Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNA expression and copy number data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 55 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 248
Signaling events mediated by Stem cell factor receptor (c-Kit) 224
Endothelins 153
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 150
EGFR-dependent Endothelin signaling events 145
Class IB PI3K non-lipid kinase events 126
IGF1 pathway 122
FOXM1 transcription factor network 119
Arf6 signaling events 108
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 248 10933 44 -0.6 0.034 1000 -1000 -0.006 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 224 17524 78 -1 0.32 1000 -1000 -0.026 -1000
Endothelins 153 14704 96 -0.81 0.17 1000 -1000 -0.025 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 150 10213 68 -0.88 0.45 1000 -1000 -0.053 -1000
EGFR-dependent Endothelin signaling events 145 3057 21 -0.31 0.048 1000 -1000 -0.038 -1000
Class IB PI3K non-lipid kinase events 126 378 3 -0.11 -1000 1000 -1000 -0.019 -1000
IGF1 pathway 122 6999 57 -0.27 0.11 1000 -1000 -0.03 -1000
FOXM1 transcription factor network 119 6104 51 -0.12 0.71 1000 -1000 0.008 -1000
Arf6 signaling events 108 6713 62 -0.31 0.081 1000 -1000 -0.006 -1000
Nongenotropic Androgen signaling 96 5014 52 -0.57 0.3 1000 -1000 -0.026 -1000
Glucocorticoid receptor regulatory network 85 9700 114 -0.95 0.29 1000 -1000 -0.048 -1000
S1P1 pathway 75 2710 36 -0.62 0.045 1000 -1000 -0.028 -1000
Signaling events mediated by PTP1B 73 5587 76 -0.37 0.19 1000 -1000 -0.037 -1000
BMP receptor signaling 72 5876 81 -0.4 0.11 1000 -1000 -0.022 -1000
PDGFR-alpha signaling pathway 70 3121 44 -0.7 0.063 1000 -1000 -0.013 -1000
Calcium signaling in the CD4+ TCR pathway 70 2200 31 -0.35 0.039 1000 -1000 -0.035 -1000
Ephrin B reverse signaling 69 3321 48 -0.18 0.061 1000 -1000 -0.032 -1000
Ras signaling in the CD4+ TCR pathway 66 1127 17 -0.2 0.033 1000 -1000 -0.007 -1000
HIF-1-alpha transcription factor network 62 4746 76 -0.4 0.07 1000 -1000 -0.014 -1000
FAS signaling pathway (CD95) 57 2696 47 -0.88 0.06 1000 -1000 -0.018 -1000
Plasma membrane estrogen receptor signaling 57 4953 86 -0.25 0.17 1000 -1000 -0.049 -1000
IL6-mediated signaling events 54 4065 75 -0.37 0.073 1000 -1000 -0.032 -1000
IL4-mediated signaling events 53 4869 91 -0.51 0.14 1000 -1000 -0.086 -1000
EPHB forward signaling 53 4530 85 -0.18 0.15 1000 -1000 -0.059 -1000
Integrins in angiogenesis 52 4441 84 -0.39 0.13 1000 -1000 -0.025 -1000
IL23-mediated signaling events 49 2989 60 -0.79 0.065 1000 -1000 -0.004 -1000
Visual signal transduction: Rods 49 2566 52 -0.43 0.074 1000 -1000 -0.008 -1000
PLK1 signaling events 46 3931 85 -0.035 0.17 1000 -1000 -0.037 -1000
E-cadherin signaling in keratinocytes 45 1959 43 -0.27 0.035 1000 -1000 -0.014 -1000
Fc-epsilon receptor I signaling in mast cells 44 4292 97 -0.36 0.04 1000 -1000 -0.039 -1000
Aurora B signaling 43 2935 67 -0.38 0.24 1000 -1000 -0.041 -1000
Signaling events mediated by the Hedgehog family 40 2109 52 -0.14 0.067 1000 -1000 -0.018 -1000
Glypican 1 network 40 1964 48 -0.39 0.07 1000 -1000 -0.017 -1000
Nectin adhesion pathway 40 2531 63 -0.075 0.054 1000 -1000 -0.023 -1000
p75(NTR)-mediated signaling 39 4963 125 -0.13 0.093 1000 -1000 -0.033 -1000
S1P5 pathway 39 679 17 -0.17 0.067 1000 -1000 -0.005 -1000
Insulin Pathway 39 2902 74 -0.28 0.091 1000 -1000 -0.032 -1000
Stabilization and expansion of the E-cadherin adherens junction 37 2740 74 -0.27 0.074 1000 -1000 -0.057 -1000
Presenilin action in Notch and Wnt signaling 36 2250 61 -0.38 0.1 1000 -1000 -0.025 -1000
TCGA08_retinoblastoma 36 293 8 -0.022 0.057 1000 -1000 -0.007 -1000
S1P4 pathway 35 893 25 -0.17 0.045 1000 -1000 -0.007 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 34 2946 85 -0.54 0.046 1000 -1000 -0.028 -1000
LPA receptor mediated events 34 3560 102 -0.35 0.094 1000 -1000 -0.067 -1000
ErbB2/ErbB3 signaling events 31 2032 65 -0.35 0.047 1000 -1000 -0.048 -1000
Syndecan-1-mediated signaling events 31 1059 34 -0.042 0.11 1000 -1000 -0.015 -1000
Signaling events regulated by Ret tyrosine kinase 31 2543 82 -0.1 0.11 1000 -1000 -0.054 -1000
IL27-mediated signaling events 31 1589 51 -0.37 0.065 1000 -1000 -0.025 -1000
Neurotrophic factor-mediated Trk receptor signaling 31 3782 120 -0.25 0.12 1000 -1000 -0.041 -1000
Regulation of nuclear SMAD2/3 signaling 30 4186 136 -0.37 0.075 1000 -1000 -0.042 -1000
ErbB4 signaling events 30 2131 69 -0.36 0.14 1000 -1000 -0.019 -1000
RXR and RAR heterodimerization with other nuclear receptor 29 1512 52 -0.38 0.1 1000 -1000 -0.012 -1000
FOXA2 and FOXA3 transcription factor networks 28 1305 46 -0.74 0.05 1000 -1000 -0.008 -1000
TCR signaling in naïve CD8+ T cells 28 2641 93 -0.04 0.082 1000 -1000 -0.041 -1000
TCGA08_rtk_signaling 28 748 26 -0.27 0.042 1000 -1000 -0.021 -1000
Syndecan-2-mediated signaling events 27 1896 69 -0.32 0.13 1000 -1000 -0.02 -1000
mTOR signaling pathway 26 1381 53 -0.051 0.044 1000 -1000 -0.027 -1000
amb2 Integrin signaling 26 2142 82 -0.53 0.13 1000 -1000 -0.018 -1000
S1P3 pathway 26 1130 42 -0.17 0.062 1000 -1000 -0.014 -1000
IL12-mediated signaling events 25 2242 87 -0.83 0.088 1000 -1000 -0.039 -1000
Thromboxane A2 receptor signaling 24 2560 105 -0.27 0.066 1000 -1000 -0.033 -1000
HIF-2-alpha transcription factor network 24 1053 43 -0.22 0.26 1000 -1000 -0.081 -1000
Syndecan-3-mediated signaling events 24 872 35 -0.37 0.074 1000 -1000 -0.017 -1000
Angiopoietin receptor Tie2-mediated signaling 24 2121 88 -0.39 0.13 1000 -1000 -0.058 -1000
IL1-mediated signaling events 23 1461 62 -0.051 0.067 1000 -1000 -0.021 -1000
Canonical Wnt signaling pathway 23 1211 51 -0.38 0.16 1000 -1000 -0.04 -1000
Osteopontin-mediated events 22 842 38 -0.35 0.14 1000 -1000 -0.006 -1000
Ceramide signaling pathway 22 1719 76 -0.25 0.083 1000 -1000 -0.014 -1000
Reelin signaling pathway 22 1257 56 -0.056 0.084 1000 -1000 -0.021 -1000
Wnt signaling 21 151 7 -0.016 0.04 1000 -1000 -0.003 -1000
Syndecan-4-mediated signaling events 21 1410 67 -0.39 0.15 1000 -1000 -0.026 -1000
Coregulation of Androgen receptor activity 20 1595 76 -0.23 0.053 1000 -1000 -0.021 -1000
Noncanonical Wnt signaling pathway 20 532 26 -0.016 0.04 1000 -1000 -0.013 -1000
Regulation of p38-alpha and p38-beta 20 1127 54 -0.32 0.071 1000 -1000 -0.039 -1000
Regulation of Telomerase 20 2109 102 -0.35 0.087 1000 -1000 -0.019 -1000
Regulation of Androgen receptor activity 20 1454 70 -0.43 0.078 1000 -1000 -0.03 -1000
Signaling mediated by p38-gamma and p38-delta 18 276 15 -0.006 0.034 1000 -1000 -0.029 -1000
E-cadherin signaling in the nascent adherens junction 18 1374 76 -0.041 0.059 1000 -1000 -0.046 -1000
IL2 signaling events mediated by PI3K 17 1007 58 -0.12 0.049 1000 -1000 -0.026 -1000
Hedgehog signaling events mediated by Gli proteins 15 1017 65 -0.17 0.077 1000 -1000 -0.02 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 15 677 45 -0.007 0.06 1000 -1000 -0.03 -1000
Signaling events mediated by PRL 15 532 34 -0.31 0.051 1000 -1000 -0.023 -1000
E-cadherin signaling events 15 77 5 0.006 0.034 1000 -1000 0.022 -1000
Caspase cascade in apoptosis 14 1054 74 -0.16 0.049 1000 -1000 -0.025 -1000
Cellular roles of Anthrax toxin 13 508 39 -0.063 0.038 1000 -1000 -0.014 -1000
ceramide signaling pathway 13 650 49 -0.072 0.053 1000 -1000 -0.017 -1000
BCR signaling pathway 13 1313 99 -0.15 0.093 1000 -1000 -0.039 -1000
JNK signaling in the CD4+ TCR pathway 12 220 17 -0.04 0.089 1000 -1000 -0.014 -1000
IFN-gamma pathway 12 872 68 -0.02 0.099 1000 -1000 -0.037 -1000
PLK2 and PLK4 events 11 33 3 0.016 0.055 1000 -1000 0.002 -1000
Class I PI3K signaling events mediated by Akt 11 790 68 -0.15 0.06 1000 -1000 -0.017 -1000
FoxO family signaling 11 755 64 0 0.15 1000 -1000 -0.017 -1000
VEGFR1 specific signals 11 645 56 -0.38 0.075 1000 -1000 -0.023 -1000
Sphingosine 1-phosphate (S1P) pathway 10 283 28 -0.17 0.053 1000 -1000 -0.012 -1000
Signaling events mediated by VEGFR1 and VEGFR2 10 1258 125 -0.38 0.075 1000 -1000 -0.033 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 9 527 54 -0.041 0.082 1000 -1000 -0.023 -1000
EPO signaling pathway 9 519 55 -0.091 0.068 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class III 8 332 40 -0.061 0.062 1000 -1000 -0.035 -1000
TRAIL signaling pathway 8 411 48 -0.002 0.046 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 7 558 75 -0.058 0.066 1000 -1000 -0.034 -1000
Circadian rhythm pathway 7 172 22 -0.021 0.1 1000 -1000 -0.009 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 7 583 83 -0.072 0.066 1000 -1000 -0.01 -1000
Arf6 trafficking events 7 513 71 -0.26 0.056 1000 -1000 -0.028 -1000
p38 MAPK signaling pathway 7 311 44 -0.016 0.066 1000 -1000 -0.012 -1000
Arf6 downstream pathway 6 264 43 -0.09 0.092 1000 -1000 -0.034 -1000
Insulin-mediated glucose transport 6 193 32 -0.099 0.053 1000 -1000 -0.009 -1000
Paxillin-independent events mediated by a4b1 and a4b7 6 249 37 -0.02 0.085 1000 -1000 -0.02 -1000
Retinoic acid receptors-mediated signaling 6 382 58 -0.055 0.08 1000 -1000 -0.018 -1000
Paxillin-dependent events mediated by a4b1 6 237 36 -0.07 0.075 1000 -1000 -0.027 -1000
PDGFR-beta signaling pathway 6 597 97 -0.035 0.08 1000 -1000 -0.041 -1000
Nephrin/Neph1 signaling in the kidney podocyte 5 171 34 -0.047 0.083 1000 -1000 -0.025 -1000
Visual signal transduction: Cones 5 210 38 0 0.069 1000 -1000 0 -1000
Class I PI3K signaling events 5 426 73 -0.008 0.059 1000 -1000 -0.023 -1000
Canonical NF-kappaB pathway 4 181 39 0 0.074 1000 -1000 -0.014 -1000
Aurora C signaling 4 31 7 0 0.078 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class I 4 471 104 -0.21 0.082 1000 -1000 -0.036 -1000
Atypical NF-kappaB pathway 4 145 31 -0.02 0.048 1000 -1000 -0.006 -1000
IL2 signaling events mediated by STAT5 4 98 22 -0.02 0.081 1000 -1000 -0.017 -1000
Aurora A signaling 3 201 60 0 0.12 1000 -1000 -0.011 -1000
TCGA08_p53 3 22 7 -0.009 0.028 1000 -1000 -0.008 -1000
LPA4-mediated signaling events 2 30 12 -0.01 0.035 1000 -1000 -0.018 -1000
Effects of Botulinum toxin 2 59 26 0 0.07 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 30 23 -0.007 0.064 1000 -1000 -0.003 -1000
Ephrin A reverse signaling 1 7 7 0 0.044 1000 -1000 0 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 1 52 33 0 0.075 1000 -1000 -0.024 -1000
BARD1 signaling events 0 48 57 -0.075 0.12 1000 -1000 -0.035 -1000
a4b1 and a4b7 Integrin signaling 0 0 5 0.033 0.054 1000 -1000 0.018 -1000
Glypican 2 network 0 0 4 0 0.032 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 25 27 0 0.078 1000 -1000 -0.032 -1000
Rapid glucocorticoid signaling 0 16 20 0 0.043 1000 -1000 0 -1000
Arf1 pathway 0 49 54 -0.001 0.062 1000 -1000 -0.013 -1000
Alternative NF-kappaB pathway 0 3 13 0 0.094 1000 -1000 0 -1000
Total 4399 267340 7203 -30 -990 131000 -131000 -3.1 -131000
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.6 0.54 -10000 0 -1 306 306
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 -0.66 155 155
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 -0.42 303 303
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 -0.45 306 306
JUN -0.26 0.31 -10000 0 -0.65 155 155
PPARGC1A -0.28 0.29 0.28 1 -0.48 314 315
USF1 -0.21 0.22 0.33 4 -0.39 285 289
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 -0.34 270 270
p38alpha-beta/HBP1 -0.25 0.28 -10000 0 -0.45 304 304
CREB1 -0.25 0.24 -10000 0 -0.43 305 305
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.24 0.24 -10000 0 -0.42 293 293
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 -0.44 300 300
KRT19 -0.22 0.23 0.33 1 -0.42 262 263
ELK4 -0.21 0.22 0.33 2 -0.4 286 288
ATF6 -0.22 0.22 0.33 4 -0.39 295 299
ATF1 -0.25 0.24 -10000 0 -0.43 307 307
p38alpha-beta/MAPKAPK2 -0.22 0.24 -10000 0 -0.42 284 284
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 -0.38 374 374
CRKL -0.32 0.17 -10000 0 -0.4 390 390
HRAS -0.23 0.15 -10000 0 -0.34 218 218
mol:PIP3 -0.27 0.17 -10000 0 -0.39 297 297
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 -0.37 328 328
AKT1 -0.3 0.18 -10000 0 -0.39 364 364
BAD -0.28 0.16 -10000 0 -0.37 331 331
megakaryocyte differentiation -0.32 0.17 -10000 0 -0.41 399 399
GSK3B -0.28 0.16 -10000 0 -0.37 336 336
RAF1 -0.19 0.13 -10000 0 -0.32 54 54
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 -1 418 418
HRAS/SPRED1 -0.19 0.14 -10000 0 -0.33 54 54
cell proliferation -0.33 0.17 -10000 0 -0.41 402 402
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 -0.4 401 401
HRAS/SPRED2 -0.19 0.14 -10000 0 -0.32 55 55
LYN/TEC/p62DOK -0.29 0.18 -10000 0 -0.4 335 335
MAPK3 -0.13 0.098 -10000 0 -0.28 16 16
STAP1 -0.32 0.18 -10000 0 -0.41 398 398
GRAP2 0.034 0.019 -10000 0 -10000 0 0
JAK2 -0.68 0.37 -10000 0 -0.85 407 407
STAT1 (dimer) -0.79 0.42 -10000 0 -0.97 418 418
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.28 0.19 -10000 0 -0.4 328 328
actin filament polymerization -0.33 0.17 -10000 0 -0.41 403 403
LYN 0.03 0.015 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.47 0.26 -10000 0 -0.58 409 409
PIK3R1 -0.021 0.17 -10000 0 -0.55 47 47
CBL/CRKL/GRB2 -0.28 0.17 -10000 0 -0.38 342 342
PI3K -0.32 0.2 -10000 0 -0.42 383 383
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 -0.42 402 402
STAT3 (dimer) -0.33 0.17 -10000 0 -0.41 396 396
positive regulation of transcription -0.11 0.083 -10000 0 -0.24 11 11
mol:GDP -0.24 0.16 -10000 0 -0.36 222 222
PIK3C2B -0.3 0.18 -10000 0 -0.42 324 324
CBL/CRKL -0.3 0.16 -10000 0 -0.38 380 380
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 -0.37 261 261
SNAI2 -0.34 0.2 -10000 0 -0.45 363 363
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 -10000 0 -10000 0 0
EPOR -0.23 0.19 -10000 0 -1.1 13 13
STAT5A (dimer) -0.48 0.26 -10000 0 -0.6 409 409
SOCS1 0.032 0.012 -10000 0 -10000 0 0
cell migration 0.32 0.17 0.41 399 -10000 0 399
SOS1 0.034 0.004 -10000 0 -10000 0 0
EPO 0.01 0.064 -10000 0 -10000 0 0
VAV1 0.038 0.025 -10000 0 -10000 0 0
GRB10 -0.34 0.18 -10000 0 -0.42 402 402
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 -0.28 17 17
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 -0.28 22 22
SHC/Grb2/SOS1 -0.27 0.18 -10000 0 -0.4 278 278
STAT5A -0.5 0.26 -10000 0 -0.61 409 409
GRB2 0.034 0.018 -10000 0 -10000 0 0
response to radiation -0.34 0.2 0.27 1 -0.44 363 364
SHC/GRAP2 0.039 0.026 -10000 0 -10000 0 0
PTPRO -0.33 0.18 -10000 0 -0.42 399 399
SH2B2 -0.33 0.18 -10000 0 -0.42 403 403
DOK1 0.036 0.016 -10000 0 -10000 0 0
MATK -0.33 0.18 -10000 0 -0.42 399 399
CREBBP -0.082 0.075 -10000 0 -0.55 1 1
BCL2 -0.43 0.51 -10000 0 -1.4 110 110
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.1 0.17 -10000 0 -0.35 140 140
PTK2B 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.17 0.29 -10000 0 -0.67 95 95
EDN1 -0.16 0.25 -10000 0 -0.54 153 153
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 -0.45 239 239
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.18 -10000 0 -0.37 138 138
ADCY4 -0.083 0.15 0.34 2 -0.3 143 145
ADCY5 -0.08 0.15 0.35 1 -0.3 139 140
ADCY6 -0.081 0.15 0.34 2 -0.3 142 144
ADCY7 -0.077 0.15 0.34 2 -0.3 137 139
ADCY1 -0.081 0.15 -10000 0 -0.3 139 139
ADCY2 -0.082 0.16 0.34 2 -0.3 142 144
ADCY3 -0.081 0.15 0.35 1 -0.3 142 143
ADCY8 -0.067 0.14 0.35 1 -0.3 103 104
ADCY9 -0.075 0.14 -10000 0 -0.3 124 124
arachidonic acid secretion -0.52 0.34 -10000 0 -0.68 384 384
ETB receptor/Endothelin-1/Gq/GTP -0.21 0.21 -10000 0 -0.37 282 282
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 -0.32 143 143
ETA receptor/Endothelin-1/Gs/GTP -0.088 0.15 -10000 0 -0.31 145 145
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 -0.35 103 103
CYSLTR1 -0.1 0.18 0.38 2 -0.35 137 139
SLC9A1 -0.068 0.12 -10000 0 -0.29 44 44
mol:GDP -0.27 0.25 -10000 0 -0.47 250 250
SLC9A3 -0.39 0.39 -10000 0 -0.69 277 277
RAF1 -0.36 0.27 -10000 0 -0.51 336 336
JUN -0.25 0.43 -10000 0 -1 117 117
JAK2 -0.1 0.17 -10000 0 -0.35 140 140
mol:IP3 -0.21 0.22 -10000 0 -0.42 205 205
ETA receptor/Endothelin-1 -0.12 0.2 -10000 0 -0.4 147 147
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 -0.4 374 374
FOS -0.68 0.43 -10000 0 -0.95 366 366
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 -0.54 203 203
BCAR1 0.029 0.013 -10000 0 -10000 0 0
PRKCB1 -0.21 0.21 -10000 0 -0.41 216 216
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 -0.44 233 233
ETA receptor/Endothelin-1/Gq/GTP -0.097 0.15 -10000 0 -0.31 132 132
MAPK14 -0.22 0.22 -10000 0 -0.41 249 249
TRPC6 -0.18 0.31 -10000 0 -0.72 93 93
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 -0.41 271 271
ETB receptor/Endothelin-2 -0.11 0.22 -10000 0 -0.33 238 238
ETB receptor/Endothelin-3 -0.42 0.27 -10000 0 -0.55 393 393
ETB receptor/Endothelin-1 -0.27 0.28 -10000 0 -0.48 297 297
MAPK3 -0.61 0.39 -10000 0 -0.84 370 370
MAPK1 -0.62 0.41 -10000 0 -0.86 370 370
Rac1/GDP -0.25 0.23 -10000 0 -0.45 235 235
cAMP biosynthetic process -0.031 0.15 0.4 5 -0.36 24 29
MAPK8 -0.18 0.3 -10000 0 -0.63 126 126
SRC 0.032 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.28 0.29 -10000 0 -0.55 232 232
p130Cas/CRK/Src/PYK2 -0.27 0.29 -10000 0 -0.56 206 206
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.25 0.23 -10000 0 -0.45 235 235
COL1A2 -0.23 0.27 0.43 1 -0.53 163 164
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.071 0.077 0.26 3 -0.4 3 6
mol:DAG -0.21 0.22 -10000 0 -0.42 205 205
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 -0.31 138 138
Gq family/GDP -0.21 0.22 -10000 0 -0.43 191 191
HRAS/GTP -0.26 0.24 -10000 0 -0.44 272 272
PRKCH -0.21 0.21 -10000 0 -0.43 197 197
RAC1 0.034 0.005 -10000 0 -10000 0 0
PRKCA -0.2 0.21 -10000 0 -0.43 174 174
PRKCB -0.21 0.21 -10000 0 -0.41 216 216
PRKCE -0.21 0.21 -10000 0 -0.43 192 192
PRKCD -0.21 0.21 -10000 0 -0.43 189 189
PRKCG -0.21 0.21 0.3 1 -0.43 194 195
regulation of vascular smooth muscle contraction -0.81 0.51 -10000 0 -1.1 366 366
PRKCQ -0.2 0.21 -10000 0 -0.43 186 186
PLA2G4A -0.59 0.4 -10000 0 -0.78 384 384
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 -0.32 143 143
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 0.22 1 -10000 0 1
NFATC2 -0.081 0.23 0.48 4 -0.55 55 59
NFATC3 -0.15 0.17 0.32 1 -0.33 188 189
CD40LG -0.67 0.53 0.79 4 -1 333 337
ITCH -0.064 0.14 -10000 0 -0.25 177 177
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 -0.7 68 75
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 -0.4 182 182
TLE4 -0.065 0.2 -10000 0 -0.64 31 31
Jun/NFAT1-c-4/p21SNFT -0.58 0.55 0.69 3 -0.96 314 317
AP-1/NFAT1-c-4 -0.8 0.68 0.92 5 -1.2 335 340
IKZF1 -0.044 0.17 0.46 10 -0.46 26 36
T-helper 2 cell differentiation -0.12 0.28 0.52 1 -0.78 45 46
AP-1/NFAT1 -0.3 0.3 0.51 7 -0.5 305 312
CALM1 -0.036 0.11 -10000 0 -0.31 1 1
EGR2 -0.8 0.76 0.73 3 -1.5 256 259
EGR3 -0.88 0.76 0.71 3 -1.4 319 322
NFAT1/FOXP3 -0.03 0.18 0.45 10 -0.41 45 55
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 -0.72 46 48
FOSL1 0.035 0.01 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.54 0.53 0.67 3 -0.92 305 308
DGKA -0.051 0.16 0.47 1 -0.43 35 36
CREM 0.033 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.76 0.55 -10000 0 -1.1 345 345
CTLA4 -0.023 0.16 0.42 15 -0.41 21 36
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 -0.93 313 314
FOS -0.35 0.27 0.26 1 -0.54 344 345
IFNG -0.096 0.3 0.57 7 -0.77 48 55
T cell activation -0.39 0.34 0.69 3 -0.71 200 203
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 0.75 290 -0.66 3 293
TNF -0.67 0.48 -10000 0 -0.98 343 343
FASLG -0.88 0.78 0.86 3 -1.4 324 327
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 4 -10000 0 4
PTPN1 -0.047 0.16 0.42 1 -0.44 34 35
NFAT1-c-4/ICER1 -0.55 0.53 0.61 1 -0.94 308 309
GATA3 0.035 0.16 -10000 0 -0.54 33 33
T-helper 1 cell differentiation -0.094 0.3 0.56 8 -0.76 48 56
IL2RA -0.25 0.31 0.74 6 -0.68 78 84
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.051 0.16 -10000 0 -0.46 28 28
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 -0.46 27 27
IRF4 0.039 0.028 -10000 0 -10000 0 0
PTGS2 -0.77 0.57 0.73 4 -1.1 350 354
CSF2 -0.67 0.53 0.79 4 -1 334 338
JunB/Fra1/NFAT1-c-4 -0.53 0.52 0.6 2 -0.9 310 312
IL4 -0.12 0.29 -10000 0 -0.82 45 45
IL5 -0.68 0.52 0.73 4 -1 333 337
IL2 -0.39 0.35 0.69 3 -0.73 191 194
IL3 -0.088 0.15 -10000 0 -0.91 13 13
RNF128 -0.21 0.33 0.28 12 -0.63 191 203
NFATC1 -0.45 0.41 0.66 3 -0.76 288 291
CDK4 0.28 0.28 0.6 83 -0.69 1 84
PTPRK -0.087 0.24 -10000 0 -0.66 59 59
IL8 -0.66 0.53 0.74 5 -1 324 329
POU2F1 0.033 0.015 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.013 -10000 0 -10000 0 0
EGFR -0.27 0.29 -10000 0 -0.54 269 269
EGF/EGFR -0.3 0.26 -10000 0 -0.44 366 366
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.19 0.21 -10000 0 -0.36 262 262
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.032 0.038 0.18 2 -0.54 2 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.15 0.27 -10000 0 -0.54 164 164
EGF/EGFR dimer/SHC -0.23 0.23 -10000 0 -0.41 285 285
mol:GDP -0.19 0.21 -10000 0 -0.36 262 262
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.14 0.26 -10000 0 -0.54 153 153
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
HRAS/GTP -0.18 0.19 -10000 0 -0.34 259 259
SHC1 0.027 0.014 -10000 0 -10000 0 0
HRAS/GDP -0.18 0.2 -10000 0 -0.35 259 259
FRAP1 -0.2 0.17 -10000 0 -0.35 262 262
EGF/EGFR dimer -0.31 0.26 -10000 0 -0.47 352 352
SOS1 0.034 0.004 -10000 0 -10000 0 0
GRB2 0.034 0.018 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.088 0.21 -10000 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 -0.34 256 256
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 -0.36 222 222
AKT1 -0.16 0.19 0.23 1 -0.36 207 208
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 -0.45 74 74
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.22 -10000 0 -0.34 219 219
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.17 0.23 -10000 0 -0.37 261 261
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.18 0.23 1 -0.35 199 200
GNB2L1 0.034 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.099 0.16 0.3 2 -0.39 64 66
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 -0.42 274 274
PI3K -0.15 0.24 -10000 0 -0.37 244 244
apoptosis 0.11 0.15 0.4 58 -0.28 2 60
HRAS/GDP 0.025 0.009 -10000 0 -10000 0 0
PRKCD -0.18 0.23 -10000 0 -0.4 234 234
RAF1/14-3-3 E -0.096 0.17 0.34 1 -0.39 74 75
BAD/14-3-3 -0.12 0.16 0.29 2 -0.43 58 60
PRKCZ -0.16 0.19 0.22 1 -0.35 224 225
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.17 -10000 0 -0.4 80 80
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 -0.41 244 244
BCAR1 0.029 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.094 0.19 -10000 0 -0.33 181 181
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 -0.43 280 280
IGF-1R heterotetramer/IGF1 -0.2 0.26 -10000 0 -0.44 258 258
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDPK1 -0.16 0.21 -10000 0 -0.36 225 225
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 1.1 127 -1 2 129
PLK1 0.23 0.2 0.68 31 -10000 0 31
BIRC5 0.37 0.25 0.69 125 -0.66 3 128
HSPA1B 0.57 0.46 1.1 149 -0.95 3 152
MAP2K1 0.17 0.13 0.35 117 -10000 0 117
BRCA2 0.6 0.49 1.2 147 -1 2 149
FOXM1 0.62 0.61 1.3 163 -1.2 3 166
XRCC1 0.57 0.47 1.1 136 -1 2 138
FOXM1B/p19 0.079 0.3 0.92 9 -1.1 3 12
Cyclin D1/CDK4 0.49 0.46 0.99 137 -0.87 10 147
CDC2 0.63 0.52 1.2 160 -1 3 163
TGFA 0.45 0.52 0.99 145 -0.93 20 165
SKP2 0.58 0.47 1.1 134 -1 2 136
CCNE1 0.087 0.063 0.22 52 -10000 0 52
CKS1B 0.62 0.5 1.2 159 -1 2 161
RB1 0.28 0.35 0.72 139 -0.76 8 147
FOXM1C/SP1 0.5 0.45 0.99 124 -1 7 131
AURKB 0.21 0.31 0.7 48 -0.84 19 67
CENPF 0.7 0.53 1.2 177 -1.3 1 178
CDK4 0.092 0.061 0.24 16 -10000 0 16
MYC 0.32 0.44 0.96 89 -0.87 10 99
CHEK2 0.17 0.13 0.35 123 -10000 0 123
ONECUT1 0.5 0.48 1 161 -0.87 7 168
CDKN2A -0.017 0.078 -10000 0 -0.23 18 18
LAMA4 0.56 0.48 1.1 125 -1.1 4 129
FOXM1B/HNF6 0.5 0.5 1 148 -1 7 155
FOS -0.12 0.65 1.1 51 -0.99 82 133
SP1 0.031 0.033 -10000 0 -0.2 6 6
CDC25B 0.58 0.47 1.1 137 -1 2 139
response to radiation 0.12 0.094 0.24 137 -10000 0 137
CENPB 0.57 0.46 1.1 135 -1 2 137
CENPA 0.64 0.51 1.2 158 -1 2 160
NEK2 0.71 0.52 1.2 189 -1.2 1 190
HIST1H2BA 0.57 0.46 1.1 137 -0.94 3 140
CCNA2 0.11 0.077 0.22 154 -10000 0 154
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 1.2 158 -1 2 160
CCNB1 0.64 0.54 1.3 156 -1 3 159
ETV5 0.54 0.52 1.1 135 -1.1 10 145
ESR1 0.38 0.61 1.1 120 -0.98 15 135
CCND1 0.51 0.51 1.1 160 -0.9 10 170
GSK3A 0.14 0.1 0.3 90 -10000 0 90
Cyclin A-E1/CDK1-2 0.21 0.13 0.37 157 -10000 0 157
CDK2 0.071 0.036 0.23 9 -10000 0 9
G2/M transition of mitotic cell cycle 0.14 0.12 0.27 180 -10000 0 180
FOXM1B/Cbp/p300 0.3 0.38 0.86 27 -1 3 30
GAS1 0.28 0.71 1.1 108 -1.1 55 163
MMP2 0.56 0.48 1.1 133 -1.2 6 139
RB1/FOXM1C 0.46 0.46 0.97 143 -0.9 9 152
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.018 0.018 -10000 0 -0.34 1 1
ARNO/beta Arrestin1-2 -0.11 0.14 -10000 0 -0.26 245 245
EGFR -0.27 0.29 -10000 0 -0.54 269 269
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 -0.47 352 352
ARRB2 0.015 0.029 -10000 0 -0.33 3 3
mol:GTP 0.013 0.029 0.12 26 -10000 0 26
ARRB1 0.03 0.027 -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 -0.001 234 234
ARAP2 0 0 -10000 0 0 250 250
mol:GDP -0.14 0.14 -10000 0 -0.27 215 215
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 242 242
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 0 137 137
KIF13B 0.027 0.029 -10000 0 -0.54 1 1
HGF/MET 0.006 0.13 -10000 0 -0.4 51 51
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.14 0.12 -10000 0 -0.25 235 235
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 0 211 211
actin filament binding 0 0 -10000 0 0 258 258
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 -0.001 151 151
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 148 148
ARF6/GDP -0.03 0.084 -10000 0 -0.27 29 29
ARF6/GDP/GULP/ACAP1 -0.16 0.18 -10000 0 -0.34 204 204
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.031 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 0 1 1
ACAP2 0 0 -10000 0 0 250 250
LHCGR/beta Arrestin2 0.022 0.048 -10000 0 -0.47 3 3
EFNA1 0.028 0.016 -10000 0 -10000 0 0
HGF 0.034 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 212 212
CYTH2 -0.002 0.002 -10000 0 -0.004 261 261
NCK1 0.034 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 152 152
endosomal lumen acidification 0 0 0.001 5 0 158 163
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 -0.007 144 144
mol:Phosphatidic acid 0 0 -10000 0 0 250 250
PIP3-E 0 0 -10000 0 0 307 307
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 -0.001 203 203
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 -0.32 352 352
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 -10000 0 -0.4 67 67
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.003 -10000 0 -0.007 363 363
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 -0.47 67 67
cell proliferation -0.3 0.21 -10000 0 -0.43 334 334
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 -0.36 176 176
MAPK1 -0.16 0.15 -10000 0 -0.39 83 83
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 -0.003 0.002 -10000 0 -0.004 347 347
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 -0.004 347 347
HRAS/GTP -0.059 0.12 -10000 0 -0.33 64 64
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 -0.004 347 347
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 66 66
HRAS/GDP -0.069 0.17 -10000 0 -0.46 66 66
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 -10000 0 -0.55 66 66
GNB1 0.034 0.011 -10000 0 -10000 0 0
RAF1 -0.086 0.11 -10000 0 -0.34 61 61
RAC1-CDC42/GDP -0.032 0.17 -10000 0 -0.44 66 66
T-DHT/AR/PELP1/Src -0.004 0.13 -10000 0 -0.33 65 65
MAP2K2 -0.12 0.11 -10000 0 -0.36 61 61
T-DHT/AR/PELP1/Src/PI3K -0.046 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 -0.48 77 77
mol:T-DHT -0.001 0.002 -10000 0 -0.004 92 92
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 -0.26 188 188
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 0.49 6 -10000 0 6
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 -0.7 42 43
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 44 -0.36 4 48
PRL -0.06 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.52 182 -10000 0 182
RELA -0.096 0.12 0.32 1 -0.3 18 19
FGG 0.23 0.23 0.45 215 -10000 0 215
GR beta/TIF2 0.11 0.14 0.3 109 -0.36 3 112
IFNG -0.39 0.34 -10000 0 -0.7 226 226
apoptosis -0.25 0.18 -10000 0 -0.54 43 43
CREB1 0.058 0.041 -10000 0 -10000 0 0
histone acetylation 0.036 0.14 0.41 35 -0.33 9 44
BGLAP -0.092 0.14 -10000 0 -0.48 9 9
GR/PKAc 0.15 0.14 0.34 53 -0.31 3 56
NF kappa B1 p50/RelA -0.16 0.2 0.48 3 -0.36 91 94
SMARCD1 0.034 0.004 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.22 185 -10000 0 185
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 -10000 0 3
GSK3B 0.001 0.027 -10000 0 -10000 0 0
NR1I3 -0.19 0.16 -10000 0 -0.55 9 9
CSN2 0.19 0.19 0.38 200 -10000 0 200
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 -0.46 191 193
IL4 -0.12 0.15 -10000 0 -0.51 10 10
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 -0.5 331 331
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.15 0.14 0.35 33 -0.4 2 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 -0.58 361 361
AP-1/NFAT1-c-4 -0.58 0.41 -10000 0 -0.82 351 351
AFP -0.18 0.2 -10000 0 -0.52 65 65
SUV420H1 0.032 0.01 -10000 0 -10000 0 0
IRF1 0.21 0.18 0.5 52 -10000 0 52
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 -1.4 326 326
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 0.3 278 -0.29 1 279
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 -0.82 351 351
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 -0.44 16 18
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.19 0.34 207 -0.36 1 208
MAPK3 0 0.024 -10000 0 -10000 0 0
MAPK1 0.009 0.023 -10000 0 -10000 0 0
ICAM1 -0.26 0.25 0.59 2 -0.52 160 162
NFKB1 -0.095 0.11 0.32 1 -0.26 24 25
MAPK8 -0.15 0.19 0.57 1 -0.35 164 165
MAPK9 0.009 0.024 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.19 -10000 0 -0.56 44 44
BAX 0.028 0.076 -10000 0 -10000 0 0
POMC -0.14 0.19 0.57 1 -0.72 13 14
EP300 0.18 0.14 0.29 281 -10000 0 281
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.52 196 -10000 0 196
proteasomal ubiquitin-dependent protein catabolic process 0.09 0.11 0.26 86 -10000 0 86
SGK1 0.23 0.17 0.36 302 -0.43 1 303
IL13 -0.29 0.25 -10000 0 -0.72 52 52
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 -0.71 20 20
IL2 -0.42 0.32 -10000 0 -0.69 252 252
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 0.59 2 -0.65 55 57
CDK5R1/CDK5 0.037 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.096 0.18 0.43 3 -0.42 25 28
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.5 225 -10000 0 225
SMARCA4 0.035 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.17 0.16 0.33 202 -10000 0 202
NF kappa B1 p50/RelA/Cbp -0.005 0.19 0.48 25 -0.37 4 29
JUN (dimer) -0.21 0.24 0.38 2 -0.46 191 193
YWHAH 0.033 0.014 -10000 0 -10000 0 0
VIPR1 -0.11 0.16 -10000 0 -0.56 24 24
NR3C1 0.19 0.2 0.39 191 -0.45 5 196
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 -0.54 43 43
cortisol/GR alpha (dimer)/Src-1 0.27 0.26 0.51 231 -10000 0 231
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 0.48 6 -0.61 178 184
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.16 0.33 200 -10000 0 200
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.25 0.5 225 -10000 0 225
mol:cortisol 0.18 0.17 0.32 243 -10000 0 243
MMP1 -0.023 0.35 -10000 0 -0.94 53 53
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.051 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 0.34 4 -0.5 293 297
GNAO1 0.003 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.25 0.26 0.41 3 -0.46 272 275
PLCG1 -0.27 0.27 0.34 5 -0.47 289 294
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 0.14 1 -10000 0 1
S1P1/S1P -0.066 0.13 0.31 5 -0.66 11 16
negative regulation of cAMP metabolic process -0.28 0.28 0.33 5 -0.48 293 298
MAPK3 -0.37 0.35 0.37 7 -0.64 308 315
calcium-dependent phospholipase C activity -0.005 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
KDR 0.029 0.011 -10000 0 -10000 0 0
PLCB2 -0.055 0.12 0.36 4 -0.57 11 15
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 4 -0.6 11 15
PTGS2 -0.62 0.53 0.46 2 -1 312 314
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 -0.48 293 298
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 -0.68 314 319
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
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 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 -10000 0 -0.31 157 157
FYN 0.03 0.037 -10000 0 -0.54 2 2
p210 bcr-abl/PTP1B -0.19 0.16 0.25 1 -0.32 241 242
EGFR -0.29 0.28 -10000 0 -0.56 269 269
EGF/EGFR -0.36 0.26 -10000 0 -0.51 348 348
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 -0.32 191 192
Insulin Receptor/Insulin -0.11 0.13 -10000 0 -0.39 30 30
HCK 0.036 0.022 -10000 0 -10000 0 0
CRK 0.031 0.01 -10000 0 -10000 0 0
TYK2 -0.18 0.16 0.44 1 -0.31 215 216
EGF -0.18 0.26 -10000 0 -0.56 164 164
YES1 0.032 0.027 -10000 0 -0.54 1 1
CAV1 -0.37 0.23 -10000 0 -0.5 362 362
TXN 0.028 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.19 0.18 -10000 0 -0.42 128 128
cell migration 0.19 0.16 0.32 241 -0.25 1 242
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 -10000 0 -0.31 219 219
Crk/p130 Cas -0.17 0.16 -10000 0 -0.32 182 182
DOK1 -0.15 0.14 0.27 1 -0.36 78 79
JAK2 -0.081 0.14 -10000 0 -0.53 31 31
Jak2/Leptin Receptor/Leptin -0.25 0.2 -10000 0 -0.44 210 210
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
PTPN1 -0.19 0.16 0.25 1 -0.32 245 246
LYN 0.03 0.015 -10000 0 -10000 0 0
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 -0.44 79 80
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 -0.43 56 56
mol:H2O2 -0.005 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.22 0.19 -10000 0 -0.41 197 197
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 -0.36 96 96
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 -0.37 86 87
STAT5A -0.14 0.16 0.26 1 -0.36 99 100
GRB2 0.034 0.018 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.18 0.16 -10000 0 -0.31 218 218
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
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.11 0.079 -10000 0 -0.28 4 4
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 -0.43 89 89
BMP7/USAG1 -0.24 0.2 -10000 0 -0.37 350 350
SMAD5/SKI -0.094 0.19 -10000 0 -0.42 82 82
SMAD1 0.004 0.09 -10000 0 -0.44 10 10
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 0.18 193 -10000 0 193
BMPR1A-1B/BAMBI 0.081 0.13 0.25 24 -0.3 38 62
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 -0.39 98 98
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 81 81
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 -0.36 101 101
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 -0.41 10 10
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 -0.43 10 10
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 0.18 1 -10000 0 1
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 -0.63 65 65
SMAD1/SMAD6 0.015 0.098 -10000 0 -0.43 10 10
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 -0.4 112 112
PPM1A 0.033 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.012 0.093 -10000 0 -0.44 9 9
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 -0.38 113 113
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
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 -0.4 64 64
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 65 65
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 -0.41 65 65
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 -0.41 65 65
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 -0.39 65 65
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 62 62
JAK1 -0.065 0.13 -10000 0 -0.4 63 63
ELK1/SRF -0.065 0.12 0.33 1 -0.35 58 59
SHB 0.035 0.018 -10000 0 -10000 0 0
SHF 0.034 0.013 -10000 0 -10000 0 0
CSNK2A1 0.063 0.025 -10000 0 -10000 0 0
GO:0007205 -0.092 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 65 65
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 64 64
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
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.008 0.058 0.26 9 -0.35 2 11
NFATC2 0.009 0.055 0.26 9 -0.34 1 10
NFATC3 0.012 0.052 0.26 9 -10000 0 9
CD40LG -0.22 0.29 0.69 10 -0.52 181 191
PTGS2 -0.32 0.36 0.67 9 -0.62 260 269
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 0.19 1 -0.54 89 90
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 -0.35 56 71
FOS -0.35 0.27 -10000 0 -0.54 344 344
IFNG -0.2 0.31 0.67 16 -0.51 183 199
AP-1/NFAT1-c-4 -0.26 0.34 0.71 11 -0.59 193 204
FASLG -0.19 0.29 0.67 15 -0.5 153 168
NFAT1-c-4/ICER1 0.015 0.098 0.41 9 -0.28 1 10
IL2RA -0.21 0.3 0.74 10 -0.52 176 186
FKBP12/FK506 0.025 0.008 -10000 0 -10000 0 0
CSF2 -0.22 0.3 0.7 11 -0.51 189 200
JunB/Fra1/NFAT1-c-4 0.039 0.11 0.41 9 -0.3 3 12
IL4 -0.22 0.29 0.66 10 -0.51 189 199
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
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 -0.55 68 68
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 -0.34 6 6
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 55 55
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 -0.34 6 6
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 -0.3 189 189
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 0.29 189 -10000 0 189
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
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.2 0.19 -9999 0 -0.35 220 220
MAP3K8 -0.048 0.19 -9999 0 -0.55 65 65
FOS -0.098 0.12 -9999 0 -0.36 29 29
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 -0.018 364 364
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 -0.006 365 365
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
HIF-1-alpha transcription factor network

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
PKM2 0.005 0.43 0.81 1 -0.76 67 68
HDAC7 0.007 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.003 0.37 0.84 3 -0.75 39 42
SMAD4 0.033 0.027 -10000 0 -0.54 1 1
ID2 0.002 0.43 -10000 0 -0.79 60 60
AP1 -0.33 0.27 -10000 0 -0.48 363 363
ABCG2 -0.014 0.44 -10000 0 -0.76 78 78
HIF1A 0.022 0.13 0.33 2 -0.44 6 8
TFF3 -0.049 0.44 -10000 0 -0.79 74 74
GATA2 0.021 0.049 -10000 0 -10000 0 0
AKT1 0.02 0.13 0.34 3 -0.22 10 13
response to hypoxia -0.004 0.11 0.25 13 -0.16 63 76
MCL1 -0.029 0.39 -10000 0 -0.75 67 67
NDRG1 -0.017 0.4 0.88 1 -0.75 66 67
SERPINE1 0.012 0.44 0.85 7 -0.76 68 75
FECH -0.002 0.42 -10000 0 -0.78 62 62
FURIN 0.006 0.43 -10000 0 -0.77 65 65
NCOA2 0.035 0.024 -10000 0 -10000 0 0
EP300 0.033 0.17 0.46 14 -0.3 33 47
HMOX1 0.009 0.44 0.87 4 -0.76 68 72
BHLHE40 -0.053 0.4 -10000 0 -0.76 68 68
BHLHE41 -0.053 0.4 -10000 0 -0.76 68 68
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 -0.76 74 74
ABCB1 -0.29 0.47 -10000 0 -0.94 162 162
TFRC 0.007 0.43 0.87 5 -0.76 68 73
CXCR4 0.01 0.43 0.87 1 -0.76 66 67
TF -0.006 0.44 -10000 0 -0.81 64 64
CITED2 -0.005 0.43 -10000 0 -0.77 69 69
HIF1A/ARNT -0.069 0.44 0.97 1 -0.91 54 55
LDHA -0.01 0.13 -10000 0 -0.74 13 13
ETS1 -0.002 0.43 -10000 0 -0.76 68 68
PGK1 0.007 0.43 0.84 3 -0.78 62 65
NOS2 -0.053 0.4 -10000 0 -0.76 68 68
ITGB2 0.007 0.43 0.86 4 -0.75 71 75
ALDOA 0.004 0.42 -10000 0 -0.75 68 68
Cbp/p300/CITED2 -0.012 0.43 0.82 1 -0.85 51 52
FOS -0.36 0.27 -10000 0 -0.55 344 344
HK2 0.003 0.43 -10000 0 -0.78 62 62
SP1 -0.019 0.094 -10000 0 -0.2 69 69
GCK 0.065 0.22 0.67 3 -0.52 2 5
HK1 0.005 0.43 -10000 0 -0.76 67 67
NPM1 0.001 0.43 -10000 0 -0.74 73 73
EGLN1 -0.023 0.4 -10000 0 -0.77 61 61
CREB1 0.04 0.01 -10000 0 -10000 0 0
PGM1 0 0.43 -10000 0 -0.78 61 61
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 -0.76 68 68
VEGFA 0.069 0.36 0.83 16 -0.63 39 55
HIF1A/JAB1 0.04 0.1 0.31 5 -0.41 4 9
CP -0.063 0.51 0.84 5 -0.82 109 114
CXCL12 -0.087 0.48 -10000 0 -0.83 105 105
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 -0.76 69 70
EGLN3 0.02 0.44 0.86 8 -0.77 65 73
CA9 0.015 0.44 0.86 5 -0.78 61 66
TERT -0.012 0.42 -10000 0 -0.75 69 69
ENO1 0.003 0.43 -10000 0 -0.76 68 68
PFKL 0.002 0.43 -10000 0 -0.78 61 61
NCOA1 0.035 0.027 -10000 0 -0.54 1 1
ADM -0.1 0.5 -10000 0 -0.8 122 122
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 -10000 0 -0.76 68 68
SLC2A1 0.07 0.36 0.84 13 -0.62 40 53
LEP -0.14 0.48 -10000 0 -0.82 123 123
HIF1A/ARNT/Cbp/p300 -0.02 0.36 0.83 1 -0.74 44 45
EPO 0.069 0.32 0.83 9 -0.73 12 21
CREBBP 0.04 0.16 0.46 14 -0.29 11 25
HIF1A/ARNT/Cbp/p300/HDAC7 -0.012 0.35 0.81 3 -0.72 40 43
PFKFB3 -0.005 0.42 -10000 0 -0.76 68 68
NT5E -0.004 0.44 -10000 0 -0.78 69 69
FAS signaling pathway (CD95)

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
SPTAN1 0.02 0.093 0.22 69 -10000 0 69
RFC1 0.02 0.088 0.21 74 -10000 0 74
PRKDC 0.04 0.11 0.23 102 -10000 0 102
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 0.26 9 -0.31 17 26
MAP2K4 -0.18 0.19 -10000 0 -0.44 95 95
mol:ceramide -0.075 0.12 0.27 1 -0.38 29 30
GSN -0.058 0.17 0.21 67 -0.34 107 174
FASLG/FAS/FADD/FAF1/Caspase 8 -0.032 0.097 0.32 3 -0.33 14 17
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 -0.45 26 28
MAP3K7 0.025 0.01 -10000 0 -10000 0 0
RB1 0.021 0.086 0.21 70 -10000 0 70
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 0.22 83 -10000 0 83
FADD -0.008 0.028 -10000 0 -10000 0 0
actin filament polymerization 0.058 0.17 0.34 108 -0.21 67 175
NFKB1 -0.1 0.12 -10000 0 -0.65 8 8
MAPK8 -0.32 0.25 -10000 0 -0.45 372 372
DFFA 0.02 0.088 0.21 70 -10000 0 70
DNA fragmentation during apoptosis 0.019 0.089 0.21 68 -10000 0 68
FAS/FADD/MET -0.031 0.15 -10000 0 -0.39 66 66
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 78 -0.2 1 79
DFFB 0.019 0.089 0.21 70 -10000 0 70
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 -0.39 32 32
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 72 -10000 0 72
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 -0.39 28 29
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
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.009 0.16 -10000 0 -0.3 104 104
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.45 144 144
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 -0.31 47 50
IGF1R 0.011 0.12 -10000 0 -0.54 21 21
E2/ER alpha (dimer)/Striatin -0.018 0.17 0.23 1 -0.33 108 109
SHC1 0.027 0.014 -10000 0 -10000 0 0
apoptosis 0.17 0.35 0.75 132 -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 -0.45 137 138
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 -0.31 50 53
IGF-1R heterotetramer 0.011 0.12 -10000 0 -0.54 21 21
PLCB1 -0.036 0.13 -10000 0 -0.3 69 69
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 -0.74 79 79
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 -0.46 107 108
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 0.18 2 -0.54 1 3
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 -0.56 68 72
PI3K 0.005 0.13 -10000 0 -0.38 48 48
GNB1 0.034 0.011 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.019 0.18 -10000 0 -0.37 88 88
SOS1 0.034 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.21 0.21 -10000 0 -0.43 208 208
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 -0.48 139 139
mol:DAG -0.035 0.12 0.26 3 -0.31 50 53
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 -0.39 12 12
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 0.48 139 -10000 0 139
GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
RhoA/GDP -0.026 0.19 -10000 0 -0.37 105 105
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 0.32 2 -0.47 138 140
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 0.4 7 -0.55 54 61
MMP2 -0.14 0.22 0.3 6 -0.55 60 66
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.023 0.3 0.68 3 -0.8 21 24
CRP 0.002 0.32 0.68 10 -0.73 30 40
cell cycle arrest -0.052 0.34 0.65 7 -0.75 53 60
TIMP1 -0.012 0.28 0.65 11 -0.62 33 44
IL6ST 0.038 0.084 -10000 0 -0.54 9 9
Rac1/GDP -0.088 0.22 0.41 8 -0.44 80 88
AP1 -0.16 0.24 0.48 5 -0.53 92 97
GAB2 0.033 0.015 -10000 0 -10000 0 0
TNFSF11 -0.005 0.32 0.7 7 -0.76 23 30
HSP90B1 0.043 0.14 -10000 0 -0.95 6 6
GAB1 0.035 0.027 -10000 0 -0.54 1 1
MAPK14 -0.13 0.2 0.32 1 -0.54 60 61
AKT1 0.032 0.092 0.34 1 -0.4 9 10
FOXO1 0.005 0.13 0.32 3 -0.43 18 21
MAP2K6 -0.12 0.2 0.36 3 -0.49 70 73
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.055 0.24 0.45 14 -0.48 67 81
MITF -0.11 0.21 0.36 5 -0.44 92 97
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 0.34 3 -0.48 22 25
STAT3 -0.071 0.36 0.66 6 -0.82 53 59
STAT1 0.035 0.12 -10000 0 -0.85 7 7
CEBPD -0.08 0.44 0.67 5 -1 71 76
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 -0.44 77 79
MAPK11 -0.12 0.2 0.32 1 -0.54 60 61
STAT3 (dimer)/FOXO1 -0.086 0.33 0.59 9 -0.7 62 71
GRB2/SOS1/GAB family -0.082 0.18 0.37 2 -0.45 44 46
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.19 0.34 3 -0.42 98 101
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 13 -0.65 19 32
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 10 -0.95 43 53
FGG -0.025 0.3 0.7 3 -0.75 28 31
macrophage differentiation -0.052 0.34 0.65 7 -0.75 53 60
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.19 -10000 0 -0.31 227 227
JUNB -0.03 0.3 0.64 3 -0.72 34 37
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 99 108
STAT1/PIAS1 -0.073 0.23 0.41 13 -0.44 74 87
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.097 -10000 0 -0.4 11 11
STAT3 (dimer) -0.069 0.35 0.66 6 -0.81 52 58
PRKCD -0.033 0.26 0.52 16 -0.54 55 71
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 0.31 2 -0.32 30 32
Rac1/GTP -0.077 0.23 0.43 10 -0.45 76 86
HCK 0.037 0.022 -10000 0 -10000 0 0
MAPKKK cascade 0.022 0.16 0.41 1 -0.56 25 26
bone resorption -0.002 0.31 0.68 9 -0.71 24 33
IRF1 -0.023 0.31 0.7 5 -0.75 27 32
mol:GDP -0.1 0.21 0.39 10 -0.43 88 98
SOS1 0.038 0.009 -10000 0 -10000 0 0
VAV1 -0.1 0.22 0.39 10 -0.44 88 98
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.2 -10000 0 -0.58 59 59
PTPN11 0.021 0.093 -10000 0 -0.81 5 5
IL6/IL6RA -0.23 0.2 -10000 0 -0.38 307 307
gp130 (dimer)/TYK2/TYK2/LMO4 0.067 0.11 0.29 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 -0.37 103 106
LMO4 0.029 0.12 0.24 4 -0.54 21 25
STAT3 (dimer)/PIAS3 -0.066 0.33 0.62 6 -0.74 55 61
MCL1 0.07 0.12 0.52 2 -10000 0 2
IL4-mediated signaling events

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
BCL2L1 -0.14 0.62 0.93 3 -1.2 85 88
STAT6 (cleaved dimer) -0.23 0.54 -10000 0 -1.1 107 107
IGHG1 0.026 0.3 0.61 20 -0.66 8 28
IGHG3 -0.15 0.58 0.78 3 -1.1 107 110
AKT1 -0.026 0.35 0.65 1 -0.75 30 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.028 0.28 0.57 6 -0.86 13 19
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 -1.2 92 97
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 0.7 19 -0.66 52 71
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 0.7 2 -0.72 81 83
SOCS3 -0.015 0.39 0.69 2 -1.1 21 23
FCER2 -0.14 0.52 0.89 4 -0.9 74 78
PARP14 0.042 0.032 -10000 0 -10000 0 0
CCL17 -0.12 0.64 1 10 -1.2 89 99
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 -1.2 106 106
IL4R/JAK1 -0.15 0.61 0.8 1 -1.1 96 97
EGR2 -0.51 0.86 0.98 4 -1.3 246 250
JAK2 0.03 0.089 0.27 1 -10000 0 1
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 0.66 9 -1.1 10 19
CCL26 -0.14 0.62 1.1 5 -1.2 89 94
IL4R -0.14 0.68 1.1 7 -1.2 98 105
PTPN6 0.015 0.044 0.2 1 -10000 0 1
IL13RA2 -0.15 0.63 0.97 4 -1.2 99 103
IL13RA1 0.031 0.091 0.26 4 -10000 0 4
IRF4 0.064 0.21 0.71 3 -0.68 7 10
ARG1 0.048 0.26 0.66 8 -0.69 13 21
CBL -0.015 0.36 0.66 6 -0.62 52 58
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 0.36 5 -10000 0 5
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 0.66 6 -0.67 50 56
mitosis -0.02 0.34 0.62 2 -0.7 30 32
STAT6 -0.15 0.76 1.2 15 -1.3 104 119
SPI1 0.043 0.033 -10000 0 -0.24 1 1
RPS6KB1 -0.003 0.33 0.65 5 -0.69 27 32
STAT6 (dimer) -0.15 0.76 1.2 15 -1.3 104 119
STAT6 (dimer)/PARP14 -0.17 0.64 -10000 0 -1.2 104 104
mast cell activation -0.006 0.027 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.018 0.36 0.62 7 -0.75 37 44
FRAP1 -0.026 0.35 0.65 1 -0.75 30 31
LTA -0.14 0.62 0.93 3 -1.2 92 95
FES 0.031 0.037 -10000 0 -0.54 2 2
T-helper 1 cell differentiation 0.14 0.74 1.3 105 -1.2 15 120
CCL11 -0.11 0.61 0.88 6 -1.1 99 105
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.01 0.34 0.62 7 -0.89 16 23
IL2RG 0.044 0.042 0.22 11 -10000 0 11
IL10 -0.1 0.63 1 11 -1.1 84 95
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 -1.2 90 94
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.061 0.55 0.98 14 -0.87 92 106
COL1A1 0.12 0.4 0.77 37 -1 20 57
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 89 89
IL2R gamma/JAK3 0.063 0.039 -10000 0 -10000 0 0
TFF3 -0.27 0.73 0.93 3 -1.3 131 134
ALOX15 -0.14 0.62 0.93 3 -1.2 92 95
MYBL1 0.049 0.054 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.094 0.54 0.81 7 -0.92 96 103
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 -0.71 40 45
mol:PI-3-4-5-P3 -0.025 0.35 0.66 1 -0.75 30 31
PI3K -0.032 0.37 0.66 1 -0.82 30 31
DOK2 0.025 0.039 -10000 0 -0.54 2 2
ETS1 0.002 0.06 0.19 2 -0.51 1 3
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 95 99
PIGR -0.39 0.84 1 11 -1.3 205 216
IGHE -0.042 0.1 0.19 7 -0.28 21 28
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 95 98
RETNLB -0.14 0.62 0.93 3 -1.1 94 97
SELP -0.29 0.82 0.98 10 -1.4 159 169
AICDA -0.14 0.59 0.94 1 -1.1 94 95
EPHB forward signaling

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
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 -0.34 193 193
HRAS/GDP -0.083 0.16 -10000 0 -0.39 43 43
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 4 9
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 -0.41 37 37
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 -0.4 44 44
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 -0.38 34 34
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 -0.28 145 145
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 -0.38 42 42
actin cytoskeleton reorganization -0.077 0.12 -10000 0 -0.32 30 30
CDC42/GDP -0.074 0.14 -10000 0 -0.38 42 42
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 -0.34 6 6
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 -0.39 8 13
MAP2K1 -0.06 0.14 -10000 0 -0.4 33 33
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 36 41
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 -0.27 179 179
RASA1 0.034 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.064 0.14 -10000 0 -0.36 42 42
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 -0.32 28 28
Rac1/GTP -0.089 0.15 -10000 0 -0.28 177 177
Ephrin B/EPHB1/Src/Paxillin -0.087 0.16 -10000 0 -0.29 177 177
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.06 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 0.28 1 -0.3 274 275
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 0.25 3 -0.34 1 4
PI4KA 0.033 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.3 0.25 -10000 0 -0.49 273 273
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 -0.56 328 328
GPR124 0.008 0.1 -10000 0 -0.54 17 17
MAPK1 -0.38 0.29 -10000 0 -0.56 345 345
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 -10000 0 -0.34 23 23
CSF1 0.034 0.008 -10000 0 -10000 0 0
PIK3C2A -0.084 0.091 -10000 0 -0.46 13 13
PI4 Kinase/Pyk2 -0.15 0.13 -10000 0 -0.27 243 243
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 -0.37 8 10
alphaV beta3/Integrin/ppsTEM5 0.04 0.081 -10000 0 -0.34 18 18
RHOA 0.033 0.007 -10000 0 -10000 0 0
VTN 0.032 0.011 -10000 0 -10000 0 0
BCAR1 0.029 0.013 -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 0.25 1 -0.34 33 34
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.069 0.041 -10000 0 -0.32 1 1
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.061 0.028 -10000 0 -0.31 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.068 -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 -0.37 8 11
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 0.31 1 -0.56 323 324
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 0.25 1 -0.34 33 34
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.28 0.53 1 4 -1.2 63 67
IL23A -0.24 0.48 1.1 6 -1 49 55
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.46 0.76 2 -1 60 62
positive regulation of T cell mediated cytotoxicity -0.27 0.52 1.1 8 -1.1 60 68
ITGA3 -0.23 0.47 0.99 5 -1 52 57
IL17F -0.18 0.35 0.71 8 -0.67 67 75
IL12B 0.007 0.082 0.3 8 -10000 0 8
STAT1 (dimer) -0.26 0.5 0.92 5 -1.1 60 65
CD4 -0.24 0.47 1 4 -1 57 61
IL23 -0.24 0.46 0.95 5 -1 49 54
IL23R -0.019 0.21 0.82 3 -1.1 10 13
IL1B -0.25 0.49 1.1 6 -1.1 57 63
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.21 0.47 0.96 6 -0.99 53 59
TYK2 0.003 0.06 0.27 3 -10000 0 3
STAT4 0.027 0.069 0.18 5 -0.54 7 12
STAT3 0.033 0.008 -10000 0 -10000 0 0
IL18RAP -0.006 0.16 -10000 0 -0.54 42 42
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 60 68
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 -0.96 49 55
ALOX12B -0.24 0.46 1 3 -1 54 57
CXCL1 -0.64 0.73 1.1 6 -1.2 294 300
T cell proliferation -0.27 0.52 1.1 8 -1.1 60 68
NFKBIA 0.033 0.01 -10000 0 -10000 0 0
IL17A -0.12 0.3 0.65 12 -0.54 48 60
PI3K -0.28 0.47 0.82 1 -1 73 74
IFNG 0.022 0.074 0.18 63 -0.12 6 69
STAT3 (dimer) -0.26 0.46 0.8 1 -0.99 72 73
IL18R1 0.04 0.03 0.2 1 -0.54 1 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.13 0.34 0.78 10 -0.69 38 48
IL18/IL18R 0.065 0.14 0.3 13 -0.34 42 55
macrophage activation -0.013 0.028 0.076 20 -0.043 40 60
TNF -0.25 0.48 1.1 5 -1.1 50 55
STAT3/STAT4 -0.26 0.48 0.81 2 -1.1 62 64
STAT4 (dimer) -0.27 0.5 0.91 4 -1.1 65 69
IL18 0.047 0.046 -10000 0 -10000 0 0
IL19 -0.2 0.47 0.95 7 -1 51 58
STAT5A (dimer) -0.27 0.49 0.92 3 -1.1 62 65
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 -1 54 58
positive regulation of humoral immune response -0.27 0.52 1.1 8 -1.1 60 68
IL23/IL23R/JAK2/TYK2 -0.28 0.54 1.1 8 -1.2 60 68
IL6 -0.79 0.67 0.94 6 -1.2 367 373
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 1 4 -1 55 59
keratinocyte proliferation -0.27 0.52 1.1 8 -1.1 60 68
NOS2 -0.25 0.46 0.96 5 -0.97 63 68
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.033 0.006 -10000 0 -10000 0 0
GNAT1/GTP 0.024 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.058 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 -0.28 218 218
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 -0.29 218 218
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 -0.27 217 217
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 -0.4 409 409
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
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 4 -0.11 46 50
BUB1B 0.094 0.063 0.16 163 -10000 0 163
PLK1 0.046 0.035 0.11 54 -10000 0 54
PLK1S1 0.023 0.019 0.06 48 -10000 0 48
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 0.17 197 -10000 0 197
WEE1 0.049 0.077 0.22 2 -0.31 16 18
cytokinesis 0.13 0.082 0.22 115 -0.39 1 116
PP2A-alpha B56 0.14 0.11 -10000 0 -0.5 2 2
AURKA 0.051 0.04 0.14 11 -0.16 2 13
PICH/PLK1 0.13 0.095 0.24 177 -10000 0 177
CENPE 0.084 0.067 0.16 170 -10000 0 170
RhoA/GTP 0.024 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.039 0.037 0.27 4 -10000 0 4
PPP2CA 0.033 0.006 -10000 0 -10000 0 0
FZR1 0.034 0.009 -10000 0 -10000 0 0
TPX2 0.08 0.039 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 48 -10000 0 48
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 -0.51 5 5
TPT1 0.014 0.059 0.13 1 -0.17 39 40
CDC25C 0.083 0.067 0.16 22 -0.22 11 33
CDC25B 0.048 0.041 -10000 0 -10000 0 0
SGOL1 0.036 0.043 0.11 46 -0.12 4 50
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 0.14 154 -10000 0 154
mitosis -0.001 0.003 0.033 2 -10000 0 2
FBXO5 0.038 0.044 0.16 22 -10000 0 22
CDC2 0.005 0.004 0.016 32 -10000 0 32
NDC80 0.11 0.074 -10000 0 -10000 0 0
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 0.089 13 -0.094 2 15
microtubule cytoskeleton organization 0.014 0.059 0.13 1 -0.17 39 40
G2/M transition DNA damage checkpoint 0 0.003 0.014 8 -10000 0 8
PPP1R12A 0.035 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.014 8 -10000 0 8
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 0.18 226 -10000 0 226
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 0.14 154 -10000 0 154
PRC1 0.1 0.074 0.18 245 -10000 0 245
ECT2 0.072 0.074 0.19 117 -10000 0 117
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 0.16 163 -10000 0 163
spindle assembly 0.036 0.03 0.1 29 -10000 0 29
spindle stabilization 0.023 0.019 0.06 48 -10000 0 48
APC/C/HCDH1 0.021 0.059 -10000 0 -0.34 13 13
MKLP2/PLK1 0.12 0.066 0.18 226 -10000 0 226
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 0.12 2 -0.16 15 17
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 48 -10000 0 48
INCENP 0.047 0.04 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.025 0.12 0.24 1 -0.33 46 47
adherens junction organization -0.026 0.13 0.23 1 -0.34 48 49
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 44 44
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 -0.29 47 47
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.028 0.18 -10000 0 -0.52 40 40
CTNND1 0.033 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.021 0.11 0.26 1 -0.32 39 40
VASP -0.021 0.12 0.24 1 -0.39 24 25
ZYX -0.026 0.12 -10000 0 -0.32 48 48
JUB -0.025 0.12 -10000 0 -0.31 54 54
EGFR(dimer) -0.16 0.2 -10000 0 -0.42 116 116
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 51 51
PIK3CA 0.032 0.011 -10000 0 -10000 0 0
PI3K -0.007 0.13 -10000 0 -0.31 51 51
FYN -0.025 0.11 0.24 1 -0.38 24 25
mol:Ca2+ -0.024 0.099 -10000 0 -0.28 44 44
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 44 44
CDH1 0.006 0.12 -10000 0 -0.54 22 22
RhoA/GDP -0.14 0.18 0.32 3 -0.38 102 105
establishment of polarity of embryonic epithelium -0.021 0.12 0.24 1 -0.38 24 25
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 -0.27 43 45
RhoA/GTP -0.006 0.1 -10000 0 -0.27 43 43
AKT2 -0.022 0.11 -10000 0 -0.29 46 46
actin cable formation -0.021 0.12 0.25 3 -0.38 24 27
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 -0.39 111 111
PIP5K1A -0.023 0.11 -10000 0 -0.32 42 42
PLCG1 -0.025 0.1 -10000 0 -0.3 44 44
Rac1/GTP -0.14 0.19 -10000 0 -0.39 115 115
homophilic cell adhesion -0.001 0.004 -10000 0 -10000 0 0
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 -0.36 44 44
AP1 -0.19 0.23 -10000 0 -0.46 159 159
mol:PIP3 0.006 0.19 0.37 21 -0.48 30 51
IKBKB 0.022 0.14 0.3 38 -0.27 33 71
AKT1 -0.006 0.2 0.33 75 -0.46 29 104
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 -0.41 23 34
mol:Ca2+ 0.014 0.16 0.32 30 -0.36 29 59
LYN 0.032 0.018 -10000 0 -10000 0 0
CBLB -0.029 0.13 -10000 0 -0.37 42 42
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 -0.34 90 156
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 0.35 20 -0.34 30 50
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 -0.43 45 45
LAT -0.026 0.12 -10000 0 -0.42 25 25
PAK2 0.009 0.16 0.38 10 -0.45 22 32
NFATC2 -0.011 0.057 -10000 0 -0.69 1 1
HRAS 0.005 0.16 0.32 9 -0.47 25 34
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 0.29 1 -0.46 26 27
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 -0.37 46 46
CHUK 0.004 0.13 0.28 23 -0.27 35 58
KLRG1 -0.024 0.12 -10000 0 -0.41 22 22
VAV1 -0.028 0.13 0.22 1 -0.36 43 44
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.028 0.12 -10000 0 -0.36 44 44
negative regulation of mast cell degranulation -0.027 0.11 -10000 0 -0.39 22 22
BTK -0.024 0.15 -10000 0 -0.49 25 25
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.047 0.17 -10000 0 -0.37 92 92
GAB2/PI3K/SHP2 -0.062 0.15 -10000 0 -0.37 73 73
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.032 0.13 -10000 0 -0.47 28 28
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 -0.58 39 39
DUSP1 -0.2 0.28 -10000 0 -0.54 208 208
NF-kappa-B/RelA 0.014 0.082 0.18 12 -0.18 17 29
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 -0.46 35 35
FER -0.028 0.12 -10000 0 -0.36 43 43
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 -0.42 26 26
PTK2 -0.015 0.18 -10000 0 -0.62 22 22
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.039 0.16 -10000 0 -0.44 47 47
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.029 0.22 0.37 15 -0.51 49 64
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 -0.38 21 22
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 90 156
SHC/Grb2/SOS1 0.01 0.14 -10000 0 -0.43 19 19
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 22 22
HCLS1 -0.028 0.13 -10000 0 -0.36 43 43
PRKCB -0.003 0.16 0.32 22 -0.36 38 60
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 -0.4 22 22
LCP2 0.037 0.023 -10000 0 -10000 0 0
PLA2G4A -0.16 0.2 -10000 0 -0.35 211 211
RASA1 0.034 0.012 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.011 0.2 0.34 66 -0.34 90 156
IKK complex 0.023 0.12 0.28 35 -0.22 17 52
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 -0.19 1 34
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 0.21 27 -0.23 139 166
BIRC5 0.12 0.076 -10000 0 -10000 0 0
DES -0.012 0.13 -10000 0 -0.58 20 20
Aurora C/Aurora B/INCENP 0.075 0.052 0.23 16 -10000 0 16
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 0.23 252 -10000 0 252
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 11 -0.43 31 42
PSMA3 0.033 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.005 -10000 0 -10000 0 0
H3F3B 0.031 0.037 -10000 0 -10000 0 0
AURKB 0.05 0.054 -10000 0 -10000 0 0
AURKC 0.036 0.019 0.18 8 -10000 0 8
CDCA8 0.11 0.074 -10000 0 -10000 0 0
cytokinesis 0.18 0.15 0.35 193 -10000 0 193
Aurora B/Septin1 0.18 0.15 0.38 127 -10000 0 127
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 0.21 2 -10000 0 2
hSgo1/Aurora B/Survivin 0.13 0.099 0.31 65 -10000 0 65
EVI5 0.036 0.026 -10000 0 -0.53 1 1
RhoA/GTP 0.22 0.14 0.36 207 -10000 0 207
SGOL1 0.073 0.065 -10000 0 -10000 0 0
CENPA 0.14 0.12 0.29 176 -10000 0 176
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 -0.43 12 12
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 0.37 239 -10000 0 239
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
NSUN2 0.027 0.093 -10000 0 -0.75 2 2
MYLK -0.071 0.17 -10000 0 -0.34 139 139
KIF23 0.12 0.075 0.2 4 -10000 0 4
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 -0.69 6 6
Chromosomal passenger complex 0.16 0.13 0.29 233 -10000 0 233
Chromosomal passenger complex/EVI5 0.14 0.11 0.37 24 -10000 0 24
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 -0.56 73 75
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 -0.48 30 32
SMO -0.016 0.18 0.44 2 -0.5 30 32
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 -0.49 31 33
STIL 0.042 0.15 0.35 26 -0.34 7 33
DHH N/PTCH2 0.049 0.01 -10000 0 -10000 0 0
DHH N/PTCH1 0.006 0.16 0.38 2 -0.32 81 83
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 0.67 2 -0.9 94 96
determination of left/right symmetry -0.016 0.18 0.44 2 -0.49 31 33
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
skeletal system development -0.11 0.39 0.67 2 -0.89 94 96
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 -0.49 31 33
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 -0.38 48 48
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 -0.49 31 33
SHH Np/Cholesterol/PTCH1 -0.01 0.12 -10000 0 -0.38 8 8
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 84 86
SMO/Vitamin D3 0.01 0.17 0.41 16 -0.46 12 28
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 37 46
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 -0.38 8 25
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 -0.4 136 136
PTCH2 0.034 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.014 0.034 -10000 0 -0.31 5 5
PTCH1 -0.009 0.18 0.47 2 -0.36 84 86
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 -0.4 64 64
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 -0.37 9 11
SLIT2 -0.039 0.19 -10000 0 -0.54 64 64
GPC1/NRG -0.002 0.13 -10000 0 -0.4 43 43
NRG1 -0.019 0.16 -10000 0 -0.54 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.07 0.039 0.25 1 -10000 0 1
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 -0.39 70 70
LCK 0.031 0.033 -10000 0 -10000 0 0
neuron differentiation -0.002 0.13 -10000 0 -0.4 43 43
PrPc/Cu2+ 0.013 0.069 -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
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.43 71 71
positive regulation of JNK cascade -0.025 0.15 -10000 0 -0.32 87 87
CDC42/GDP -0.019 0.2 0.46 1 -0.42 90 91
Rac1/GDP -0.019 0.2 -10000 0 -0.42 90 90
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 86 86
nectin-3/I-afadin -0.024 0.17 -10000 0 -0.39 85 85
RAPGEF1 -0.043 0.2 0.47 1 -0.46 83 84
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.22 -10000 0 -0.51 85 85
PDGFB-D/PDGFRB 0.034 0.006 -10000 0 -10000 0 0
TLN1 -0.039 0.12 0.2 3 -0.47 22 25
Rap1/GTP -0.03 0.14 -10000 0 -0.33 79 79
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 90 91
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 -0.34 106 106
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.4 3 3
positive regulation of lamellipodium assembly -0.021 0.16 -10000 0 -0.33 88 88
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 -0.54 98 98
ITGB3 0.035 0.019 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.046 -10000 0 -0.4 3 3
FARP2 -0.045 0.24 0.48 1 -0.53 80 81
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 -0.4 3 3
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 87 87
alphaV/beta3 Integrin/Talin -0.005 0.13 0.3 1 -0.46 20 21
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.25 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 -0.52 86 87
RAP1/GDP -0.015 0.19 -10000 0 -0.39 84 84
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 88 88
PTPRM -0.035 0.14 -10000 0 -0.29 84 84
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
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.049 0.011 -10000 0 -10000 0 0
Necdin/E2F1 -0.045 0.18 -10000 0 -0.38 111 111
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 98 101
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 0.18 7 -10000 0 7
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 0.18 34 -10000 0 34
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 81 81
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 -0.39 81 81
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 -0.35 81 81
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 71 79
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 0.29 7 -0.33 74 81
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 -0.33 78 78
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 70 77
MAPK9 -0.025 0.13 0.28 7 -0.32 71 78
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 -0.34 81 81
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.027 0.14 -10000 0 -0.3 74 74
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 -0.39 101 101
BAD -0.025 0.15 0.4 9 -0.33 73 82
RIPK2 0.029 0.021 0.18 6 -10000 0 6
NGFR -0.054 0.2 -10000 0 -0.54 75 75
CYCS -0.008 0.13 0.26 7 -0.29 72 79
ADAM17 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.003 0.12 -10000 0 -0.31 61 61
BCL2L11 -0.025 0.15 0.4 9 -0.33 73 82
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 74 83
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 -0.27 2 2
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 -0.26 75 75
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 -0.32 284 284
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 0.36 23 -10000 0 23
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 19 -10000 0 19
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 40 40
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 -0.49 8 8
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 -0.33 5 5
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
Stabilization and expansion of the E-cadherin adherens junction

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
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 -0.32 1 6
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 26 26
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 7 7
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 0.34 17 -0.29 1 18
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
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.036 0.085 -10000 0 -0.41 14 14
HDAC1 0.023 0.028 -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 -0.34 338 338
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 14 14
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 -0.34 338 338
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 -0.51 14 14
DVL1 -0.039 0.094 -10000 0 -0.36 28 28
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.081 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 0.37 1 -0.48 13 14
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
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 -0.2 15 43
RB1 0.005 0.072 0.23 13 -0.2 31 44
CDK4 -0.003 0.073 0.21 35 -0.21 13 48
CDK6 -0.005 0.073 0.21 33 -0.22 16 49
G1/S progression 0.003 0.087 0.21 53 -0.23 15 68
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.012 -10000 0 -10000 0 0
CDC42/GTP -0.067 0.14 -10000 0 -0.31 62 62
PLCG1 -0.073 0.13 -10000 0 -0.33 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.033 0.01 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.045 0.017 -10000 0 -10000 0 0
cell migration -0.067 0.14 -10000 0 -0.31 62 62
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.07 0.13 -10000 0 -0.34 49 49
MAPK1 -0.077 0.13 -10000 0 -0.33 56 56
S1P/S1P5/Gi -0.081 0.14 -10000 0 -0.25 186 186
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
CDC42/GDP 0.024 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.034 0.051 0.19 49 -10000 0 49
S1P/S1P4/Gi -0.081 0.14 -10000 0 -0.25 186 186
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.062 -10000 0 -0.54 6 6
S1P/S1P4/G12/G13 0.039 0.014 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
CDC42 0.033 0.007 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 0.005 0.13 -10000 0 -0.38 52 52
CRKL -0.002 0.11 0.37 1 -0.41 14 15
mol:PIP3 0.009 0.064 0.49 7 -10000 0 7
AKT1 0.021 0.08 0.39 11 -10000 0 11
PTK2B 0.027 0.014 -10000 0 -10000 0 0
RAPGEF1 -0.003 0.11 0.35 1 -0.43 10 11
RANBP10 0.03 0.012 -10000 0 -10000 0 0
PIK3CA 0.033 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 -0.43 352 352
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 -0.42 10 11
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.032 0.008 -10000 0 -10000 0 0
PTEN 0.026 0.067 -10000 0 -0.54 7 7
ELK1 -0.019 0.084 0.26 15 -0.21 34 49
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.006 0.064 -10000 0 -0.26 5 5
PAK1 0.046 0.099 0.44 12 -10000 0 12
HGF/MET/RANBP10 0.021 0.12 -10000 0 -0.34 50 50
HRAS -0.032 0.2 -10000 0 -0.58 58 58
DOCK1 -0.004 0.11 0.43 2 -0.44 10 12
GAB1 -0.003 0.12 -10000 0 -0.41 17 17
CRK -0.003 0.11 0.37 1 -0.45 10 11
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 34 49
HGF/MET/MUC20 0.008 0.12 -10000 0 -0.34 51 51
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 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.012 0.097 -10000 0 -0.29 41 41
MET/MUC20 -0.017 0.13 -10000 0 -0.39 52 52
RAP1B 0.003 0.11 0.32 2 -0.41 9 11
RAP1A -0.004 0.1 0.51 1 -0.42 9 10
HGF/MET/RANBP9 0.027 0.12 -10000 0 -0.34 48 48
RAF1 -0.025 0.19 -10000 0 -0.55 58 58
STAT3 -0.007 0.11 -10000 0 -0.42 16 16
cell proliferation 0.025 0.15 0.34 11 -0.38 37 48
RPS6KB1 0.001 0.061 -10000 0 -0.3 11 11
MAPK3 -0.037 0.081 0.55 4 -10000 0 4
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 86 86
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 56 57
MET -0.022 0.17 -10000 0 -0.54 50 50
MAP4K1 0.002 0.12 0.39 1 -0.44 15 16
PTK2 0.027 0.014 -10000 0 -10000 0 0
MAP2K2 -0.022 0.18 0.48 1 -0.51 58 59
BAD 0.018 0.074 0.39 7 -10000 0 7
MAP2K4 -0.013 0.12 0.35 1 -0.39 22 23
SHP2/GRB2/SOS1/GAB1 0.02 0.14 -10000 0 -0.36 51 51
INPPL1 0.032 0.01 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
SH3KBP1 0.033 0.027 -10000 0 -0.54 1 1
HGS -0.015 0.077 -10000 0 -0.25 44 44
PLCgamma1/PKC 0.024 0.006 -10000 0 -10000 0 0
HGF 0.035 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 51 51
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 -0.26 1 4
AP1 -0.22 0.19 -10000 0 -0.33 345 345
mol:PIP3 -0.15 0.16 -10000 0 -0.29 276 276
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 -0.28 17 17
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 -0.23 13 18
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 44 44
ADCY6 -0.047 0.094 -10000 0 -0.22 44 44
ADCY7 -0.037 0.091 -10000 0 -0.27 19 19
ADCY1 -0.046 0.093 -10000 0 -0.28 14 14
ADCY2 -0.05 0.1 -10000 0 -0.24 47 47
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 0.15 2 -0.26 2 4
HRAS 0.034 0.013 -10000 0 -10000 0 0
NFKBIA 0.027 0.061 0.27 3 -0.27 2 5
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 -0.13 1 1
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 0.15 2 -0.28 10 12
EGFR/PI3K-beta/Gab1 -0.15 0.17 -10000 0 -0.3 276 276
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 -10000 0 -0.21 5 5
GNAI3 0.02 0.023 -10000 0 -0.22 4 4
GNAI1 -0.11 0.17 -10000 0 -0.34 184 184
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 -0.28 27 28
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 0.37 8 -0.4 229 237
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 -0.19 5 5
PI3K-beta -0.01 0.089 -10000 0 -0.37 8 8
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 0.21 9 -0.26 1 10
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 4 4
MAPKKK cascade -0.054 0.1 -10000 0 -0.24 61 61
contractile ring contraction involved in cytokinesis 0.008 0.068 -10000 0 -0.27 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.021 0.039 -10000 0 -0.31 4 4
GNA15 0.016 0.014 -10000 0 -10000 0 0
GNA12 0.034 0.005 -10000 0 -10000 0 0
GNA13 0.031 0.01 -10000 0 -10000 0 0
MAPT -0.015 0.08 0.23 5 -0.24 13 18
GNA11 0.015 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.051 0.11 -10000 0 -0.91 7 7
MMP2 0.016 0.053 0.27 2 -0.47 5 7
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.005 0.015 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.1 -10000 0 -0.29 13 13
NFATC4 -0.028 0.08 0.28 3 -10000 0 3
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 27 27
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 0.23 6 -0.26 7 13
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.037 0.093 -10000 0 -0.32 27 27
RAF1 -0.038 0.096 -10000 0 -0.3 17 17
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 0.27 6 -0.26 3 9
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.26 0.28 -10000 0 -0.65 125 125
FOS -0.33 0.26 -10000 0 -0.49 366 366
NRAS 0.034 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.087 -10000 0 -0.3 27 27
MAPK3 -0.16 0.21 -10000 0 -0.5 94 94
MAPK1 -0.18 0.24 -10000 0 -0.55 111 111
JAK2 -0.033 0.089 0.26 2 -0.29 26 28
NF2 0.003 0.069 -10000 0 -0.68 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.08 -10000 0 -0.28 24 24
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 -0.29 31 31
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 -0.38 88 88
myelination -0.021 0.089 0.35 5 -10000 0 5
PPP3CB -0.033 0.086 0.25 2 -0.28 9 11
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 -0.28 24 24
SOS1 0.033 0.004 -10000 0 -10000 0 0
MAP2K2 -0.054 0.1 -10000 0 -0.32 18 18
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 -0.59 53 53
heart morphogenesis -0.036 0.087 -10000 0 -0.3 27 27
RAS family/GDP 0.029 0.11 -10000 0 -0.29 7 7
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 27 27
CDC42 0.033 0.007 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 81 -0.34 8 89
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 51 51
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 32 -0.37 11 43
Syndecan-1/CD147 0.093 0.15 0.31 29 -0.32 10 39
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 22 -0.37 34 56
regulation of cell adhesion 0.061 0.12 0.27 21 -0.33 6 27
HPSE 0.045 0.04 -10000 0 -10000 0 0
positive regulation of cell migration 0.087 0.14 0.27 81 -0.34 8 89
SDC1 0.087 0.13 0.26 93 -0.32 4 97
Syndecan-1/Collagen 0.087 0.14 0.27 81 -0.34 8 89
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 0.26 96 -0.34 8 104
MMP1 0.11 0.077 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.028 0.081 -10000 0 -0.43 10 10
Crk/p130 Cas/Paxillin -0.082 0.14 -10000 0 -0.38 69 69
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 -0.29 47 47
GRB7 0.029 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.11 0.17 -10000 0 -0.3 59 59
MAPKKK cascade 0.057 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 -0.35 73 73
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 -10000 0 -10000 0 0
DOK6 0.032 0.049 -10000 0 -0.54 3 3
PXN 0.034 0.003 -10000 0 -10000 0 0
neurite development 0.043 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 -0.37 8 12
HRAS/GTP 0.092 0.16 0.3 4 -0.32 44 48
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 -10000 0 -0.31 63 63
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 -0.38 3 9
PI3K -0.039 0.26 0.31 8 -0.54 76 84
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 0.25 12 -0.34 3 15
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 -0.33 4 10
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 -10000 0 -10000 0 0
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 72 75
RET9/GFRalpha1/GDNF 0.038 0.15 -10000 0 -0.34 63 63
GFRalpha1/GDNF 0.039 0.17 -10000 0 -0.39 66 66
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 0.53 41 -0.59 39 80
IL12B 0.042 0.027 0.2 11 -10000 0 11
IL12A 0.005 0.061 0.14 6 -0.4 11 17
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 0.23 1 -10000 0 1
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 0.79 24 -1 22 46
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 -0.72 19 21
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 -0.11 9 111
T cell differentiation 0 0.009 0.02 27 -0.024 19 46
STAT3 (dimer) 0.023 0.21 0.48 6 -0.69 22 28
STAT5A (dimer) 0.023 0.21 0.48 6 -0.67 24 30
STAT4 (dimer) 0.021 0.21 0.5 6 -0.67 25 31
STAT4 0.027 0.069 0.18 5 -0.54 7 12
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 0.7 14 -1.3 33 47
IL18 0.019 0.036 0.14 26 -10000 0 26
positive regulation of mast cell cytokine production 0.024 0.2 0.46 7 -0.67 22 29
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 -0.41 142 142
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 0.18 7 -10000 0 7
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 0.46 100 -10000 0 100
SHC 2-3/Grb2 -0.13 0.23 -10000 0 -0.51 100 100
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 -0.14 0.24 -10000 0 -0.53 117 117
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 0.28 3 -0.3 13 16
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 0.18 34 -10000 0 34
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 -0.3 15 15
ELMO1 0.034 0.005 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.042 0.032 -10000 0 -0.29 4 4
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.013 -10000 0 -10000 0 0
DOCK1 0.03 0.044 -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 -0.33 79 79
mol:GDP -0.008 0.15 0.34 6 -0.44 17 23
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 -0.29 14 15
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 -0.26 12 12
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 -0.26 15 15
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 0.29 6 -0.29 14 20
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 -0.38 48 48
FRS3 0.033 0.006 -10000 0 -10000 0 0
FAIM 0.033 0.006 -10000 0 -10000 0 0
GAB1 0.033 0.027 -10000 0 -0.54 1 1
RASGRF1 -0.052 0.14 -10000 0 -0.34 76 76
SOS1 0.034 0.004 -10000 0 -10000 0 0
MCF2L -0.083 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 -0.3 13 18
NGF (dimer)/TRKA/GRIT 0.02 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.025 0.22 0.42 1 -0.75 26 27
NGF (dimer)/TRKA/NEDD4-2 0.03 0.058 -10000 0 -0.26 15 15
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 -0.21 20 20
NGF (dimer)/TRKA -0.059 0.14 -10000 0 -0.36 81 81
Rac1/GTP -0.05 0.098 -10000 0 -0.28 40 40
FRS2 family/SHP2/CRK family 0.082 0.046 -10000 0 -0.3 1 1
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.4 107 108
AKT1 0.038 0.02 -10000 0 -10000 0 0
GSC -0.095 0.4 -10000 0 -1.3 46 46
NKX2-5 0.045 0.05 -10000 0 -10000 0 0
muscle cell differentiation 0 0.12 0.47 17 -10000 0 17
SMAD2-3/SMAD4/SP1 0.053 0.12 -10000 0 -0.31 13 13
SMAD4 -0.028 0.084 -10000 0 -0.26 28 28
CBFB 0.03 0.014 -10000 0 -10000 0 0
SAP18 0.032 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 -0.75 20 20
AP1 -0.26 0.29 -10000 0 -0.42 331 331
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 -0.19 1 1
SMAD3/SMAD4/GR -0.045 0.14 -10000 0 -0.39 52 52
GATA3 0.038 0.16 -10000 0 -0.53 33 33
SKI/SIN3/HDAC complex/NCoR1 0.017 0.083 -10000 0 -0.41 12 12
MEF2C/TIF2 0.008 0.15 0.34 3 -0.53 25 28
endothelial cell migration -0.058 0.11 0.57 7 -10000 0 7
MAX 0.025 0.024 -10000 0 -10000 0 0
RBBP7 0.037 0.022 -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 -0.33 30 30
DCP1A 0.033 0.008 -10000 0 -10000 0 0
SKI 0.033 0.007 -10000 0 -10000 0 0
SERPINE1 0.058 0.11 -10000 0 -0.57 7 7
SMAD3/SMAD4/ATF2 0.004 0.092 -10000 0 -0.29 9 9
SMAD3/SMAD4/ATF3 -0.09 0.2 -10000 0 -0.41 132 132
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 0.29 1 -0.41 328 329
SMAD3/SMAD4/IRF7 0.021 0.094 -10000 0 -0.29 9 9
TFE3 0.03 0.046 -10000 0 -10000 0 0
COL1A2 0.075 0.13 0.41 8 -0.71 5 13
mesenchymal cell differentiation -0.005 0.093 0.26 15 -10000 0 15
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 -0.29 10 10
IRF7 0.039 0.024 -10000 0 -10000 0 0
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 -0.54 29 38
SMAD2-3/SMAD4 0.009 0.11 -10000 0 -0.31 20 20
Cbp/p300/Src-1 0.062 0.039 -10000 0 -0.32 2 2
IGHV3OR16-13 -0.007 0.07 -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 -0.4 296 296
SMAD2 0.02 0.053 -10000 0 -0.23 1 1
SMAD3 -0.015 0.063 -10000 0 -0.22 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.07 -10000 0 -0.31 6 6
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 -0.3 14 14
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 -0.48 121 121
MYC/MIZ-1 0.008 0.098 -10000 0 -0.41 25 25
SMAD3/SMAD4 0.032 0.097 0.32 12 -0.38 3 15
IL10 -0.006 0.12 0.4 1 -0.38 25 26
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 -0.38 24 25
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 -0.29 13 13
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 -0.54 29 38
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 -0.28 10 10
SMAD3/SMAD4/GATA3 0.027 0.15 -10000 0 -0.41 32 32
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 48 48
SMAD3/SMAD4/SP1-3 0.061 0.11 -10000 0 -0.33 5 5
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 -0.35 27 27
ITGB5 -0.003 0.084 0.33 1 -0.45 3 4
TGIF/SIN3/HDAC complex/CtBP 0.024 0.07 -10000 0 -0.33 12 12
SMAD3/SMAD4/AR -0.044 0.16 -10000 0 -0.39 72 72
AR -0.04 0.19 -10000 0 -0.54 66 66
negative regulation of cell growth -0.022 0.12 -10000 0 -0.38 23 23
SMAD3/SMAD4/MYOD 0.004 0.096 -10000 0 -0.28 17 17
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 -0.35 11 11
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.11 -10000 0 -0.36 22 22
TFDP1 0.033 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.25 0.3 -10000 0 -0.42 330 330
SMAD3/SMAD4/RUNX2 0.006 0.093 -10000 0 -0.27 15 15
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
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.38 4 14
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 0.28 1 -0.32 34 35
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 0.44 33 -10000 0 33
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 -0.33 3 3
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 -0.38 7 7
NRG1 -0.015 0.12 -10000 0 -0.4 41 41
NRG3 0.035 0.043 -10000 0 -0.54 2 2
NRG2 -0.35 0.27 -10000 0 -0.54 339 339
NRG4 0.034 0.013 -10000 0 -10000 0 0
heart development 0.12 0.14 0.44 33 -10000 0 33
neural crest cell migration 0.003 0.11 -10000 0 -0.38 7 7
ERBB2 0.021 0.028 0.3 1 -0.37 1 2
WWOX/E4ICDs 0.028 0.1 0.34 6 -0.34 3 9
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 0.36 4 -0.34 1 5
ErbB4/ErbB4/betacellulin/betacellulin 0.022 0.12 0.31 6 -0.35 18 24
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 0.35 28 -0.34 3 31
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.1 -10000 0 -0.3 34 34
STAT5A 0.11 0.12 0.41 32 -10000 0 32
ErbB4/EGFR/neuregulin 1 beta -0.15 0.18 -10000 0 -0.46 60 60
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 28 -0.36 1 29
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 0.45 31 -10000 0 31
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 0.28 1 -0.43 26 27
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 0.42 11 -0.42 5 16
RXR and RAR heterodimerization with other nuclear receptor

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
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 -0.26 262 262
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 -10000 0 -10000 0 0
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 -10000 0 0
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 75 75
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 98 98
RXRs/FXR 0.084 0.065 -10000 0 -0.31 4 4
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
FOXA2 and FOXA3 transcription factor networks

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
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 0.79 2 -0.76 3 5
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 -0.74 15 15
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 -0.65 44 45
PKLR 0.035 0.19 -10000 0 -0.79 2 2
APOA1 0.022 0.22 -10000 0 -0.88 3 3
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 -0.22 1 1
CPT1A 0.025 0.21 0.68 5 -0.7 3 8
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 -0.26 372 372
IGFBP1 0.015 0.14 -10000 0 -0.66 4 4
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 -0.36 49 50
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 -0.22 1 1
G6PC -0.098 0.12 -10000 0 -10000 0 0
SLC2A2 0.047 0.16 -10000 0 -1.1 1 1
INS 0.022 0.015 0.25 1 -10000 0 1
FOXA1 -0.003 0.23 0.38 3 -0.53 73 76
FOXA3 -0.12 0.14 0.3 1 -0.26 124 125
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 -0.84 3 4
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.089 0.16 0.34 70 -0.4 11 81
FYN 0.061 0.16 0.4 28 -0.4 18 46
LAT/GRAP2/SLP76 0.071 0.16 0.43 26 -0.41 11 37
IKBKB 0.029 0.013 -10000 0 -10000 0 0
AKT1 0.059 0.16 0.35 54 -0.31 29 83
B2M 0.037 0.011 -10000 0 -10000 0 0
IKBKG 0.034 0.071 0.19 50 -10000 0 50
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 0.47 25 -0.41 28 53
TRPV6 0.013 0.22 1.3 10 -0.54 17 27
CD28 0.028 0.084 0.18 14 -0.55 10 24
SHC1 0.072 0.18 0.34 77 -0.45 16 93
receptor internalization 0.024 0.19 0.36 26 -0.39 65 91
PRF1 0.037 0.16 0.54 10 -0.79 6 16
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 0.33 50 -0.31 36 86
LAT 0.055 0.17 0.4 30 -0.44 16 46
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D 0.04 0.036 0.21 8 -10000 0 8
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 0.43 31 -0.33 15 46
HLA-A 0.041 0.025 0.22 2 -10000 0 2
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 0.22 91 -0.13 2 93
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.01 0.048 -10000 0 -0.18 16 16
PRKCA 0.041 0.1 0.31 29 -0.22 5 34
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 0.044 1 -10000 0 1
TCR/CD3/MHC I/CD8 0.024 0.13 0.31 21 -0.3 48 69
ORAI1 -0.02 0.17 -10000 0 -1.1 10 10
CSK 0.045 0.16 0.4 20 -0.43 16 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 0.37 26 -0.42 17 43
VAV1 0.043 0.16 0.44 19 -0.42 20 39
Monovalent TCR/CD3 0.023 0.1 0.27 22 -0.37 21 43
CBL 0.03 0.011 -10000 0 -10000 0 0
LCK 0.062 0.16 0.39 30 -0.41 14 44
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 25 -0.42 24 49
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 15 15
HRAS 0.034 0.013 -10000 0 -10000 0 0
GO:0035030 0.042 0.14 0.38 27 -0.38 14 41
CD8A 0.003 0.006 0.046 2 -10000 0 2
CD8B 0.041 0.026 -10000 0 -10000 0 0
PTPRC 0.035 0.035 0.18 19 -10000 0 19
PDK1/PKC theta 0.07 0.19 0.42 56 -0.39 18 74
CSK/PAG1 0.064 0.16 0.38 31 -0.45 12 43
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 0.46 19 -0.42 16 35
STIM1 0.004 0.1 1.2 3 -10000 0 3
RAS family/GTP 0.076 0.11 0.28 55 -0.18 10 65
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.021 0.19 0.36 26 -0.41 65 91
mol:DAG -0.016 0.068 0.13 2 -0.28 13 15
RAP1A/GDP 0.036 0.048 0.13 56 -10000 0 56
PLCG1 0.032 0.008 -10000 0 -10000 0 0
CD247 0.022 0.11 -10000 0 -0.55 15 15
cytotoxic T cell degranulation 0.038 0.16 0.53 10 -0.75 6 16
RAP1A/GTP 0.002 0.016 -10000 0 -0.06 27 27
mol:PI-3-4-5-P3 0.054 0.17 0.44 28 -0.35 28 56
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.023 0.12 0.32 10 -0.41 10 20
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 0.3 12 -0.4 11 23
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 0.15 5 -0.2 13 18
PRKCE 0.045 0.11 0.3 33 -0.22 9 42
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 75 -10000 0 75
RAS family/GDP 0 0.009 -10000 0 -10000 0 0
MAP3K14 0.028 0.14 0.28 50 -0.24 32 82
PDPK1 0.063 0.16 0.38 56 -0.3 25 81
TCR/CD3/MHC I/CD8/Fyn 0.013 0.17 0.38 15 -0.54 18 33
TCGA08_rtk_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
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 -0.29 23 28
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 0.31 23 -0.3 1 24
PI3K -0.068 0.16 0.32 9 -0.31 102 111
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 -0.18 8 15
AKT2 0.034 0.006 -10000 0 -10000 0 0
PTEN 0.026 0.067 -10000 0 -0.54 7 7
Syndecan-2-mediated signaling events

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
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 0.2 87 -0.3 16 103
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 0.34 3 -0.33 17 20
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 -0.27 16 16
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 0.23 4 -0.3 16 20
angiogenesis 0.024 0.073 0.23 1 -0.33 16 17
MMP2 0.028 0.039 -10000 0 -0.54 2 2
IL8 0.048 0.053 -10000 0 -0.54 1 1
calcineurin-NFAT signaling pathway 0.016 0.065 -10000 0 -0.33 16 16
mTOR 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
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 0.28 3 -0.29 68 71
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 -0.28 34 37
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.057 -10000 0 -0.2 14 14
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 -0.24 11 11
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 -0.33 22 26
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 1 -0.002 61 62
EIF4B -0.008 0.096 0.29 4 -0.32 15 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.016 0.098 -10000 0 -0.3 14 14
eIF4E/eIF4G1/eIF4A1 -0.002 0.069 -10000 0 -0.3 18 18
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 11 -0.21 12 23
FKBP1A 0.034 0.012 -10000 0 -10000 0 0
RHEB/GTP 0.005 0.1 0.25 3 -0.26 32 35
mol:Amino Acids 0 0.001 0.001 1 -0.002 61 62
FKBP12/Rapamycin 0.025 0.009 -10000 0 -10000 0 0
PDPK1 -0.051 0.12 0.25 4 -0.29 85 89
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 -0.26 1 1
TSC1/TSC2 -0.003 0.12 0.29 3 -0.3 34 37
tumor necrosis factor receptor activity 0 0.001 0.002 61 -0.001 1 62
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 0.24 5 -0.3 73 78
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 0.4 2 -0.44 18 20
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 12 -0.003 6 18
EEF2 0.02 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.016 0.24 -10000 0 -0.97 29 29
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.28 1 1
alphaM/beta2 Integrin/Talin -0.02 0.072 -10000 0 -10000 0 0
AGER -0.035 0.051 -10000 0 -0.59 1 1
RAP1A 0.034 0.005 -10000 0 -10000 0 0
SELPLG 0.034 0.028 -10000 0 -0.54 1 1
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.1 0.14 -10000 0 -0.37 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 -0.35 7 7
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 0.32 3 -0.5 4 7
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 -0.36 299 300
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 -10000 0 -10000 0 0
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 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA/Plg 0.01 0.091 -10000 0 -0.36 1 1
RhoA/GTP 0.043 0.1 -10000 0 -0.42 11 11
positive regulation of phagocytosis 0.036 0.083 0.3 2 -0.35 3 5
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 8 -0.44 5 13
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 0.48 1 -0.6 7 8
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 0.27 2 -0.36 2 4
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 7 -0.42 10 17
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 -0.47 121 121
SELP -0.1 0.24 -10000 0 -0.54 117 117
S1P3 pathway

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
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 0.44 1 -0.53 7 8
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
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.011 0.096 0.36 7 -0.31 9 16
TBX21 -0.13 0.37 0.72 6 -1 54 60
B2M 0.038 0.013 0.2 1 -10000 0 1
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 -0.75 46 48
IL12RB2 0.03 0.076 0.26 6 -0.55 1 7
GADD45G -0.062 0.26 0.7 3 -0.69 42 45
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 0.24 2 -10000 0 2
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 -0.58 50 60
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 6 -0.58 66 72
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 0.21 5 -10000 0 5
CD3E -0.001 0.033 -10000 0 -10000 0 0
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 0.79 1 -0.8 19 20
CCL4 -0.087 0.25 0.71 2 -0.7 30 32
HLA-A 0.043 0.026 0.21 1 -10000 0 1
IL18/IL18R 0.058 0.14 0.4 11 -0.36 42 53
NOS2 -0.086 0.26 0.6 9 -0.58 70 79
IL12/IL12R/TYK2/JAK2/SPHK2 0.008 0.099 0.35 8 -0.32 9 17
IL1R1 -0.17 0.43 0.71 2 -1.1 73 75
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 -0.66 34 38
lysosomal transport -0.042 0.24 0.64 4 -0.61 37 41
FOS -0.83 0.6 0.57 1 -1.2 367 368
STAT4 (dimer) -0.034 0.27 0.63 9 -0.64 48 57
STAT5A (dimer) -0.061 0.26 0.58 8 -0.59 60 68
GZMA -0.093 0.25 0.57 7 -0.57 71 78
GZMB -0.092 0.26 0.71 6 -0.77 26 32
HLX 0.025 0.038 -10000 0 -0.54 2 2
LCK -0.086 0.27 0.69 9 -0.62 63 72
TCR/CD3/MHC II/CD4 -0.12 0.16 0.25 9 -0.42 66 75
IL2/IL2R 0.088 0.056 0.37 4 -0.32 1 5
MAPK14 -0.06 0.28 0.64 7 -0.72 47 54
CCR5 -0.068 0.28 0.71 10 -0.71 47 57
IL1B 0.014 0.071 0.23 2 -0.55 5 7
STAT6 -0.039 0.18 0.39 7 -0.66 27 34
STAT4 0.027 0.069 0.18 5 -0.54 7 12
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 0.24 3 -10000 0 3
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 -0.36 7 16
IL2RB 0.035 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.26 0.62 9 -0.59 48 57
IL2RG 0.043 0.035 -10000 0 -10000 0 0
IL12 0.007 0.089 0.28 4 -0.41 11 15
STAT5A 0.032 0.026 -10000 0 -0.54 1 1
CD247 -0.003 0.11 -10000 0 -0.55 15 15
IL2 0.033 0.027 -10000 0 -0.54 1 1
SPHK2 0.034 0.005 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.006 0.093 0.22 3 -0.56 11 14
IL12/IL12R/TYK2/JAK2 -0.1 0.27 0.68 8 -0.64 67 75
MAP2K3 -0.071 0.29 0.63 7 -0.75 50 57
RIPK2 0.029 0.021 0.18 6 -10000 0 6
MAP2K6 -0.063 0.27 0.63 8 -0.7 47 55
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 -10000 0 -0.55 42 42
IL12Rbeta1/TYK2 0.029 0.047 0.25 1 -10000 0 1
EOMES 0.042 0.1 -10000 0 -0.61 3 3
STAT1 (dimer) -0.013 0.26 0.67 15 -0.58 42 57
T cell proliferation -0.031 0.22 0.54 9 -0.53 45 54
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.037 0.031 0.21 1 -0.56 1 2
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 -0.61 40 42
ATF2 -0.057 0.26 0.63 4 -0.68 45 49
Thromboxane A2 receptor signaling

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
TGM2 0.046 0.042 0.19 1 -10000 0 1
GNB1/GNG2 -0.019 0.054 -10000 0 -0.18 48 48
AKT1 0.059 0.13 0.4 20 -0.28 12 32
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 45 61
LYN 0.026 0.052 0.26 3 -10000 0 3
RhoA/GTP 0.025 0.067 0.19 15 -0.14 8 23
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK 0.058 0.17 0.49 18 -0.34 45 63
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 -0.63 14 14
G beta5/gamma2 -0.014 0.075 -10000 0 -0.24 45 45
PRKCH 0.053 0.18 0.51 15 -0.36 45 60
DNM1 0.034 0.008 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.015 0.029 -10000 0 -0.53 1 1
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
PTGDR 0.03 0.06 -10000 0 -0.54 5 5
G12 family/GTP 0.004 0.11 -10000 0 -0.3 44 44
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 0.52 16 -0.37 46 62
cell morphogenesis 0.044 0.012 -10000 0 -10000 0 0
PLCB2 0.051 0.22 0.71 8 -0.5 47 55
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 0.52 15 -0.37 46 61
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 0.69 9 -0.51 48 57
LCK 0.038 0.061 0.25 6 -10000 0 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.044 0.042 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.098 -10000 0 -0.41 20 20
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.04 0.042 -10000 0 -10000 0 0
MAPK14 0.052 0.13 0.41 19 -0.23 39 58
TGM2/GTP 0.056 0.2 0.59 13 -0.41 40 53
MAPK11 0.05 0.13 0.42 19 -0.23 38 57
ARHGEF1 0.046 0.11 0.31 23 -0.19 16 39
GNAI2 0.033 0.01 -10000 0 -10000 0 0
JNK cascade 0.059 0.19 0.53 16 -0.38 47 63
RAB11/GDP 0.031 0.01 -10000 0 -10000 0 0
ICAM1 0.058 0.15 0.45 20 -0.28 45 65
cAMP biosynthetic process 0.054 0.17 0.51 14 -0.34 41 55
Gq family/GTP/EBP50 0.033 0.048 0.16 1 -0.22 6 7
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 -0.3 38 41
VCAM1 0.053 0.16 0.46 18 -0.31 47 65
TP beta/Gq family/GDP/G beta5/gamma2 0.012 0.12 -10000 0 -0.63 14 14
platelet activation 0.063 0.16 0.48 19 -0.3 39 58
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 -0.55 14 14
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 0.54 15 -0.42 46 61
EGFR -0.27 0.29 -10000 0 -0.54 269 269
TXA2/TP alpha 0.058 0.21 0.67 9 -0.46 45 54
Gq family/GTP 0.009 0.052 0.22 1 -0.22 18 19
YES1 0.029 0.057 0.26 2 -0.43 1 3
GNAI2/GTP 0.03 0.04 -10000 0 -10000 0 0
PGD2/DP 0.023 0.044 -10000 0 -0.4 5 5
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 0.5 17 -0.35 40 57
PRKCB 0.053 0.17 0.51 14 -0.35 47 61
PRKCE 0.055 0.17 0.54 13 -0.35 45 58
PRKCD 0.054 0.18 0.52 15 -0.38 46 61
PRKCG 0.056 0.18 0.51 16 -0.38 46 62
muscle contraction 0.055 0.22 0.61 12 -0.47 47 59
PRKCZ 0.057 0.17 0.5 16 -0.34 46 62
ARR3 0.035 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.044 0.049 -10000 0 -0.26 2 2
PRKCQ 0.06 0.18 0.46 24 -0.35 46 70
MAPKKK cascade 0.054 0.2 0.66 9 -0.44 46 55
SELE 0.049 0.18 0.46 19 -0.38 49 68
TP beta/GNAI2/GDP/G beta/gamma 0.062 0.049 -10000 0 -0.35 1 1
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
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.037 0.1 0.46 3 -0.63 5 8
oxygen homeostasis 0.026 0.03 0.2 3 -10000 0 3
TCEB2 0.031 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.13 0.14 0.43 26 -0.35 2 28
EPO 0.22 0.25 0.68 58 -0.52 1 59
FIH (dimer) 0.056 0.031 0.26 1 -10000 0 1
APEX1 0.058 0.038 0.24 2 -10000 0 2
SERPINE1 0.26 0.25 0.72 45 -0.51 3 48
FLT1 -0.016 0.17 -10000 0 -0.66 23 23
ADORA2A 0.26 0.25 0.67 74 -0.5 3 77
germ cell development 0.25 0.23 0.69 39 -0.52 2 41
SLC11A2 0.26 0.24 0.7 42 -0.5 4 46
BHLHE40 0.18 0.23 0.62 52 -0.49 4 56
HIF1AN 0.056 0.031 0.26 1 -10000 0 1
HIF2A/ARNT/SIRT1 0.17 0.19 0.55 39 -0.4 2 41
ETS1 0.041 0.034 -10000 0 -0.54 1 1
CITED2 0.005 0.15 -10000 0 -0.81 13 13
KDR -0.006 0.15 -10000 0 -0.67 16 16
PGK1 0.26 0.24 0.72 40 -0.53 2 42
SIRT1 0.036 0.008 -10000 0 -10000 0 0
response to hypoxia 0.002 0.006 -10000 0 -10000 0 0
HIF2A/ARNT 0.23 0.26 0.76 26 -0.56 4 30
EPAS1 0.16 0.18 0.47 65 -0.33 8 73
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 -0.54 2 22
FXN 0.25 0.24 0.65 59 -0.48 3 62
POU5F1 0.25 0.24 0.7 38 -0.54 2 40
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 14 -0.54 1 15
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 -10000 0 -10000 0 0
SLC2A1 0.25 0.24 0.68 56 -0.52 2 58
TWIST1 0.21 0.29 0.63 62 -0.55 29 91
ELK1 0.04 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.14 0.18 0.55 21 -0.4 2 23
VEGFA 0.26 0.25 0.72 47 -0.5 4 51
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.013 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.13 0.17 -10000 0 -0.56 19 19
Syndecan-3/Neurocan 0.043 0.1 -10000 0 -0.47 16 16
POMC 0.035 0.031 -10000 0 -0.54 1 1
EGFR -0.27 0.29 -10000 0 -0.54 269 269
Syndecan-3/EGFR -0.12 0.18 -10000 0 -0.48 31 31
AGRP 0.03 0.015 -10000 0 -10000 0 0
NCSTN 0.028 0.014 -10000 0 -10000 0 0
PSENEN 0.035 0.015 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.032 0.027 -10000 0 -0.54 1 1
APH1A 0.031 0.028 -10000 0 -10000 0 0
NCAN 0.039 0.028 -10000 0 -10000 0 0
long-term memory 0.041 0.096 -10000 0 -0.45 13 13
Syndecan-3/IL8 0.049 0.11 -10000 0 -0.47 16 16
PSEN1 0.033 0.007 -10000 0 -10000 0 0
Src/Cortactin 0.04 0.021 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.54 2 2
limb bud formation -0.001 0.089 -10000 0 -0.48 16 16
MC4R 0.034 0.013 -10000 0 -10000 0 0
SRC 0.033 0.008 -10000 0 -10000 0 0
PTN -0.37 0.27 0.18 1 -0.54 355 356
FGFR/FGF/Syndecan-3 -0.001 0.09 -10000 0 -0.49 16 16
neuron projection morphogenesis -0.12 0.16 -10000 0 -0.55 19 19
Syndecan-3/AgRP 0.034 0.1 -10000 0 -0.47 16 16
Syndecan-3/AgRP/MC4R 0.05 0.1 -10000 0 -0.46 15 15
Fyn/Cortactin 0.038 0.03 -10000 0 -0.28 2 2
SDC3 -0.002 0.091 -10000 0 -0.49 16 16
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.048 0.11 -10000 0 -0.46 16 16
IL8 0.048 0.053 -10000 0 -0.54 1 1
Syndecan-3/Fyn/Cortactin 0.043 0.099 -10000 0 -0.46 13 13
Syndecan-3/CASK -0.003 0.087 -10000 0 -0.47 16 16
alpha-MSH/MC4R 0.049 0.027 -10000 0 -0.4 1 1
Gamma Secretase 0.074 0.054 -10000 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 -0.66 21 21
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 -0.66 34 34
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 -0.59 21 21
ETS1 0.031 0.056 -10000 0 -0.29 11 11
PXN 0.038 0.2 -10000 0 -0.68 24 24
ITGB1 0.033 0.006 -10000 0 -10000 0 0
NOS3 0.012 0.2 -10000 0 -0.74 24 24
RAC1 0.034 0.005 -10000 0 -10000 0 0
TNF 0.038 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 0.41 1 -0.58 24 25
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
IL1-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
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 -0.37 21 21
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 -0.42 33 33
TOLLIP 0.033 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.011 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.038 0.067 -10000 0 -0.35 1 1
JUN -0.051 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 -0.38 48 48
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.022 0.14 -10000 0 -0.41 35 35
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 -0.35 111 111
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 -0.39 12 12
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
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.043 0.26 4 -10000 0 4
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 0.23 5 -0.55 15 20
MACF1 0.034 0.006 -10000 0 -10000 0 0
CTNNB1 0.15 0.11 0.35 27 -0.41 3 30
WIF1 -0.38 0.26 -10000 0 -0.54 370 370
beta catenin/RanBP3 0.041 0.15 0.5 41 -0.4 3 44
KREMEN2 0.1 0.076 -10000 0 -10000 0 0
DKK1 0.007 0.18 0.18 15 -0.54 44 59
beta catenin/beta TrCP1 0.16 0.1 0.35 25 -0.41 2 27
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 0.35 9 -0.57 14 23
Axin1/APC/GSK3 0.065 0.059 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.06 0.076 0.37 1 -0.54 1 2
HNF1A 0.027 0.041 0.25 6 -10000 0 6
CTBP1 0.025 0.038 0.24 4 -10000 0 4
MYC 0.096 0.44 0.62 128 -1.3 29 157
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 0.24 5 -0.54 7 12
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 0.53 35 -0.52 15 50
LEF1 0.054 0.068 0.27 8 -10000 0 8
DVL1 0.08 0.058 -10000 0 -10000 0 0
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.097 0.17 0.32 6 -0.59 15 21
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 0.74 97 -1.2 14 111
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 0.27 62 -0.3 1 63
CREBBP 0.023 0.044 0.25 3 -0.55 1 4
Osteopontin-mediated events

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
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 0.37 14 -10000 0 14
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 91 92
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 -10000 0 -0.28 4 4
ITGAV 0.04 0.029 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.047 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 0.31 9 -0.3 5 14
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 0.33 15 -0.28 4 19
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 -10000 0 -10000 0 0
NFKBIA 0.077 0.099 0.35 22 -10000 0 22
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 0.5 10 -0.53 1 11
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 12 -0.29 11 23
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 0.29 7 -0.27 10 17
MMP2 -0.13 0.17 0.47 1 -0.41 73 74
Ceramide signaling pathway

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
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 13 -0.27 9 22
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 0.59 7 -10000 0 7
BAD -0.013 0.07 0.18 3 -0.32 6 9
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 -10000 0 -0.35 6 6
NSMAF 0.028 0.028 -10000 0 -0.54 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.074 0.28 4 -0.35 4 8
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 -0.28 140 140
BID -0.014 0.19 -10000 0 -0.66 35 35
MAP3K1 -0.011 0.073 0.2 1 -0.31 8 9
EIF2A -0.005 0.073 0.27 7 -0.25 5 12
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 5 -0.25 9 14
FADD 0.028 0.1 0.28 2 -0.3 16 18
KSR1 -0.006 0.073 0.21 6 -0.33 5 11
MAPK8 -0.008 0.07 -10000 0 -0.27 10 10
PRKRA -0.012 0.071 0.2 1 -0.32 6 7
PDGFA -0.019 0.16 -10000 0 -0.54 46 46
TRAF2 0.035 0.012 0.18 3 -10000 0 3
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 86 86
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 0.22 28 -0.25 6 34
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 0.22 5 -0.3 5 10
TNF-alpha/TNFR1A/FAN 0.057 0.036 -10000 0 -0.33 1 1
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.022 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 0.24 173 -0.22 3 176
NF kappa B1/RelA/I kappa B alpha 0.075 0.031 -10000 0 -0.3 1 1
AIFM1 0.026 0.082 0.21 32 -0.24 7 39
BCL2 -0.072 0.22 -10000 0 -0.54 93 93
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.51 25 25
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 0.24 2 -0.29 20 22
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 0.25 1 -0.32 22 23
GRIN2A/RELN/LRP8/DAB1/Fyn 0.084 0.095 -10000 0 -0.28 20 20
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 93 101
RELN/LRP8 0.07 0.091 -10000 0 -0.32 20 20
GRIN2B/RELN/LRP8/DAB1/Fyn 0.08 0.11 -10000 0 -0.31 29 29
PI3K 0.005 0.13 -10000 0 -0.38 48 48
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 28 32
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.048 0.068 -10000 0 -0.55 1 1
RELN/VLDLR 0.029 0.16 -10000 0 -0.31 80 80
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.016 0.13 -10000 0 -0.37 47 47
FZD6 0.007 0.11 -10000 0 -0.54 18 18
WNT6 0.033 0.04 -10000 0 -0.54 2 2
WNT4 0.04 0.033 0.18 27 -10000 0 27
FZD3 0.014 0.091 -10000 0 -0.54 13 13
WNT5A 0.01 0.13 -10000 0 -0.54 25 25
WNT11 0.024 0.079 0.18 10 -0.54 9 19
Syndecan-4-mediated signaling events

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
PTK2 0.12 0.12 0.28 7 -0.63 4 11
Syndecan-4/Syndesmos 0.13 0.12 0.4 4 -0.72 4 8
positive regulation of JNK cascade 0.062 0.18 0.41 1 -0.66 6 7
Syndecan-4/ADAM12 0.15 0.13 0.41 5 -0.76 4 9
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 0.41 1 -0.72 5 6
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 0.4 3 -0.76 4 7
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 0.41 4 -0.76 4 8
Syndecan-4/RANTES 0.13 0.13 0.39 2 -0.76 4 6
ITGB1 0.033 0.006 -10000 0 -10000 0 0
LAMA1 0.033 0.01 -10000 0 -10000 0 0
LAMA3 -0.15 0.27 -10000 0 -0.54 161 161
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 0.38 2 -0.69 5 7
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 0.4 2 -0.7 7 9
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 0.21 3 -10000 0 3
cell migration -0.012 0.008 -10000 0 -10000 0 0
PRKCD 0.016 0.035 -10000 0 -10000 0 0
vasculogenesis 0.14 0.12 0.41 4 -0.72 4 8
SDC4 0.11 0.12 -10000 0 -0.81 4 4
Syndecan-4/Tenascin C 0.14 0.12 0.4 3 -0.76 4 7
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.12 0.12 0.39 2 -0.76 4 6
MMP9 0.094 0.078 0.2 4 -10000 0 4
Rac1/GTP 0.092 0.072 0.27 50 -10000 0 50
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 -0.65 8 11
Coregulation of Androgen receptor activity

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
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 -0.35 64 64
CARM1 0.035 0.014 0.18 4 -10000 0 4
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 -0.31 85 85
FHL2 -0.11 0.32 -10000 0 -0.98 58 58
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 -0.38 68 68
XRCC6 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.057 0.17 -10000 0 -0.36 83 83
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 -0.36 65 65
AR -0.069 0.2 -10000 0 -0.56 66 66
UBA3 0 0.001 -10000 0 -10000 0 0
PATZ1 0.031 0.01 -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 -0.32 63 63
RPS6KA3 0.034 0.037 -10000 0 -0.54 2 2
T-DHT/AR/ARA70 -0.039 0.14 -10000 0 -0.36 66 66
LATS2 0.02 0.076 -10000 0 -0.54 9 9
T-DHT/AR/PRX1 -0.034 0.13 -10000 0 -0.33 66 66
Cyclin D3/CDK11 p58 0.025 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 -0.35 71 71
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF 0 0 -10000 0 -10000 0 0
ZMIZ1 0.004 0.053 -10000 0 -10000 0 0
CCND3 0.033 0.006 -10000 0 -10000 0 0
TGIF1 0.03 0.027 -10000 0 -0.54 1 1
FKBP4 0.038 0.026 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
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 26 26
PLCG1 0.004 0.13 -10000 0 -0.42 26 26
YES1 -0.003 0.13 0.25 1 -0.36 44 45
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 0.34 5 -0.42 25 30
MAP3K7 -0.006 0.11 0.25 1 -0.35 25 26
mol:Ca2+ 0.005 0.12 -10000 0 -0.4 26 26
mol:IP3 0.005 0.13 -10000 0 -0.41 26 26
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 -0.38 26 27
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.016 0.13 -10000 0 -0.37 47 47
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
GNAS -0.006 0.13 0.25 1 -0.35 44 45
GO:0007205 -0.001 0.12 0.26 1 -0.41 26 27
WNT6 0.033 0.04 -10000 0 -0.54 2 2
WNT4 0.04 0.033 0.18 27 -10000 0 27
NFAT1/CK1 alpha 0.016 0.14 -10000 0 -0.44 23 23
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 0.24 1 -0.46 22 23
Regulation of p38-alpha and p38-beta

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
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 -0.23 241 241
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 -0.33 31 31
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 -10000 0 -10000 0 0
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 30 33
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 37 39
positive regulation of innate immune response 0.001 0.16 0.47 2 -0.42 35 37
LCK 0.048 0.044 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.014 0.15 0.58 1 -0.42 30 31
p38alpha-beta/MKP5 0.009 0.15 0.58 1 -0.41 31 32
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 72 72
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 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
Telomerase catalytic core complex 0.002 0.18 -10000 0 -0.75 11 11
RAD9A 0.031 0.01 -10000 0 -10000 0 0
AP1 -0.31 0.27 -10000 0 -0.46 362 362
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 11 11
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 -0.78 8 8
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 0.2 12 -10000 0 12
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 -0.64 10 10
Mad/Max 0.055 0.018 -10000 0 -10000 0 0
TERT -0.006 0.18 -10000 0 -0.89 8 8
CCND1 0.034 0.26 0.56 11 -1 14 25
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 4 -0.32 10 14
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 -0.53 7 7
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 -0.74 11 11
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 -0.47 352 352
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 -0.78 8 8
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 -0.62 11 11
Smad3/Myc 0.005 0.081 -10000 0 -0.34 25 25
911 complex 0.061 0.026 -10000 0 -10000 0 0
IFNG 0.065 0.073 -10000 0 -0.22 9 9
Telomerase/PinX1 0.011 0.16 -10000 0 -0.62 11 11
Telomerase/AKT1/mTOR/p70S6K 0.022 0.12 0.3 1 -0.49 15 16
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 -0.66 9 9
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 -0.64 10 10
E2F1 0.054 0.048 0.21 1 -10000 0 1
ZNFX1 0.033 0.017 -10000 0 -10000 0 0
PIF1 0.039 0.028 -10000 0 -10000 0 0
NCL 0.034 0.006 -10000 0 -10000 0 0
DKC1 0.035 0.011 0.18 3 -10000 0 3
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.017 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 0.004 1 -10000 0 1
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.003 0.063 -10000 0 -0.41 10 10
FOXO1 -0.023 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 -0.33 8 13
AR/GR -0.04 0.14 -10000 0 -0.29 92 92
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 -0.36 7 8
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 -10000 0 -10000 0 0
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 0.004 1 -10000 0 1
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 0.18 4 -10000 0 4
NR2C2 0.035 0.014 -10000 0 -10000 0 0
KLK2 0.013 0.078 0.34 3 -10000 0 3
AR -0.025 0.1 -10000 0 -0.27 61 61
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 -0.32 4 6
T-DHT/AR/Hsp90 -0.011 0.098 0.36 2 -0.36 11 13
GSK3B 0.033 0.01 -10000 0 -10000 0 0
NR2C1 0.033 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 S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.006 0.029 0.36 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 23 63
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 -0.28 23 63
MAP2K6 0.015 0.098 0.25 45 -0.3 25 70
MAPT 0.013 0.067 0.27 8 -0.26 9 17
MAPK13 0.017 0.027 -10000 0 -0.4 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.062 -10000 0 -0.33 17 17
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.038 0.15 -10000 0 -0.43 44 44
KLHL20 0.042 0.12 0.31 41 -0.26 14 55
CYFIP2 0.05 0.047 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.12 0.31 7 -0.3 26 33
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 -0.17 14 14
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.049 0.095 -10000 0 -0.31 26 26
RAPGEF1 -0.031 0.14 0.31 2 -0.4 40 42
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 44 45
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 -0.2 13 13
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 -0.26 13 13
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 -0.32 33 33
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 0.3 7 -0.3 25 32
actin cytoskeleton organization 0.037 0.094 0.26 43 -0.19 13 56
CDC42/GDP 0 0.12 0.3 7 -0.3 25 32
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 0.31 7 -0.34 33 40
CDC42/GTP/IQGAP1 0.043 0.013 -10000 0 -10000 0 0
JUP 0.033 0.01 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.007 0.12 0.32 5 -0.31 24 29
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 -0.11 4 36
Rap1/GTP 0.012 0.087 0.26 3 -0.31 3 6
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.059 0.092 -10000 0 -0.3 21 21
CCND1 0.017 0.08 0.24 23 -0.28 11 34
VAV2 -0.02 0.19 0.39 3 -0.62 20 23
RAP1/GDP 0.009 0.1 0.31 3 -0.35 4 7
adherens junction assembly -0.035 0.16 -10000 0 -0.43 47 47
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.033 0.006 -10000 0 -10000 0 0
PIP5K1C 0.034 0.009 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.044 0.089 -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 60 -0.41 19 79
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
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 -0.4 42 43
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 0.35 1 -0.49 44 45
FRAP1 -0.036 0.24 0.38 1 -0.53 57 58
FOXO3 0.005 0.18 0.38 3 -0.52 28 31
AKT1 0.002 0.2 0.38 1 -0.54 33 34
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 -0.5 8 9
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 -10000 0 0
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 0.48 2 -0.92 31 33
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 15 16
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 15 16
Rac1/GDP -0.011 0.096 -10000 0 -0.31 44 44
T cell proliferation 0.028 0.12 0.31 1 -0.35 15 16
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 15 16
NF kappa B1 p50/RelA -0.008 0.22 0.37 1 -0.52 39 40
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 15 16
GRB2 0.032 0.02 -10000 0 -10000 0 0
IL2 0.032 0.029 -10000 0 -0.54 1 1
PIK3CA 0.032 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.014 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 -0.83 104 105
Hedgehog signaling events mediated by Gli proteins

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 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 -0.57 47 47
GNAO1 0.03 0.012 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.029 0.093 -10000 0 -0.4 22 22
SMO 0.012 0.12 -10000 0 -0.54 22 22
ARRB2 0.032 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.03 0.11 0.29 1 -0.48 9 10
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.008 -10000 0 -10000 0 0
GNAI2 0.034 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.077 0.032 -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 -0.65 27 27
SAP30 0.033 0.009 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 -10000 0 -0.54 22 22
MIM/GLI2A 0.033 0.029 0.31 1 -10000 0 1
IFT88 0.031 0.027 -10000 0 -0.54 1 1
GNAI3 0.034 0.006 -10000 0 -10000 0 0
GLI2 0.016 0.084 -10000 0 -0.41 10 10
GLI3 0.017 0.11 0.3 1 -0.47 11 12
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 -0.46 14 14
GLI2/Su(fu) 0.019 0.11 -10000 0 -0.49 10 10
FOXA2 0.016 0.12 -10000 0 -0.66 14 14
neural tube patterning -0.043 0.2 -10000 0 -0.57 47 47
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 -0.57 47 47
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 -0.6 12 13
GLI3A/CBP 0.001 0.12 -10000 0 -0.36 49 49
KIF3A 0.033 0.006 -10000 0 -10000 0 0
GLI1 -0.045 0.21 -10000 0 -0.59 47 47
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 -0.69 18 18
MIM/GLI1 -0.024 0.18 -10000 0 -0.58 33 33
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 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
BAG4 0.028 0.016 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.047 0.14 -10000 0 -0.44 17 17
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 -0.42 16 33
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CD247 0.029 0.11 -10000 0 -0.55 15 15
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 -0.32 36 45
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 -0.33 38 46
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 17 19
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.12 -10000 0 -0.33 42 42
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 0.36 18 -0.37 15 33
NFKB1 0.03 0.035 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.053 0.035 -10000 0 -10000 0 0
CASP6 0.053 0.15 -10000 0 -0.56 13 13
CASP7 0.019 0.19 0.4 16 -0.49 37 53
RELA 0.03 0.034 -10000 0 -10000 0 0
CASP2 0.033 0.006 -10000 0 -10000 0 0
CASP3 0.016 0.19 0.4 15 -0.49 38 53
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 0.26 2 -0.38 26 28
BCL2 -0.007 0.18 0.48 5 -0.55 23 28
Signaling events mediated by PRL

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
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 -0.44 19 19
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 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.034 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
Caspase cascade in apoptosis

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.035 0.074 0.32 1 -0.35 7 8
ACTA1 0.007 0.083 0.24 3 -0.34 4 7
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 11 -0.48 1 12
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BIRC2 0.03 0.011 -10000 0 -10000 0 0
BAX 0.035 0.012 -10000 0 -10000 0 0
CASP10 -0.003 0.04 0.24 8 -0.35 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 91 92
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 0.26 5 -0.2 19 24
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 0.32 1 -0.46 2 3
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 0.18 3 -10000 0 3
ICAD/CAD 0.017 0.062 0.28 2 -0.47 1 3
CASP7 0.016 0.082 0.26 22 -0.31 4 26
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 19 -0.26 5 24
actin filament polymerization 0.016 0.13 0.31 11 -0.3 9 20
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.023 0.046 0.21 8 -0.22 4 12
SATB1 -0.011 0.16 -10000 0 -0.81 12 12
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 -0.53 20 22
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 0.39 2 -0.57 13 15
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 19 -0.001 27 46
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM 0.015 0.11 0.34 1 -0.46 9 10
LMNA 0.022 0.082 0.34 2 -0.35 10 12
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.088 -10000 0 -0.31 18 18
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 0.31 8 -0.32 11 19
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
Cellular roles of Anthrax toxin

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
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 0.11 3 -0.29 143 146
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 -10000 0 -0.25 3 3
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
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 7 10
NFKBIA 0.033 0.007 -10000 0 -10000 0 0
BIRC3 0.016 0.11 -10000 0 -0.54 17 17
BAX 0.007 0.052 0.26 3 -0.18 8 11
EnzymeConsortium:3.1.4.12 0.003 0.032 0.09 4 -0.097 21 25
IKBKB 0.012 0.13 0.3 4 -0.44 16 20
MAP2K2 0.011 0.059 0.23 10 -0.22 2 12
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 0.31 11 -0.44 20 31
MAP2K4 0.007 0.052 0.2 2 -0.24 5 7
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 -0.21 3 21
CRADD 0.034 0.005 -10000 0 -10000 0 0
mol:ceramide 0.008 0.05 0.16 3 -0.15 20 23
I-kappa-B-alpha/RELA/p50/ubiquitin 0.043 0.014 -10000 0 -10000 0 0
MADD 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.054 0.2 2 -0.24 7 9
TRADD 0.03 0.012 -10000 0 -10000 0 0
RELA/p50 0.034 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.06 0.23 11 -0.24 1 12
MAPK1 0.01 0.068 0.23 11 -0.22 7 18
p50/RELA/I-kappa-B-alpha 0.048 0.016 -10000 0 -10000 0 0
FADD 0.026 0.14 0.3 8 -0.45 19 27
KSR1 0.011 0.057 0.2 14 -0.18 7 21
MAPK8 0.004 0.056 0.28 3 -0.24 5 8
TRAF2 0.035 0.012 0.18 3 -10000 0 3
response to radiation 0 0 0.003 2 -10000 0 2
CHUK -0.007 0.12 0.27 1 -0.44 21 22
TNF R/SODD 0.038 0.023 -10000 0 -10000 0 0
TNF 0.038 0.023 -10000 0 -10000 0 0
CYCS 0.025 0.07 0.18 23 -0.18 7 30
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 0.18 24 -0.18 9 33
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
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 0.33 9 -0.35 27 36
IKBKB 0.05 0.092 0.35 8 -0.35 2 10
AKT1 0.062 0.12 0.32 46 -0.25 2 48
IKBKG 0.056 0.077 0.33 8 -0.28 3 11
CALM1 0.031 0.086 0.28 8 -0.39 6 14
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
MAP3K1 0.068 0.14 0.37 9 -0.49 12 21
MAP3K7 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.031 0.091 0.29 7 -0.36 9 16
DOK1 0.036 0.016 -10000 0 -10000 0 0
AP-1 -0.073 0.11 0.32 1 -0.24 73 74
LYN 0.03 0.015 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
SHC1 0.027 0.014 -10000 0 -10000 0 0
BCR complex 0.041 0.07 0.26 3 -0.4 10 13
CD22 0.015 0.088 0.28 6 -0.45 11 17
CAMK2G 0.029 0.084 0.26 10 -0.37 6 16
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 4 4
GO:0007205 0.032 0.092 0.29 7 -0.37 9 16
SYK 0.038 0.026 -10000 0 -10000 0 0
ELK1 0.033 0.09 0.28 8 -0.4 6 14
NFATC1 0.064 0.11 0.29 19 -0.38 10 29
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 8 17
HRAS 0.044 0.095 0.27 14 -0.35 8 22
NFKBIA 0.043 0.052 0.21 9 -0.13 8 17
NF-kappa-B/RelA/I kappa B beta 0.047 0.048 0.21 9 -10000 0 9
RasGAP/Csk 0.064 0.079 0.35 2 -0.39 6 8
mol:GDP 0.032 0.089 0.28 7 -0.38 7 14
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 0.21 9 -10000 0 9
GRB2 0.034 0.018 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.049 0.15 0.4 7 -0.46 16 23
PIK3R1 -0.02 0.17 -10000 0 -0.54 47 47
mol:IP3 0.03 0.09 0.3 6 -0.37 9 15
CSK 0.034 0.011 -10000 0 -10000 0 0
FOS -0.15 0.14 0.27 1 -0.37 58 59
CHUK 0.053 0.084 0.34 7 -0.34 5 12
IBTK 0.033 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.054 0.091 0.31 3 -0.37 5 8
PTPN6 0.031 0.1 0.29 11 -0.43 11 22
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 0.3 5 -0.45 11 16
ubiquitin-dependent protein catabolic process 0.046 0.052 0.21 9 -0.13 10 19
BTK 0.017 0.09 -10000 0 -0.96 4 4
CD19 0.022 0.092 0.26 9 -0.43 11 20
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 0.36 11 -0.42 12 23
SH3BP5 0.018 0.094 -10000 0 -0.54 14 14
PIK3AP1 0.029 0.096 0.33 6 -0.41 9 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.047 0.095 0.31 4 -0.44 7 11
RAF1 0.042 0.09 0.26 13 -0.37 5 18
RasGAP/p62DOK/SHIP 0.054 0.071 0.3 1 -0.35 7 8
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 68 69
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 19 -0.49 6 25
NF-kappa-B/RelA 0.093 0.088 0.37 8 -0.23 1 9
Calcineurin 0.042 0.091 -10000 0 -0.38 5 5
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 0.32 6 -0.42 10 16
SOS1 0.034 0.004 -10000 0 -10000 0 0
Bam32/HPK1 0.065 0.16 -10000 0 -0.63 16 16
DAPP1 0.031 0.16 -10000 0 -0.71 16 16
cytokine secretion 0.063 0.11 0.28 22 -0.36 10 32
mol:DAG 0.03 0.09 0.3 6 -0.37 9 15
PLCG2 0.021 0.073 -10000 0 -0.54 8 8
MAP2K1 0.039 0.087 0.27 7 -0.37 4 11
B-cell antigen/BCR complex/FcgammaRIIB 0.046 0.074 0.28 3 -0.43 7 10
mol:PI-3-4-5-P3 0.031 0.1 0.31 20 -0.3 6 26
ETS1 0.026 0.081 0.3 3 -0.34 7 10
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 -0.38 7 19
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 0.19 27 -0.14 1 28
PTPRC 0.035 0.035 -10000 0 -10000 0 0
PDPK1 0.038 0.096 0.28 32 -0.22 4 36
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
JNK signaling in the CD4+ TCR 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
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 -0.3 92 92
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
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 4 -0.28 37 41
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 0.31 25 -0.27 5 30
AKT1 0.018 0.11 0.32 10 -0.32 17 27
MAP2K1 0.026 0.074 0.31 4 -10000 0 4
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 0.41 8 -0.59 5 13
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 0.3 31 -0.27 5 36
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 4 31
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 -0.39 36 39
MAPK1 0.01 0.2 -10000 0 -0.7 33 33
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 0.38 18 -0.35 4 22
SMAD7 0.022 0.071 0.23 8 -0.17 12 20
CBL/CRKL/C3G 0.069 0.069 0.33 3 -10000 0 3
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 17 28
PRKCD 0.018 0.11 0.32 11 -0.32 13 24
RAP1B 0.033 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.004 0.097 0.17 4 -0.28 37 41
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 -0.27 3 29
SOCS1 0.018 0.1 -10000 0 -1 5 5
mol:GDP 0.064 0.065 0.31 3 -10000 0 3
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 0.33 3 -0.27 6 9
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 4 -0.28 37 41
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
PLK2 and PLK4 events

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
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
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.016 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.041 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 0.27 10 -0.28 2 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 -0.42 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.054 -10000 0 -0.33 9 9
CHUK 0.02 0.061 -10000 0 -0.34 8 8
BAD/BCL-XL 0.056 0.074 0.31 1 -0.6 1 2
mTORC2 0.042 0.01 -10000 0 -10000 0 0
AKT2 0.017 0.006 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.043 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 -0.58 1 3
TSC1/TSC2 0.025 0.08 0.35 3 -0.38 4 7
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.078 0.35 2 -0.55 1 3
glucose import -0.15 0.15 0.21 1 -0.31 237 238
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.055 0.18 2 -0.64 1 3
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 -0.34 9 10
p27Kip1/14-3-3 family 0.031 0.044 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
KPNA1 0.034 0.005 -10000 0 -10000 0 0
HSP90AA1 0.033 0.006 -10000 0 -10000 0 0
YWHAG 0.034 0.008 -10000 0 -10000 0 0
RHEB 0.034 0.009 -10000 0 -10000 0 0
CREBBP 0.03 0.027 -10000 0 -0.54 1 1
FoxO family signaling

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
G6PC 0.003 0.098 -10000 0 -10000 0 0
PLK1 0.13 0.22 0.68 10 -0.86 4 14
CDKN1B 0.099 0.18 0.56 5 -0.45 14 19
FOXO3 0.11 0.23 0.56 21 -0.62 16 37
KAT2B 0.02 0.031 0.086 37 -0.058 10 47
FOXO1/SIRT1 0.006 0.1 -10000 0 -0.33 10 10
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 -0.34 11 11
MAPK10 0.024 0.06 0.23 4 -0.29 10 14
mol:GTP 0 0.004 -10000 0 -10000 0 0
FOXO4 0.044 0.12 0.41 4 -0.39 7 11
response to oxidative stress 0.023 0.033 0.091 38 -0.063 8 46
FOXO3A/SIRT1 0.085 0.2 0.47 14 -0.6 15 29
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 -0.31 10 10
mol:GDP 0.023 0.033 0.091 38 -0.063 8 46
RAN 0.034 0.005 -10000 0 -10000 0 0
GADD45A 0.082 0.21 0.5 1 -0.8 15 16
YWHAQ 0.034 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.036 0.15 -10000 0 -0.53 21 21
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 0.23 5 -0.27 1 6
MAPK9 0.029 0.04 0.23 4 -10000 0 4
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 10 -0.55 12 22
RBL2 0.035 0.32 0.56 2 -0.78 48 50
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 -0.84 4 25
FOXO1-3a-4/beta catenin 0.096 0.22 0.56 9 -0.4 44 53
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.1 -10000 0 -0.3 10 10
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
SGK1 0.02 0.031 0.086 37 -0.058 10 47
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 0.65 26 -1.1 26 52
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
VEGFR1 specific signals

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
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 -0.3 4 4
VEGFR1 homodimer/NRP1/VEGFR 121 0.042 0.044 -10000 0 -0.3 3 3
CaM/Ca2+ 0.037 0.041 -10000 0 -0.29 4 4
HIF1A 0.039 0.055 -10000 0 -0.54 4 4
GAB1 0.033 0.027 -10000 0 -0.54 1 1
AKT1 -0.008 0.099 -10000 0 -0.36 4 4
PLCG1 0.019 0.042 -10000 0 -0.31 4 4
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 0.36 3 -10000 0 3
mol:Ca2+ 0.019 0.041 -10000 0 -0.3 4 4
MAPK3 -0.006 0.035 0.25 1 -10000 0 1
MAPK1 -0.006 0.037 0.25 1 -10000 0 1
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 -0.3 41 41
PRKCA -0.004 0.04 0.26 1 -10000 0 1
PRKCB -0.002 0.039 -10000 0 -0.28 4 4
VEGFR1 homodimer/PLGF homodimer 0.038 0.039 -10000 0 -0.34 4 4
VEGFA 0.05 0.047 -10000 0 -10000 0 0
VEGFB 0.033 0.007 -10000 0 -10000 0 0
mol:IP3 0.019 0.042 -10000 0 -0.3 4 4
RASA1 0.02 0.043 -10000 0 -0.31 4 4
NRP2 0.035 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer 0.021 0.043 -10000 0 -0.39 4 4
VEGFB homodimer 0.033 0.007 -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 25 25
PTPN11 0.034 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.035 0.11 -10000 0 -0.3 41 41
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 -0.29 3 3
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 -0.29 3 3
VEGFR1 homodimer/NRP2 0.038 0.04 -10000 0 -0.34 4 4
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.034 0.005 -10000 0 -10000 0 0
SPHK1 0.033 0.06 -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 -0.24 4 4
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.17 0.28 -10000 0 -0.54 183 183
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
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.049 0.027 -10000 0 -0.4 1 1
AKT1 0.026 0.14 0.37 2 -0.47 13 15
PTK2B 0.015 0.084 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 -10000 0 0
endothelial cell proliferation 0.051 0.13 0.39 11 -0.44 8 19
mol:Ca2+ 0.02 0.091 0.37 1 -0.5 4 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.068 0.093 -10000 0 -0.45 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 -0.29 3 3
SHC1 0.027 0.014 -10000 0 -10000 0 0
SHC2 0.006 0.12 -10000 0 -0.54 24 24
HRAS/GDP 0.031 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 -0.31 19 19
VEGFR1 homodimer 0.032 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.056 0.1 -10000 0 -0.44 4 4
GRB10 0.017 0.11 -10000 0 -0.61 7 7
PTPN11 0.034 0.004 -10000 0 -10000 0 0
GRB2 0.034 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 26 26
mol:GDP 0.043 0.09 -10000 0 -0.43 4 4
mol:NADP 0.031 0.11 0.59 1 -0.45 10 11
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 -0.45 10 11
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 -0.58 4 4
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 -0.48 7 7
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 -0.33 6 6
FES 0.018 0.095 -10000 0 -0.56 4 4
GAB1 0.041 0.1 -10000 0 -0.41 5 5
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 40 40
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 35 35
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 -0.31 19 19
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 23 23
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.049 0.092 -10000 0 -0.33 6 6
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 -0.45 10 11
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 -0.51 10 11
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.12 -10000 0 -0.32 36 36
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
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.033 0.006 -10000 0 -10000 0 0
VLDLR -0.041 0.19 -10000 0 -0.54 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 -0.37 22 22
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 -0.31 3 3
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
EPO signaling 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
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 0.27 12 -0.32 1 13
RAP1A 0.016 0.067 0.3 3 -10000 0 3
GAB1 0.017 0.066 0.3 2 -10000 0 2
MAPK14 0.048 0.073 0.27 12 -10000 0 12
EPO 0.046 0.052 -10000 0 -10000 0 0
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 -10000 0 -0.32 90 90
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 0.26 15 -0.3 1 16
GAB1/SHIP/PIK3R1/SHP2/SHC 0.002 0.086 -10000 0 -0.37 1 1
TEC 0.016 0.067 0.3 3 -10000 0 3
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 -0.31 119 119
SH2B3 0.033 0.016 -10000 0 -10000 0 0
NFKB1 0.048 0.073 0.27 12 -10000 0 12
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 -10000 0 -10000 0 0
VAV2 0.018 0.068 0.3 4 -10000 0 4
CBL 0.014 0.066 0.3 3 -10000 0 3
SHC/Grb2/SOS1 0.03 0.059 -10000 0 -10000 0 0
STAT5A 0.028 0.1 -10000 0 -0.32 1 1
GRB2 0.034 0.018 -10000 0 -10000 0 0
STAT5 (dimer) 0.025 0.15 -10000 0 -0.37 15 15
LYN/PLCgamma2 0.029 0.061 0.25 1 -0.4 8 9
PTPN11 0.034 0.004 -10000 0 -10000 0 0
BTK 0.02 0.071 0.3 3 -10000 0 3
BCL2 -0.091 0.36 -10000 0 -0.82 98 98
Signaling events mediated by HDAC Class III

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
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 -0.13 1 1
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 0.14 8 -0.4 2 10
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 0.13 1 -10000 0 1
SIRT1/FOXO3a 0.022 0.032 0.19 1 -0.21 2 3
SIRT1 0.03 0.012 0.22 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.053 0.029 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.052 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 -0.34 50 50
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 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
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 -0.4 19 19
MAP2K4 0.015 0.085 -10000 0 -0.4 12 12
IKBKB 0.029 0.013 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.028 0.018 -10000 0 -10000 0 0
SMPD1 0.004 0.057 -10000 0 -0.27 18 18
IKBKG 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.014 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.022 0.086 -10000 0 -0.4 19 19
TRAIL/TRAILR3 0.023 0.086 -10000 0 -0.4 19 19
TRAIL/TRAILR1 0.023 0.085 -10000 0 -0.39 19 19
TRAIL/TRAILR4 0.023 0.085 -10000 0 -0.4 19 19
TRAIL/TRAILR1/DAP3/GTP 0.031 0.066 -10000 0 -0.31 13 13
IKK complex 0.024 0.074 -10000 0 -0.42 5 5
RIPK1 0.033 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.01 -10000 0 -10000 0 0
MAPK3 0 0.078 -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 -0.3 13 13
mol:ceramide 0.004 0.057 -10000 0 -0.26 18 18
FADD 0.028 0.015 -10000 0 -10000 0 0
MAPK8 -0.001 0.1 -10000 0 -0.4 17 17
TRAF2 0.035 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 -0.4 19 19
TRAIL (trimer) 0.011 0.11 -10000 0 -0.54 19 19
TNFRSF10C 0.028 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.035 0.064 -10000 0 -0.29 9 9
TRAIL/TRAILR2/FADD 0.032 0.074 -10000 0 -0.34 14 14
cell death 0.004 0.056 -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 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
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 -0.4 2 2
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 -0.17 1 1
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 -0.4 50 50
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 -0.4 106 106
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 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
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 -0.38 1 1
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
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.033 0.007 -10000 0 -10000 0 0
NFATC1 0.042 0.086 0.35 3 -0.4 5 8
NFATC2 0.002 0.074 0.29 1 -0.25 16 17
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 -0.27 6 8
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 -10000 0 0
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 -0.28 6 8
CALM1 0.033 0.008 -10000 0 -10000 0 0
RAN 0.034 0.005 -10000 0 -10000 0 0
MAP3K1 0.036 0.046 -10000 0 -0.54 2 2
CAMK4 0.035 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.009 -10000 0 -10000 0 0
YWHAH 0.033 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.053 0.04 -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 -0.4 8 9
PRKCH 0.029 0.051 -10000 0 -0.54 4 4
CABIN1/Cbp/p300 0.04 0.031 -10000 0 -0.4 1 1
CASP3 0.033 0.008 -10000 0 -10000 0 0
PIM1 0.035 0.015 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.009 -10000 0 -10000 0 0
apoptosis -0.003 0.058 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.04 0.047 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.01 0.064 -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 -0.38 5 6
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.066 0.063 -10000 0 -10000 0 0
NR4A1 0.024 0.14 -10000 0 -0.49 24 24
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 -0.31 5 5
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 -10000 0 -0.54 2 2
MEF2D 0.027 0.016 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.018 -10000 0 -10000 0 0
NFATc/p38 alpha 0.057 0.085 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
Arf6 trafficking events

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
SLC2A4 -0.26 0.28 -10000 0 -0.54 253 253
CLTC 0.034 0.056 0.26 1 -0.42 3 4
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 -0.41 1 2
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 -0.33 5 9
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 0.29 2 -0.42 3 5
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 -0.33 19 19
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 -0.34 30 30
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 0.29 2 -0.38 4 6
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 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
TRAF6/ASK1 0.008 0.07 -10000 0 -0.28 26 26
TRAF2/ASK1 0.022 0.087 -10000 0 -0.29 34 34
ATM 0.03 0.012 -10000 0 -10000 0 0
MAP2K3 -0.016 0.14 0.28 1 -0.41 31 32
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.13 0.32 1 -0.36 41 42
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 -0.37 30 30
TAK1/TAB family -0.002 0.021 -10000 0 -0.21 1 1
RAC1/OSM/MEKK3 0.057 0.023 -10000 0 -10000 0 0
TRAF2 0.035 0.012 0.18 3 -10000 0 3
RAC1/OSM/MEKK3/MKK3 0.008 0.12 -10000 0 -0.34 24 24
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
Arf6 downstream pathway

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
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 -0.16 1 1
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 0.25 8 -0.33 1 9
MAPK3 0.071 0.078 0.22 16 -10000 0 16
ARF6/GTP/NME1/Tiam1 0.092 0.067 0.26 8 -10000 0 8
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 10 -10000 0 10
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 -0.16 1 1
cortical actin cytoskeleton organization 0.056 0.079 0.25 8 -0.33 1 9
RAC1 0.034 0.005 -10000 0 -10000 0 0
liver development 0.048 0.045 -10000 0 -0.16 1 1
ARF6/GTP 0.048 0.045 -10000 0 -0.16 1 1
RhoA/GTP 0.062 0.041 -10000 0 -10000 0 0
mol:GDP 0.051 0.076 0.2 99 -10000 0 99
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 0.25 8 -0.33 1 9
ruffle organization 0.021 0.05 -10000 0 -0.24 1 1
regulation of epithelial cell migration 0.048 0.045 -10000 0 -0.16 1 1
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 0.25 8 -0.33 1 9
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.075 0.14 0.38 1 -0.28 41 42
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 58 59
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 -0.3 60 61
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
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.027 0.026 -10000 0 -10000 0 0
CRKL 0.033 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 -10000 0 -10000 0 0
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 -0.32 44 44
PIK3CA 0.033 0.008 -10000 0 -10000 0 0
PI3K 0.005 0.13 -10000 0 -0.38 48 48
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 -10000 0 -0.34 11 11
p130Cas/Crk/Dock1 0.04 0.071 0.37 1 -0.28 14 15
VCAM1 0.023 0.086 -10000 0 -0.54 11 11
RHOA 0.033 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.081 0.035 -10000 0 -10000 0 0
BCAR1 -0.007 0.061 0.39 2 -0.3 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 -0.33 44 44
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.034 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 -0.45 1 1
NCOR2 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.027 -10000 0 -0.4 2 2
RXRs/RARs/NRIP1/9cRA 0.022 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 -0.36 1 1
RARA 0.021 0.023 0.2 1 -0.24 1 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.092 -10000 0 -0.35 13 13
PRKCA 0.033 0.019 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.027 0.13 0.46 2 -0.54 9 11
RXRG 0.021 0.033 -10000 0 -0.32 3 3
RXRA 0.039 0.054 0.22 1 -0.26 4 5
RXRB 0.027 0.019 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.027 -10000 0 -0.4 2 2
RBP1 0.007 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 -0.49 3 3
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.026 0.11 -10000 0 -0.43 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.096 0.25 6 -0.31 11 17
RXRs/RARs/NRIP1/9cRA/HDAC3 0.027 0.13 0.46 2 -0.56 9 11
positive regulation of DNA binding 0.059 0.055 -10000 0 -0.26 3 3
NRIP1 0.02 0.19 0.56 2 -1.1 9 11
RXRs/RARs 0.029 0.12 0.38 2 -0.54 5 7
RXRs/RXRs/DNA/9cRA 0.026 0.056 -10000 0 -0.37 1 1
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 S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.033 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 57 57
PIK3CA 0.033 0.008 -9999 0 -10000 0 0
PI3K 0.005 0.13 -9999 0 -0.38 48 48
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 57 57
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.039 0.085 0.3 2 -0.33 7 9
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 0.41 13 -0.78 29 42
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 -0.39 8 12
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 2 2
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 58 58
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 0.35 5 -0.42 10 15
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 0.33 2 -0.43 13 15
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 0.39 19 -0.68 29 48
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 -0.51 17 17
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 -0.42 19 19
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 0.35 4 -0.49 30 34
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
Nephrin/Neph1 signaling in the kidney podocyte

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
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 -10000 0 0
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 S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.047 0.037 -10000 0 -0.3 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 0.25 16 -0.31 2 18
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 0.24 1 -0.31 2 3
GNAT2/GDP 0.056 0.096 -10000 0 -0.28 30 30
GNB5 0.032 0.026 -10000 0 -0.54 1 1
mol:GMP (4 units) 0.021 0.046 0.2 1 -0.31 5 6
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 0.18 1 -10000 0 1
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 -0.28 7 7
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.033 0.01 -10000 0 -10000 0 0
RGS9 0.001 0.13 -10000 0 -0.54 27 27
PDE6C 0.034 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
Class I PI3K signaling events

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
ARF5/GTP -0.005 0.054 0.26 10 -10000 0 10
DAPP1 0.033 0.11 0.31 4 -0.32 20 24
Src family/SYK family/BLNK-LAT/BTK-ITK 0.044 0.14 0.42 9 -0.45 17 26
mol:DAG 0.041 0.095 0.28 30 -0.2 1 31
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 0.21 19 -0.16 1 20
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.035 0.012 -10000 0 -10000 0 0
ZAP70 0.038 0.024 -10000 0 -10000 0 0
mol:IP3 0.026 0.071 0.24 20 -0.23 1 21
LYN 0.03 0.015 -10000 0 -10000 0 0
ARF1/GDP 0.037 0.077 0.43 1 -0.37 6 7
RhoA/GDP 0.05 0.059 0.3 6 -10000 0 6
PDK1/Src/Hsp90 0.059 0.026 -10000 0 -10000 0 0
BLNK 0.039 0.026 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.035 0.083 0.35 8 -0.35 3 11
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 0.3 8 -10000 0 8
Src family/SYK family/BLNK-LAT 0.042 0.091 0.31 11 -0.36 6 17
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 -0.31 18 18
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 -0.28 1 24
LCK 0.048 0.044 -10000 0 -10000 0 0
BTK -0.002 0.059 0.31 7 -10000 0 7
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 0.33 7 -0.34 8 15
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 0.18 6 -10000 0 6
IKBKG 0.019 0.14 -10000 0 -0.39 42 42
IKK complex/A20 0.04 0.15 -10000 0 -0.44 18 18
NEMO/A20/RIP2 0.029 0.021 0.18 6 -10000 0 6
XPO1 0.034 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.03 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 C 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
INCENP 0.045 0.04 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.078 0.055 0.24 19 -10000 0 19
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.017 0.032 -10000 0 -0.31 4 4
AURKB 0.056 0.058 -10000 0 -10000 0 0
AURKC 0.036 0.019 0.18 8 -10000 0 8
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 -0.31 1 1
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 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
RELA 0.028 0.042 -10000 0 -0.23 7 7
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 -10000 0 0
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 -0.37 7 7
HDAC1 0.034 0.005 -10000 0 -10000 0 0
HDAC3 0.03 0.013 -10000 0 -10000 0 0
HDAC2 0.033 0.017 -10000 0 -10000 0 0
YY1 0.016 0.015 -10000 0 -0.28 1 1
HDAC8 0.035 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 -0.29 3 3
YY1/SAP30/HDAC1 0.05 0.054 -10000 0 -0.3 1 1
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 -0.38 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.032 0.042 -10000 0 -10000 0 0
nuclear export -0.056 0.028 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GATAD2B 0.028 0.014 -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 -0.34 4 4
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 -10000 0 0
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 1 1
NFKBIA 0.033 0.037 -10000 0 -0.28 1 1
MAPK14 0.034 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.03 0.016 -10000 0 -10000 0 0
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.038 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 -0.38 48 48
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 0.34 3 -0.42 4 7
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
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.046 0.055 -10000 0 -0.3 7 7
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 -10000 0 -10000 0 0
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 -0.29 18 18
BRCA1 0.036 0.021 -10000 0 -10000 0 0
centrosome duplication 0.056 0.049 -10000 0 -10000 0 0
regulation of centrosome cycle 0.092 0.064 0.25 1 -10000 0 1
spindle assembly 0.051 0.087 -10000 0 -0.29 18 18
TDRD7 0.034 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.072 0.28 5 -10000 0 5
CENPA 0.061 0.056 0.16 64 -0.23 1 65
Aurora A/PP2A 0.052 0.037 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.028 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
TCGA08_p53

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
CDKN2A 0.027 0.046 -10000 0 -10000 0 0
TP53 -0.002 0.055 -10000 0 -0.26 1 1
Senescence -0.006 0.06 -10000 0 -0.26 1 1
Apoptosis -0.006 0.06 -10000 0 -0.26 1 1
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
LPA4-mediated signaling events

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
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
Effects of Botulinum toxin

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
STX1A 0.012 0.019 -10000 0 -10000 0 0
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 0.092 12 -0.12 11 23
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
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.032 0.026 -10000 0 -0.54 1 1
SMAD2 -0.007 0.05 -10000 0 -0.25 8 8
SMAD3 0.027 0.045 0.29 2 -10000 0 2
SMAD3/SMAD4 0.058 0.065 -10000 0 -0.42 4 4
SMAD4/Ubc9/PIASy 0.058 0.034 -10000 0 -0.34 1 1
SMAD2/SMAD2/SMAD4 0.064 0.074 -10000 0 -0.3 2 2
PPM1A 0.033 0.006 -10000 0 -10000 0 0
CALM1 0.033 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.009 0.057 -10000 0 -0.28 6 6
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
Ephrin A reverse signaling

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
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
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.034 0.004 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.031 0.01 -10000 0 -10000 0 0
TCEB1 0.028 0.013 -10000 0 -10000 0 0
HIF1A/p53 0.046 0.06 -10000 0 -0.27 7 7
HIF1A 0.03 0.05 -10000 0 -0.27 6 6
COPS5 0.028 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.07 0.05 -10000 0 -10000 0 0
FIH (dimer) 0.034 0.005 -10000 0 -10000 0 0
CDKN2A 0.053 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 -0.47 6 6
ARNT 0.027 0.014 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.032 0.009 -10000 0 -10000 0 0
HIF1A/p19ARF 0.059 0.068 0.26 3 -0.27 6 9
BARD1 signaling events

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
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 -10000 0 -0.54 1 1
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 0.34 8 -0.4 2 10
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 0.25 1 -10000 0 1
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 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
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
Glypican 2 network

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
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
Sumoylation by RanBP2 regulates transcriptional repression

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
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 -0.26 3 3
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
Rapid glucocorticoid 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
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 -10000 0 -10000 0 0
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 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
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 -0.19 2 3
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 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.009 0.02 -10000 0 -0.19 1 1
ARF1/GTP 0.015 0.014 -10000 0 -10000 0 0
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 -10000 0 0
AP2M1 0.034 0.009 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.008 -10000 0 -10000 0 0
Rac/GTP 0.028 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.033 0.024 -10000 0 -10000 0 0
ARFIP2 0.021 0.026 -10000 0 -10000 0 0
COPA 0.028 0.014 -10000 0 -10000 0 0
RAC1 0.034 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.016 0.032 -10000 0 -0.2 3 3
ARF1/GTP/ARHGAP10 0.018 0.01 -10000 0 -10000 0 0
GGA3 0.032 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.016 0.041 -10000 0 -0.23 9 9
AP2A1 0.034 0.013 -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 -0.25 13 13
Arfaptin 2/Rac/GDP 0.041 0.016 -10000 0 -10000 0 0
CYTH2 -0.001 0.002 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.021 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.025 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.024 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 -10000 0 -10000 0 0
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 -10000 0 -10000 0 0
GOSR2 0.013 0.018 -10000 0 -0.26 1 1
USO1 0.012 0.024 -10000 0 -0.31 2 2
GBF1 0.013 0.02 -10000 0 -0.31 1 1
ARF1/GTP/Arfaptin 2 0.036 0.022 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.062 0.026 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.048 0.015 -10000 0 -0.17 1 1
FBXW11 0.033 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.007 -10000 0 -10000 0 0
CHUK 0.034 0.005 -10000 0 -10000 0 0
NF kappa B2 p100/RelB 0.094 0.036 -10000 0 -10000 0 0
NFKB1 0.034 0.005 -10000 0 -10000 0 0
MAP3K14 0.033 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelB 0.051 0.017 -10000 0 -10000 0 0
RELB 0.036 0.02 -10000 0 -10000 0 0
NFKB2 0.035 0.012 -10000 0 -10000 0 0
NF kappa B2 p52/RelB 0.047 0.018 0.23 1 -10000 0 1
regulation of B cell activation 0.047 0.017 0.23 1 -10000 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/2841012/2.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/2859781/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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