0.014 -10000 0 -10000 0 0
TRADD 0.03 0.012 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.028 0.018 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.002 0.081 -10000 0 -0.37 15 15
CFLAR 0.033 0.026 -10000 0 -0.54 1 1
MAPK1 0.001 0.076 -10000 0 -0.4 18 18
TRAIL/TRAILR1/FADD/TRADD/RIP 0.046 0.079 -10000 0 -0.29 14 14
mol:ceramide 0.004 0.057 -10000 0 -0.26 18 18
FADD 0.028 0.015 -10000 0 -10000 0 0
MAPK8 -0.001 0.1 -10000 0 -0.4 17 17
TRAF2 0.035 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 0.014 -10000 0 -10000 0 0
CASP10 0.024 0.077 0.34 3 -0.34 5 8
JNK cascade 0.023 0.085 -10000 0 -0.38 20 20
TRAIL (trimer) 0.011 0.11 -10000 0 -0.54 19 19
TNFRSF10C 0.028 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.035 0.064 -10000 0 -0.29 9 9
TRAIL/TRAILR2/FADD 0.032 0.074 -10000 0 -0.34 14 14
cell death 0.004 0.056 -10000 0 -0.26 18 18
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.002 0.081 -10000 0 -0.36 16 16
TRAILR2 (trimer) 0.027 0.016 -10000 0 -10000 0 0
CASP8 0.02 0.056 -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
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.073 0.038 -9999 0 -0.32 1 1
HDAC3 0.034 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.049 0.011 -9999 0 -10000 0 0
GATA1/HDAC5 0.049 0.012 -9999 0 -10000 0 0
GATA2/HDAC5 0.053 0.026 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.023 0.12 -9999 0 -0.34 50 50
HDAC9 0.035 0.017 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.033 0.11 -9999 0 -0.34 40 40
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 0.042 0.033 -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 0.048 0.024 -9999 0 -0.4 1 1
Histones 0.024 0.051 -9999 0 -0.28 4 4
ADRBK1 0.032 0.01 -9999 0 -10000 0 0
HDAC4 0.033 0.007 -9999 0 -10000 0 0
XPO1 0.034 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.045 0.033 -9999 0 -0.32 3 3
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 0.019 -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 0.06 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 -0.012 0.16 -9999 0 -0.54 40 40
SUMO1/HDAC4 0.051 0.051 -9999 0 -0.25 3 3
SRF 0.034 0.006 -9999 0 -10000 0 0
HDAC4/YWHAB 0.046 0.015 -9999 0 -10000 0 0
Tubulin 0.042 0.061 -9999 0 -0.4 9 9
HDAC4/14-3-3 E 0.045 0.019 -9999 0 -10000 0 0
GNB1 0.034 0.011 -9999 0 -10000 0 0
RANGAP1 0.038 0.03 -9999 0 -10000 0 0
BCL6/BCoR 0.004 0.13 -9999 0 -0.39 52 52
HDAC4/HDAC3/SMRT (N-CoR2) 0.066 0.017 -9999 0 -10000 0 0
HDAC4/SRF 0.065 0.022 -9999 0 -10000 0 0
HDAC4/ER alpha -0.027 0.2 -9999 0 -0.39 110 110
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.023 0.05 -9999 0 -0.28 4 4
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 -0.024 0.17 -9999 0 -0.54 51 51
HDAC4/CaMK II delta B 0.033 0.007 -9999 0 -10000 0 0
Hsp90/HDAC6 0.049 0.01 -9999 0 -10000 0 0
ESR1 -0.058 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 0.05 -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 0.024 0.076 -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 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
chromatin modification 0.1 0.086 -10000 0 -10000 0 0
CLOCK 0.039 0.01 -10000 0 -10000 0 0
TIMELESS/CRY2 0.069 0.069 -10000 0 -10000 0 0
DEC1/BMAL1 0.052 0.025 -10000 0 -0.4 1 1
ATR 0.034 0.006 -10000 0 -10000 0 0
NR1D1 0.04 0.053 -10000 0 -10000 0 0
ARNTL 0.037 0.028 -10000 0 -0.54 1 1
TIMELESS 0.059 0.091 -10000 0 -10000 0 0
NPAS2 0.041 0.02 -10000 0 -10000 0 0
CRY2 0.034 0.005 -10000 0 -10000 0 0
mol:CO -0.021 0.03 -10000 0 -0.11 54 54
CHEK1 0.087 0.075 -10000 0 -10000 0 0
mol:HEME 0.021 0.03 0.11 54 -10000 0 54
PER1 0.024 0.063 -10000 0 -0.54 6 6
BMAL/CLOCK/NPAS2 0.088 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 0.086 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.1 0.087 -10000 0 -10000 0 0
mol:NADPH 0.021 0.03 0.11 54 -10000 0 54
PER1/TIMELESS 0.059 0.074 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.035 0.01 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.027 0.026 -10000 0 -10000 0 0
CRKL 0.033 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
DOCK1 0.03 0.044 -10000 0 -0.54 3 3
ITGA4 0.04 0.029 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.085 0.033 -10000 0 -10000 0 0
EPO 0.054 0.05 0.18 70 -10000 0 70
alpha4/beta7 Integrin 0.054 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 0.053 0.023 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.063 0.037 -10000 0 -10000 0 0
lamellipodium assembly -0.004 0.11 -10000 0 -0.38 17 17
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.4 44 44
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 -0.02 0.17 -10000 0 -0.54 47 47
MADCAM1 0.034 0.013 -10000 0 -10000 0 0
cell adhesion 0.082 0.032 -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 0.021 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 -10000 0 -0.54 11 11
RHOA 0.033 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.081 0.035 -10000 0 -10000 0 0
BCAR1 -0.007 0.061 0.39 2 -0.3 11 13
EPOR 0.034 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.03 0.011 -10000 0 -10000 0 0
GIT1 0.032 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.11 -10000 0 -0.39 17 17
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.033 0.007 -10000 0 -10000 0 0
NFATC1 0.042 0.086 0.38 2 -0.4 5 7
NFATC2 0.002 0.074 0.29 1 -0.24 18 19
NFATC3 0.013 0.008 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.031 0.062 0.26 2 -0.26 8 10
Exportin 1/Ran/NUP214 0.066 0.017 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.054 0.065 -10000 0 -0.26 2 2
BCL2/BAX -0.035 0.17 -10000 0 -0.4 93 93
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 0.006 -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 -0.072 0.22 -10000 0 -0.54 93 93
FKBP8 0.034 0.009 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.037 0.059 0.26 6 -10000 0 6
KPNB1 0.032 0.009 -10000 0 -10000 0 0
KPNA2 0.058 0.06 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
SFN 0.032 0.04 -10000 0 -0.54 2 2
MAP3K8 -0.04 0.19 -10000 0 -0.54 65 65
NFAT4/CK1 alpha 0.028 0.038 -10000 0 -0.33 1 1
MEF2D/NFAT1/Cbp/p300 0.032 0.1 -10000 0 -0.31 19 19
CABIN1 0.031 0.061 0.26 2 -0.26 8 10
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 0.04 -10000 0 -0.4 2 2
YWHAB 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.032 0.026 -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 0.099 0.32 1 -0.42 7 8
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 0.064 -10000 0 -10000 0 0
BAD/BCL-XL 0.047 0.014 -10000 0 -10000 0 0
PRKCD 0.035 0.017 -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 0.034 0.006 -10000 0 -10000 0 0
PRKCQ 0.039 0.03 -10000 0 -10000 0 0
FKBP38/BCL2 -0.034 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 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.057 0.087 0.34 1 -0.38 5 6
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 0.054 0.086 0.34 1 -0.4 4 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.066 0.063 -10000 0 -0.26 2 2
NR4A1 0.024 0.14 -10000 0 -0.48 25 25
GSK3B 0.034 0.01 -10000 0 -10000 0 0
positive T cell selection 0.013 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.006 0.062 -10000 0 -0.29 6 6
RCH1/ KPNB1 0.062 0.046 -10000 0 -10000 0 0
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
PRKACA 0.034 0.006 -10000 0 -10000 0 0
AKAP5 0.04 0.051 0.18 32 -0.54 2 34
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 0.085 0.34 1 -0.38 5 6
CREBBP 0.028 0.029 -10000 0 -0.54 1 1
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
Retinoic acid receptors-mediated signaling

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
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.034 0.006 -10000 0 -10000 0 0
VDR 0.032 0.037 -10000 0 -0.54 2 2
Cbp/p300/PCAF 0.039 0.024 -10000 0 -0.34 1 1
EP300 0.032 0.009 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0 0.088 -10000 0 -0.3 17 17
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.008 0.12 0.27 4 -0.26 56 60
RAR alpha/9cRA/Cyclin H 0.077 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 -0.24 54 54
CDC2 0 0.003 -10000 0 -10000 0 0
response to UV 0.001 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.046 0.047 -10000 0 -0.25 4 4
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 0.022 0.12 0.38 1 -0.52 10 11
NCOA2 0.028 0.015 -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 0.032 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 -0.32 3 3
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 0.092 -10000 0 -0.24 45 45
PRKCA 0.033 0.019 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.027 0.13 0.41 4 -0.54 9 13
RXRG 0.021 0.033 -10000 0 -0.32 3 3
RXRA 0.039 0.054 0.22 1 -0.26 4 5
RXRB 0.027 0.019 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RBP1 0.007 0.13 -10000 0 -0.54 26 26
CRBP1/9-cic-RA 0.005 0.094 -10000 0 -0.4 26 26
RARB -0.055 0.21 -10000 0 -0.54 80 80
PRKCG 0.035 0.015 -10000 0 -10000 0 0
MNAT1 0.033 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.009 0.11 -10000 0 -0.37 10 10
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.026 0.11 -10000 0 -0.4 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.096 0.25 6 -0.28 16 22
RXRs/RARs/NRIP1/9cRA/HDAC3 0.027 0.13 0.41 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 0.35 5 -0.4 13 18
RXRs/RXRs/DNA/9cRA 0.026 0.056 0.27 2 -0.31 4 6
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 0.05 -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 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
CRKL 0.033 0.008 -9999 0 -10000 0 0
Rac1/GDP 0.03 0.013 -9999 0 -10000 0 0
DOCK1 0.03 0.044 -9999 0 -0.54 3 3
ITGA4 0.04 0.029 -9999 0 -10000 0 0
RAC1 0.034 0.005 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.054 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 0.025 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.059 0.023 -9999 0 -10000 0 0
lamellipodium assembly -0.032 0.16 -9999 0 -0.44 56 56
PIK3CA 0.033 0.008 -9999 0 -10000 0 0
PI3K 0.005 0.13 -9999 0 -0.4 44 44
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 -0.02 0.17 -9999 0 -0.54 47 47
ARF6/GTP 0.068 0.033 -9999 0 -10000 0 0
cell adhesion 0.073 0.029 -9999 0 -10000 0 0
CRKL/CBL 0.044 0.018 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.058 0.024 -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 0.03 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.072 0.034 -9999 0 -10000 0 0
BCAR1 0.029 0.013 -9999 0 -10000 0 0
mol:GDP -0.07 0.033 -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 0.03 -9999 0 -10000 0 0
Rac1/GTP -0.038 0.18 -9999 0 -0.49 56 56
Class I PI3K signaling events

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
ARF5/GTP -0.005 0.054 0.26 10 -10000 0 10
DAPP1 0.033 0.11 0.28 8 -0.32 20 28
Src family/SYK family/BLNK-LAT/BTK-ITK 0.044 0.14 0.39 12 -0.44 19 31
mol:DAG 0.041 0.095 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 0.078 -10000 0 -0.37 6 6
PLCG2 0.021 0.073 -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 0.055 0.28 10 -10000 0 10
ARF1/GTP 0.003 0.05 0.28 10 -10000 0 10
RHOA 0.033 0.007 -10000 0 -10000 0 0
YES1 0.032 0.027 -10000 0 -0.54 1 1
RAP1A/GTP -0.004 0.055 0.25 10 -10000 0 10
ADAP1 -0.006 0.052 0.27 10 -10000 0 10
ARAP3 -0.006 0.055 0.28 10 -10000 0 10
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PREX1 0.055 0.079 -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 0.037 0.017 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.54 2 2
ARF6 0.034 0.005 -10000 0 -10000 0 0
FGR 0.033 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.058 0.22 17 -0.16 1 18
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.035 0.012 -10000 0 -10000 0 0
ZAP70 0.038 0.024 -10000 0 -10000 0 0
mol:IP3 0.026 0.071 0.25 18 -0.23 1 19
LYN 0.03 0.015 0.18 2 -10000 0 2
ARF1/GDP 0.037 0.077 0.43 1 -0.37 6 7
RhoA/GDP 0.05 0.059 0.31 5 -10000 0 5
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
BLNK 0.039 0.026 0.18 17 -10000 0 17
actin cytoskeleton reorganization 0.035 0.083 0.37 7 -0.35 3 10
SRC 0.033 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 0.065 -10000 0 -0.52 7 7
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.06 0.29 11 -10000 0 11
RhoA/GTP -0.005 0.057 0.33 6 -10000 0 6
Src family/SYK family/BLNK-LAT 0.042 0.091 0.31 11 -0.34 7 18
BLK 0.039 0.044 -10000 0 -10000 0 0
PDPK1 0.031 0.01 -10000 0 -10000 0 0
CYTH1 -0.006 0.052 0.27 10 -10000 0 10
HCK 0.036 0.022 -10000 0 -10000 0 0
CYTH3 -0.006 0.052 0.27 10 -10000 0 10
CYTH2 -0.006 0.052 0.27 10 -10000 0 10
KRAS 0.035 0.018 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.014 0.031 0.26 1 -10000 0 1
SGK1 0.019 0.044 0.38 3 -10000 0 3
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.031 0.079 0.34 2 -0.36 7 9
SOS1 0.034 0.004 -10000 0 -10000 0 0
SYK 0.039 0.026 -10000 0 -10000 0 0
ARF6/GDP 0.033 0.064 0.34 8 -10000 0 8
mol:PI-3-4-5-P3 -0.006 0.059 0.32 10 -10000 0 10
ARAP3/RAP1A/GTP -0.004 0.055 0.25 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 0.052 0.039 0.29 2 -10000 0 2
PLEKHA1 -0.008 0.021 -10000 0 -0.34 2 2
Rac1/GDP 0.048 0.078 -10000 0 -0.37 6 6
LAT 0.035 0.025 -10000 0 -10000 0 0
Rac1/GTP 0.027 0.082 -10000 0 -0.38 7 7
ITK -0.003 0.06 0.32 6 -0.29 2 8
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.042 0.11 0.34 23 -0.26 3 26
LCK 0.048 0.044 -10000 0 -10000 0 0
BTK -0.002 0.059 0.31 7 -10000 0 7
Arf6 trafficking events

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
SLC2A4 -0.26 0.28 -10000 0 -0.54 253 253
CLTC 0.034 0.056 -10000 0 -0.42 3 3
calcium ion-dependent exocytosis 0.015 0.043 -10000 0 -0.37 2 2
Dynamin 2/GTP 0.03 0.013 -10000 0 -10000 0 0
EXOC4 0.034 0.005 -10000 0 -10000 0 0
CD59 0.02 0.045 -10000 0 -0.32 3 3
CPE -0.042 0.13 -10000 0 -0.34 84 84
CTNNB1 0.029 0.052 -10000 0 -0.54 4 4
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 0.045 0.25 1 -0.29 3 4
TSHR 0.015 0.028 -10000 0 -0.34 3 3
INS 0.008 0.099 -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 0.022 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 0.008 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 0.041 0.033 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.036 0.053 -10000 0 -0.36 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.031 0.011 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.045 0.082 0.35 5 -10000 0 5
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 0.035 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.026 0.04 -10000 0 -0.29 2 2
clathrin heavy chain/ACAP1 0.03 0.069 0.29 4 -0.37 3 7
JIP4/KLC1 0.056 0.024 -10000 0 -10000 0 0
EXOC1 0.034 0.005 -10000 0 -10000 0 0
exocyst 0.036 0.054 -10000 0 -0.36 3 3
RALA/GTP 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.016 -10000 0 -10000 0 0
receptor recycling 0.025 0.004 -10000 0 -10000 0 0
CTNNA1 0.032 0.056 0.37 1 -10000 0 1
NME1 0.016 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0.037 0.065 0.32 1 -0.42 3 4
IL2RA 0.027 0.047 -10000 0 -0.36 3 3
VAMP3 0.017 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.1 0.13 -10000 0 -0.34 17 17
EXOC6 0.033 0.027 -10000 0 -0.54 1 1
PLD1 0.005 0.062 -10000 0 -0.28 21 21
PLD2 0.016 0.016 -10000 0 -0.27 1 1
EXOC5 0.034 0.006 -10000 0 -10000 0 0
PIP5K1C 0.019 0.037 -10000 0 -0.42 1 1
SDC1 0.037 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 0.085 -10000 0 -0.36 5 5
mol:Phosphatidic acid 0.012 0.035 -10000 0 -0.35 1 1
endocytosis -0.041 0.009 -10000 0 -10000 0 0
SCAMP2 0.033 0.007 -10000 0 -10000 0 0
ADRB2 -0.11 0.15 -10000 0 -0.41 14 14
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 0.069 0.3 1 -0.38 4 5
RALA 0.034 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.04 0.085 0.34 2 -0.38 3 5
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.008 0.07 -10000 0 -0.28 26 26
TRAF2/ASK1 0.022 0.087 -10000 0 -0.34 26 26
ATM 0.03 0.012 -10000 0 -10000 0 0
MAP2K3 -0.016 0.14 0.28 1 -0.4 34 35
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.13 0.32 1 -0.38 35 36
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 0.025 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 0.021 0.1 -10000 0 -0.4 26 26
TAK1/TAB family -0.002 0.021 -10000 0 -0.16 4 4
RAC1/OSM/MEKK3 0.057 0.023 -10000 0 -10000 0 0
TRAF2 0.035 0.012 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.008 0.12 -10000 0 -0.34 23 23
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 0.069 -10000 0 -0.54 5 5
CCM2 0.034 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.047 0.046 -10000 0 -0.34 5 5
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 0.041 0.094 -10000 0 -0.3 31 31
OSM/MEKK3 0.044 0.018 -10000 0 -10000 0 0
TAOK1 0.016 0.013 -10000 0 -10000 0 0
TAOK2 0.015 0.008 -10000 0 -10000 0 0
TAOK3 0.016 0.007 -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 0.003 0.13 -10000 0 -0.54 26 26
MAP3K10 0.032 0.039 -10000 0 -0.54 2 2
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TRX/ASK1 0.009 0.082 -10000 0 -0.32 28 28
GADD45/MTK1/MTK1 0.066 0.059 -10000 0 -0.29 10 10
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.047 0.032 -10000 0 -10000 0 0
KIRREL 0.032 0.018 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.047 0.032 -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 0.28 71 -0.24 2 73
mol:Ca2+ 0.066 0.047 -10000 0 -10000 0 0
mol:DAG 0.067 0.047 -10000 0 -10000 0 0
NPHS2 0.033 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 0.032 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.083 0.053 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.055 0.045 -10000 0 -0.23 2 2
NPHS1 0.049 0.032 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.056 0.043 -10000 0 -0.24 2 2
TJP1 0.032 0.026 -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 0.069 0.048 -10000 0 -10000 0 0
CD2AP 0.034 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.068 0.049 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.056 0.12 0.3 67 -0.31 13 80
cytoskeleton organization 0.033 0.055 0.27 9 -10000 0 9
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
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.047 0.037 -10000 0 -0.3 3 3
RGS9BP 0.054 0.065 -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 0.23 1 -0.34 2 3
mol:ADP 0.008 0.019 0.14 1 -0.4 1 2
GNAT2 0.031 0.045 -10000 0 -0.54 3 3
RGS9-1/Gbeta5/R9AP 0.049 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 0.033 0.03 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.026 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.056 0.075 0.28 9 -0.31 2 11
Cone PDE6 0.069 0.1 -10000 0 -0.28 27 27
Cone Metarhodopsin II 0.021 0.015 -10000 0 -0.31 1 1
Na + (4 Units) 0.056 0.046 -10000 0 -0.31 2 2
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 0.035 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 0.1 -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 0.034 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 0.033 0.03 -10000 0 -0.54 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.075 0.14 0.38 1 -0.29 35 36
CaM/Ca2+ 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.035 0.017 -10000 0 -10000 0 0
AKT2 0.034 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 54 55
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 0.07 -10000 0 -0.4 14 14
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 0.035 0.017 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.025 0.005 -10000 0 -10000 0 0
RHOQ 0.033 0.026 -10000 0 -0.54 1 1
GYS1 0.017 0.021 0.25 3 -10000 0 3
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.033 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 0.025 0.077 -10000 0 -0.37 8 8
VAMP2 0.031 0.011 -10000 0 -10000 0 0
SLC2A4 -0.099 0.14 0.42 1 -0.31 54 55
STX4 0.031 0.01 -10000 0 -10000 0 0
GSK3B 0.027 0.014 -10000 0 -10000 0 0
SFN 0.032 0.04 -10000 0 -0.54 2 2
LNPEP 0.035 0.016 -10000 0 -10000 0 0
YWHAE 0.031 0.01 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.039 0.085 0.3 2 -0.34 6 8
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 0.026 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 0.046 0.094 0.35 3 -0.36 9 12
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
FGR 0.01 0.1 -10000 0 -0.45 17 17
mol:Ca2+ 0.037 0.092 0.34 3 -0.38 11 14
MYC 0.048 0.23 0.45 7 -0.78 29 36
SHC1 0.027 0.014 -10000 0 -10000 0 0
HRAS/GDP 0.049 0.046 0.27 1 -10000 0 1
LRP1/PDGFRB/PDGFB 0.065 0.023 -10000 0 -10000 0 0
GRB10 0.03 0.051 -10000 0 -0.54 4 4
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0.037 0.093 0.34 3 -0.38 11 14
PTEN 0.026 0.067 -10000 0 -0.54 7 7
GRB2 0.034 0.018 -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 0.047 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 0.02 0.12 0.37 16 -0.34 1 17
GAB1 0.039 0.1 0.33 4 -0.41 7 11
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.038 0.096 0.36 5 -0.35 6 11
PDGFB-D/PDGFRB 0.06 0.037 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.049 0.018 -10000 0 -0.17 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.03 0.078 -10000 0 -0.37 4 4
positive regulation of MAPKKK cascade 0.05 0.01 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.037 0.094 0.34 3 -0.38 11 14
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.033 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.043 0.02 -10000 0 -10000 0 0
SHB 0.035 0.018 -10000 0 -10000 0 0
BLK -0.035 0.17 -10000 0 -0.41 59 59
PTPN2 0.034 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.05 0.011 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -10000 0 -10000 0 0
VAV2 0.039 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 0.025 0.096 -10000 0 -0.49 11 11
PDGFRB 0.034 0.009 -10000 0 -10000 0 0
ACP1 0.034 0.006 -10000 0 -10000 0 0
HCK 0.024 0.076 -10000 0 -0.62 4 4
ABL1 0.033 0.096 0.33 4 -0.39 8 12
PDGFB-D/PDGFRB/CBL 0.033 0.11 0.35 1 -0.43 13 14
PTPN1 0.037 0.03 -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 0.059 0.055 -10000 0 -10000 0 0
cell proliferation 0.051 0.21 0.42 11 -0.68 29 40
SLA 0.029 0.025 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.05 0.06 0.42 3 -10000 0 3
SRC 0.021 0.06 -10000 0 -0.62 2 2
PI3K -0.011 0.066 -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 0.047 0.096 0.35 3 -0.37 9 12
LYN 0.021 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 0.026 -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 0.094 0.34 3 -0.38 11 14
PLCG1 0.037 0.095 0.34 3 -0.39 11 14
NHERF/PDGFRB 0.074 0.05 -10000 0 -10000 0 0
YES1 0.009 0.11 -10000 0 -0.54 14 14
cell migration 0.073 0.05 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.066 0.056 -10000 0 -10000 0 0
SLC9A3R2 0.032 0.015 -10000 0 -10000 0 0
SLC9A3R1 0.059 0.058 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.08 0.07 -10000 0 -0.31 4 4
FYN 0.006 0.1 -10000 0 -0.57 7 7
DOK1 0.036 0.05 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.009 -10000 0 -10000 0 0
PDGFB 0.033 0.015 -10000 0 -10000 0 0
RAC1 0.024 0.16 0.38 2 -0.5 28 30
PRKCD 0.037 0.054 0.33 2 -10000 0 2
FER 0.035 0.053 0.39 1 -10000 0 1
MAPKKK cascade 0.051 0.1 0.36 22 -10000 0 22
RASA1 0.035 0.052 0.39 1 -10000 0 1
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0.007 -10000 0 -10000 0 0
p62DOK/Csk 0.054 0.044 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.05 0.019 -10000 0 -0.17 1 1
chemotaxis 0.033 0.095 0.33 4 -0.38 8 12
STAT1-3-5/STAT1-3-5 0.079 0.049 -10000 0 -0.29 1 1
Bovine Papilomavirus E5/PDGFRB 0.025 0.007 -10000 0 -10000 0 0
PTPRJ 0.035 0.017 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.035 0.009 -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 -0.34 8 14
ERC1 0.033 0.013 -10000 0 -10000 0 0
RIP2/NOD2 0.053 0.051 0.26 3 -10000 0 3
NFKBIA 0.014 0.022 -10000 0 -0.33 1 1
BIRC2 0.031 0.011 -10000 0 -10000 0 0
IKBKB 0.029 0.013 -10000 0 -10000 0 0
RIPK2 0.029 0.021 -10000 0 -10000 0 0
IKBKG 0.019 0.14 -10000 0 -0.39 42 42
IKK complex/A20 0.04 0.15 -10000 0 -0.42 21 21
NEMO/A20/RIP2 0.029 0.021 -10000 0 -10000 0 0
XPO1 0.034 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.03 0.15 -10000 0 -0.43 26 26
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 0.025 0.13 -10000 0 -0.41 21 21
BCL10/MALT1/TRAF6 0.064 0.021 -10000 0 -10000 0 0
NOD2 0.059 0.061 -10000 0 -10000 0 0
NFKB1 0.036 0.007 -10000 0 -10000 0 0
RELA 0.036 0.007 -10000 0 -10000 0 0
MALT1 0.033 0.01 -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 0.034 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 0.009 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
IKK complex 0.033 0.15 -10000 0 -0.43 22 22
CYLD 0.03 0.012 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.036 0.14 -10000 0 -0.42 20 20
Aurora A signaling

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
Aurora A/GADD45A 0.046 0.055 -10000 0 -0.29 8 8
BIRC5 0.12 0.075 -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 0.023 0.041 0.3 3 -10000 0 3
NDEL1 0.031 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.04 0.035 -10000 0 -10000 0 0
NDEL1/TACC3 0.095 0.066 0.26 2 -10000 0 2
GADD45A 0.025 0.072 -10000 0 -0.54 8 8
GSK3B 0.003 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.056 0.049 -10000 0 -10000 0 0
MDM2 0.033 0.01 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.11 0.059 -10000 0 -10000 0 0
TP53 0.022 0.059 -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 0.07 0.27 2 -10000 0 2
G2/M transition of mitotic cell cycle 0.04 0.034 -10000 0 -10000 0 0
AURKA 0.032 0.041 -10000 0 -10000 0 0
AURKB 0.044 0.054 0.14 64 -0.14 12 76
CDC25B 0.035 0.047 -10000 0 -10000 0 0
G2/M transition checkpoint 0.016 0.028 -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 -0.28 22 22
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 0.092 0.064 0.25 1 -10000 0 1
spindle assembly 0.051 0.087 -10000 0 -0.28 22 22
TDRD7 0.034 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.072 0.28 8 -10000 0 8
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 0.028 0.036 0.27 1 -10000 0 1
negative regulation of DNA binding 0.022 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 0.034 0.012 -10000 0 -10000 0 0
Ajuba/Aurora A 0.016 0.028 -10000 0 -10000 0 0
mitotic prometaphase 0.006 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.041 -10000 0 -10000 0 0
TACC1 0.001 0.12 -10000 0 -0.54 24 24
TACC3 0.096 0.073 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.069 0.037 -10000 0 -10000 0 0
Aurora A/RasGAP 0.051 0.037 -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 0.003 0.027 -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 0.034 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.063 0.25 3 -10000 0 3
PAK1 0.043 0.046 -10000 0 -10000 0 0
CKAP5 0.035 0.015 -10000 0 -10000 0 0
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 -0.01 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.064 -10000 0 -0.29 2 2
SUMO1 0.034 0.005 -10000 0 -10000 0 0
ZFPM1 0.029 0.015 -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 0.041 0.044 -10000 0 -0.25 1 1
SAP18 0.032 0.009 -10000 0 -10000 0 0
RELA 0.028 0.042 -10000 0 -0.23 8 8
HDAC1/Smad7 0.064 0.019 -10000 0 -10000 0 0
RANGAP1 0.038 0.03 -10000 0 -10000 0 0
HDAC3/TR2 0.044 0.041 -10000 0 -0.29 1 1
NuRD/MBD3 Complex 0.04 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 0.042 0.033 -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 0.094 -10000 0 -0.37 13 13
RBBP7 0.037 0.022 -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 0.007 -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 0.032 0.016 -10000 0 -10000 0 0
SAP30 0.034 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 0.051 -10000 0 -0.36 2 2
YY1/HDAC2 0.034 0.047 -10000 0 -0.23 6 6
YY1/HDAC1 0.034 0.051 -10000 0 -0.24 7 7
NuRD/MBD2 Complex (MeCP1) 0.039 0.058 -10000 0 -0.25 5 5
PPARG -0.21 0.16 -10000 0 -0.31 340 340
HDAC8/hEST1B 0.057 0.029 -10000 0 -10000 0 0
UBE2I 0.031 0.01 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.032 0.009 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.044 0.039 -10000 0 -10000 0 0
MBD3L2 0.033 0.026 -10000 0 -0.54 1 1
ubiquitin-dependent protein catabolic process 0.064 0.019 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
NuRD/MBD3/MBD3L2 Complex 0.04 0.081 -10000 0 -0.35 9 9
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.03 0.013 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
YY1 0.016 0.015 -10000 0 -0.28 1 1
HDAC8 0.035 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 0.008 -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 0.054 -10000 0 -0.22 6 6
EP300 0.032 0.009 -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 0.061 -10000 0 -0.27 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.032 0.042 -10000 0 -0.26 1 1
nuclear export -0.056 0.028 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GATAD2B 0.028 0.014 -10000 0 -10000 0 0
GATAD2A 0.037 0.022 -10000 0 -10000 0 0
GATA2/HDAC3 0.049 0.046 -10000 0 -10000 0 0
GATA1/HDAC1 0.05 0.009 -10000 0 -10000 0 0
GATA1/HDAC3 0.045 0.039 -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 0.04 0.076 -10000 0 -0.31 7 7
positive regulation of chromatin silencing 0.072 0.048 -10000 0 -10000 0 0
SIN3B 0.035 0.014 -10000 0 -10000 0 0
MTA2 0.034 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 0.053 0.05 -10000 0 -0.25 3 3
HDAC complex 0.082 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 0.058 -10000 0 -0.25 5 5
Ran/GTP/Exportin 1 0.051 0.05 -10000 0 -0.26 3 3
NF kappa B/RelA/I kappa B alpha 0.031 0.048 -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 0.014 -10000 0 -10000 0 0
FBXW11 0.033 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.033 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.052 -10000 0 -0.26 2 2
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 0.038 0.023 -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 0.033 0.008 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.022 0.015 0.26 1 -10000 0 1
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
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 0.041 0.057 -10000 0 -0.29 2 2
SRC 0.033 0.008 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.4 44 44
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 0.007 -10000 0 -10000 0 0
SYK 0.039 0.026 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.017 0.1 -10000 0 -0.28 37 37
cell death 0.04 0.055 -10000 0 -0.28 2 2
NF kappa B1 p105/c-Rel 0.033 0.022 -10000 0 -10000 0 0
LCK 0.048 0.044 -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 0.081 0.069 -10000 0 -10000 0 0
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
JAK3 0.034 0.006 -10000 0 -10000 0 0
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
JAK1 0.034 0.007 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.065 0.11 0.31 8 -0.37 9 17
SHC1 0.028 0.014 -10000 0 -10000 0 0
SP1 0.036 0.049 -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 0.035 -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 0.1 -10000 0 -0.77 9 9
LCK 0.049 0.044 -10000 0 -10000 0 0
GRB2 0.034 0.018 -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 0.46 4 -0.45 1 5
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.042 -10000 0 -0.34 7 7
ADCY3 -0.007 0.007 -10000 0 -10000 0 0
ADCY8 -0.004 0.015 -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 0.07 0.23 17 -10000 0 17
Arf6 downstream pathway

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
PLAUR 0.099 0.13 0.42 8 -10000 0 8
regulation of axonogenesis -0.021 0.05 0.24 1 -10000 0 1
myoblast fusion -0.065 0.074 -10000 0 -0.25 9 9
mol:GTP 0.048 0.045 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.09 0.066 -10000 0 -10000 0 0
ARF1/GTP 0.052 0.044 -10000 0 -10000 0 0
mol:GM1 0.033 0.04 -10000 0 -10000 0 0
mol:Choline 0.017 0.076 -10000 0 -0.32 20 20
lamellipodium assembly 0.056 0.079 -10000 0 -0.33 1 1
MAPK3 0.071 0.078 0.23 10 -10000 0 10
ARF6/GTP/NME1/Tiam1 0.092 0.067 -10000 0 -10000 0 0
ARF1 0.027 0.014 -10000 0 -10000 0 0
ARF6/GDP 0.065 0.074 0.25 9 -10000 0 9
ARF1/GDP 0.056 0.069 -10000 0 -10000 0 0
ARF6 0.054 0.026 -10000 0 -10000 0 0
RAB11A 0.033 0.006 -10000 0 -10000 0 0
TIAM1 0.04 0.014 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.073 0.079 0.23 12 -10000 0 12
actin filament bundle formation -0.075 0.064 -10000 0 -10000 0 0
KALRN 0.042 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 0.045 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.056 0.079 -10000 0 -0.33 1 1
RAC1 0.034 0.005 -10000 0 -10000 0 0
liver development 0.048 0.045 -10000 0 -10000 0 0
ARF6/GTP 0.048 0.045 -10000 0 -10000 0 0
RhoA/GTP 0.062 0.041 -10000 0 -10000 0 0
mol:GDP 0.051 0.076 0.22 2 -10000 0 2
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 0.087 -10000 0 -0.35 20 20
RAB11FIP3 0.031 0.01 -10000 0 -10000 0 0
tube morphogenesis 0.056 0.079 -10000 0 -0.33 1 1
ruffle organization 0.021 0.05 -10000 0 -0.24 1 1
regulation of epithelial cell migration 0.048 0.045 -10000 0 -10000 0 0
PLD2 0.042 0.045 -10000 0 -0.36 1 1
PIP5K1A 0.021 0.05 -10000 0 -0.24 1 1
mol:Phosphatidic acid 0.017 0.076 -10000 0 -0.32 20 20
Rac1/GTP 0.056 0.08 -10000 0 -0.33 1 1
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 0.019 0.14 12 -10000 0 12
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.053 0.029 -10000 0 -10000 0 0
STXBP1 0.034 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.023 0.031 -10000 0 -0.16 1 1
RAB3GAP2/RIMS1/UNC13B 0.057 0.038 -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 0.042 0.035 -10000 0 -10000 0 0
mol:ACh 0 0.032 0.091 13 -0.12 11 24
RAB3GAP2 0.028 0.014 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.041 0.055 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.023 0.031 -10000 0 -0.16 1 1
UNC13B 0.034 0.014 -10000 0 -10000 0 0
CHRNA1 0.035 0.01 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.053 0.077 0.18 12 -0.33 9 21
SNAP25 0.007 0.035 -10000 0 -0.3 5 5
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 0.07 0.1 -10000 0 -0.54 8 8
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.033 0.015 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.041 0.055 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.043 0.022 -9999 0 -0.34 1 1
EFNA5 0.033 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 0.044 0.022 -9999 0 -0.34 1 1
EPHA5 0.034 0.005 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.034 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.014 -10000 0 -10000 0 0
MDM2/SUMO1 0.049 0.052 -10000 0 -0.25 3 3
HDAC4 0.033 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.014 -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 0.053 0.05 -10000 0 -0.25 3 3
RANGAP1 0.038 0.03 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.078 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 0.047 -10000 0 -0.23 5 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.01 -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
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 8 8
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 0.053 0.054 -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 0.034 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 0.034 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.031 -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 0.075 0.059 -10000 0 -0.32 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.057 0.065 -10000 0 -0.3 2 2
VHL 0.036 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 0.059 0.064 -10000 0 -0.54 1 1
EGLN2 0.035 0.017 -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 0.064 -10000 0 -0.48 5 5
ARNT 0.027 0.014 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.032 0.009 -10000 0 -10000 0 0
HIF1A/p19ARF 0.059 0.068 0.26 3 -0.27 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 0.025 -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 0.024 -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 0.003 -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 0.036 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.035 0.052 0.17 1 -0.17 4 5
AP2 0.049 0.017 0.26 1 -10000 0 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.043 0.015 -10000 0 -10000 0 0
CLTB 0.033 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.019 -10000 0 -10000 0 0
CD4 0.032 0.009 -10000 0 -10000 0 0
CLTA 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.008 0.14 2 -10000 0 2
mol:PI-4-5-P2 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP 0.015 0.014 -10000 0 -0.1 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.011 0.022 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 0.007 0.02 -10000 0 -0.2 1 1
ARF1/GDP 0.002 0.022 -10000 0 -0.11 5 5
AP2M1 0.034 0.009 0.18 1 -10000 0 1
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 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.032 -10000 0 -0.23 5 5
ARF1/GDP/Membrin 0.018 0.049 -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 0.024 0.032 -10000 0 -10000 0 0
PLD2 0.008 0.02 -10000 0 -0.2 1 1
ARF-GAP1/v-SNARE 0.009 0.008 0.14 2 -10000 0 2
PIP5K1A 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP/Membrin/GBF1/p115 0.015 0.024 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.02 -10000 0 -0.2 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.008 0.14 2 -10000 0 2
GOSR2 0.013 0.018 -10000 0 -0.26 1 1
USO1 0.012 0.024 -10000 0 -0.31 2 2
GBF1 0.013 0.02 -10000 0 -0.31 1 1
ARF1/GTP/Arfaptin 2 0.036 0.022 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.062 0.026 0.25 1 -10000 0 1
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 0.026 -10000 0 -0.54 1 1
SMAD2 -0.007 0.05 -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 -0.29 2 2
MAPK3 0.032 0.009 -10000 0 -10000 0 0
MAPK1 0.032 0.008 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
CTDSP1 0.034 0.005 -10000 0 -10000 0 0
CTDSP2 0.034 0.006 -10000 0 -10000 0 0
CTDSPL 0.031 0.036 -10000 0 -0.54 2 2
KPNB1 0.032 0.009 -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 0.058 0.06 -10000 0 -10000 0 0
PIAS4 0.035 0.016 -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 0.034 0.006 -10000 0 -10000 0 0
UBE2L3 0.033 0.008 -10000 0 -10000 0 0
FANCD2 0.024 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.089 0.059 0.33 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 0.048 0.033 -10000 0 -10000 0 0
MRE11A 0.03 0.011 -10000 0 -10000 0 0
DNA-PK 0.056 0.031 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.025 0.11 -10000 0 -0.42 15 15
FANCF 0.033 0.006 -10000 0 -10000 0 0
BRCA1 0.036 0.021 -10000 0 -10000 0 0
CCNE1 0.058 0.056 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.068 0.047 0.26 8 -10000 0 8
FANCG 0.034 0.011 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.052 0.025 -10000 0 -10000 0 0
FANCE 0.033 0.027 0.18 1 -0.54 1 2
FANCC 0.036 0.016 -10000 0 -10000 0 0
NBN 0.028 0.016 -10000 0 -10000 0 0
FANCA 0.061 0.064 -10000 0 -10000 0 0
DNA repair 0.075 0.1 0.33 9 -0.4 2 11
BRCA1/BARD1/ubiquitin 0.052 0.025 -10000 0 -10000 0 0
BARD1/DNA-PK 0.072 0.04 -10000 0 -10000 0 0
FANCL 0.034 0.004 -10000 0 -10000 0 0
mRNA polyadenylation -0.048 0.022 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.074 -10000 0 -0.31 3 3
BRCA1/BACH1/BARD1/TopBP1 0.068 0.028 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.078 0.038 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.063 0.032 -10000 0 -10000 0 0
BRCA1/BACH1 0.036 0.021 -10000 0 -10000 0 0
BARD1 0.037 0.023 -10000 0 -10000 0 0
PCNA 0.037 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.069 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.067 0.028 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.12 0.071 0.35 2 -10000 0 2
BARD1/DNA-PK/P53 0.077 0.05 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.052 0.025 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.048 0.039 -10000 0 -0.32 2 2
FA complex 0.042 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 0.035 0.012 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.075 0.037 -10000 0 -10000 0 0
BRCA1/BARD1 0.097 0.064 0.35 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 0.074 -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 0.025 -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 0.04 0.029 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.054 0.022 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.053 0.023 -9999 0 -9999 0 0
Aurora C signaling

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
INCENP 0.045 0.04 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.078 0.055 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.017 0.032 -9999 0 -0.31 4 4
AURKB 0.056 0.058 -9999 0 -10000 0 0
AURKC 0.036 0.019 -9999 0 -10000 0 0
Glypican 2 network

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
MDK 0.044 0.037 -9999 0 -9999 0 0
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine 0.032 0.026 -9999 0 -9999 0 0
neuron projection morphogenesis 0.032 0.026 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.048 0.015 -10000 0 -9999 0 0
FBXW11 0.033 0.007 -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 0.007 -10000 0 -9999 0 0
CHUK 0.034 0.005 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.094 0.036 -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 0.017 -10000 0 -9999 0 0
RELB 0.036 0.02 -10000 0 -9999 0 0
NFKB2 0.035 0.012 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.047 0.018 0.23 1 -9999 0 1
regulation of B cell activation 0.047 0.017 0.23 1 -9999 0 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 513 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 0.035 0.035 0.035 0.18
105_BMP4 0.035 0.035 0.035 0.035
105_BMP6 0.035 0.035 0.035 0.035
105_BMP7 0.035 0.035 0.035 0.035
105_BMP2 0.035 0.035 0.035 0.035
131_RELN/VLDLR 0.089 0.089 -0.32 0.18
30_TGFB1/TGF beta receptor Type II 0.034 0.034 0.034 0.034
84_STAT5B -0.21 -0.0037 -0.03 -0.21
84_STAT5A -0.21 -0.0037 -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/3023103/2.GDAC_MergeDataFiles.Finished/BRCA-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BRCA-TP/3139796/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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