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

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

Summary

There were 52 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Signaling mediated by p38-alpha and p38-beta 248
Signaling events mediated by Stem cell factor receptor (c-Kit) 247
EGFR-dependent Endothelin signaling events 179
Endothelins 168
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 163
IGF1 pathway 136
Class IB PI3K non-lipid kinase events 136
Arf6 signaling events 134
S1P1 pathway 104
Nongenotropic Androgen signaling 103
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 10943 44 -0.72 0.016 1000 -1000 -0.035 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 247 19318 78 -1.1 0.35 1000 -1000 -0.05 -1000
EGFR-dependent Endothelin signaling events 179 3779 21 -0.45 0.016 1000 -1000 -0.042 -1000
Endothelins 168 16165 96 -0.82 0.029 1000 -1000 -0.05 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 163 11095 68 -1 0.48 1000 -1000 -0.074 -1000
IGF1 pathway 136 7794 57 -0.37 0.15 1000 -1000 -0.064 -1000
Class IB PI3K non-lipid kinase events 136 408 3 -0.17 -1000 1000 -1000 -0.001 -1000
Arf6 signaling events 134 8311 62 -0.45 0.018 1000 -1000 -0.037 -1000
S1P1 pathway 104 3765 36 -0.67 0.016 1000 -1000 -0.053 -1000
Nongenotropic Androgen signaling 103 5400 52 -0.58 0.28 1000 -1000 -0.038 -1000
Signaling events mediated by PTP1B 99 7594 76 -0.48 0.2 1000 -1000 -0.055 -1000
HIF-1-alpha transcription factor network 98 7469 76 -0.51 0.054 1000 -1000 -0.041 -1000
Calcium signaling in the CD4+ TCR pathway 97 3035 31 -0.53 0.026 1000 -1000 -0.046 -1000
FOXM1 transcription factor network 92 4710 51 -0.84 0.017 1000 -1000 -0.092 -1000
Glucocorticoid receptor regulatory network 88 10128 114 -1.2 0.3 1000 -1000 -0.049 -1000
Ras signaling in the CD4+ TCR pathway 77 1311 17 -0.23 0.013 1000 -1000 -0.03 -1000
PDGFR-alpha signaling pathway 76 3346 44 -0.84 0.046 1000 -1000 -0.049 -1000
BMP receptor signaling 72 5878 81 -0.59 0.039 1000 -1000 -0.065 -1000
Ephrin B reverse signaling 72 3469 48 -0.26 0.13 1000 -1000 -0.043 -1000
FAS signaling pathway (CD95) 69 3268 47 -0.96 0.071 1000 -1000 -0.033 -1000
IL6-mediated signaling events 67 5057 75 -0.52 0.052 1000 -1000 -0.057 -1000
Integrins in angiogenesis 63 5299 84 -0.57 0.053 1000 -1000 -0.055 -1000
Plasma membrane estrogen receptor signaling 62 5384 86 -0.35 0.17 1000 -1000 -0.055 -1000
IL4-mediated signaling events 61 5556 91 -0.63 0.24 1000 -1000 -0.17 -1000
Fc-epsilon receptor I signaling in mast cells 58 5637 97 -0.51 0.039 1000 -1000 -0.068 -1000
E-cadherin signaling in keratinocytes 50 2153 43 -0.37 0.044 1000 -1000 -0.05 -1000
p75(NTR)-mediated signaling 49 6161 125 -0.25 0.016 1000 -1000 -0.059 -1000
Glypican 1 network 49 2355 48 -0.55 0.061 1000 -1000 -0.031 -1000
IL23-mediated signaling events 45 2737 60 -0.92 0.019 1000 -1000 -0.11 -1000
ErbB2/ErbB3 signaling events 42 2763 65 -0.48 0.03 1000 -1000 -0.045 -1000
Nectin adhesion pathway 42 2679 63 -0.1 0.016 1000 -1000 -0.055 -1000
Stabilization and expansion of the E-cadherin adherens junction 42 3147 74 -0.37 0.08 1000 -1000 -0.072 -1000
Signaling events regulated by Ret tyrosine kinase 41 3402 82 -0.17 0.018 1000 -1000 -0.063 -1000
Insulin Pathway 41 3086 74 -0.39 0.046 1000 -1000 -0.058 -1000
ErbB4 signaling events 40 2823 69 -0.5 0.11 1000 -1000 -0.065 -1000
Visual signal transduction: Rods 40 2105 52 -0.58 0.029 1000 -1000 -0.068 -1000
EPHB forward signaling 39 3339 85 -0.26 0.12 1000 -1000 -0.07 -1000
Presenilin action in Notch and Wnt signaling 36 2212 61 -0.53 0.04 1000 -1000 -0.054 -1000
TCGA08_retinoblastoma 36 289 8 -0.045 0.022 1000 -1000 -0.012 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 35 3049 85 -0.54 0.035 1000 -1000 -0.067 -1000
Neurotrophic factor-mediated Trk receptor signaling 35 4284 120 -0.42 0.18 1000 -1000 -0.052 -1000
Signaling events mediated by the Hedgehog family 34 1803 52 -0.22 0.14 1000 -1000 -0.062 -1000
S1P5 pathway 34 588 17 -0.25 0.078 1000 -1000 -0.033 -1000
RXR and RAR heterodimerization with other nuclear receptor 34 1786 52 -0.53 0.088 1000 -1000 -0.041 -1000
Ceramide signaling pathway 32 2474 76 -0.35 0.098 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 31 4324 136 -0.51 0.065 1000 -1000 -0.042 -1000
Syndecan-3-mediated signaling events 31 1085 35 -0.51 0.016 1000 -1000 -0.059 -1000
IL27-mediated signaling events 31 1584 51 -0.52 0.039 1000 -1000 -0.051 -1000
TCGA08_rtk_signaling 30 784 26 -0.37 0.028 1000 -1000 -0.016 -1000
S1P3 pathway 29 1233 42 -0.25 0.041 1000 -1000 -0.034 -1000
Syndecan-2-mediated signaling events 28 1993 69 -0.46 0.046 1000 -1000 -0.042 -1000
LPA receptor mediated events 28 2860 102 -0.51 0.045 1000 -1000 -0.057 -1000
Sphingosine 1-phosphate (S1P) pathway 25 713 28 -0.25 0.03 1000 -1000 -0.031 -1000
amb2 Integrin signaling 25 2054 82 -0.62 0.049 1000 -1000 -0.06 -1000
Signaling events mediated by VEGFR1 and VEGFR2 25 3140 125 -0.52 0.059 1000 -1000 -0.068 -1000
Angiopoietin receptor Tie2-mediated signaling 24 2169 88 -0.55 0.068 1000 -1000 -0.093 -1000
Wnt signaling 23 164 7 -0.029 0.012 1000 -1000 -0.014 -1000
S1P4 pathway 23 597 25 -0.25 0.03 1000 -1000 -0.03 -1000
FOXA2 and FOXA3 transcription factor networks 22 1041 46 -0.85 0.075 1000 -1000 -0.016 -1000
mTOR signaling pathway 22 1212 53 -0.072 0.042 1000 -1000 -0.045 -1000
Reelin signaling pathway 22 1280 56 -0.1 0.044 1000 -1000 -0.059 -1000
IL1-mediated signaling events 22 1378 62 -0.12 0.082 1000 -1000 -0.059 -1000
Regulation of Telomerase 22 2247 102 -0.51 0.067 1000 -1000 -0.066 -1000
E-cadherin signaling events 22 113 5 -0.039 0.013 1000 -1000 -0.029 -1000
Osteopontin-mediated events 21 802 38 -0.51 0.061 1000 -1000 -0.064 -1000
Thromboxane A2 receptor signaling 21 2256 105 -0.37 0.097 1000 -1000 -0.051 -1000
Canonical Wnt signaling pathway 21 1079 51 -0.53 0.2 1000 -1000 -0.044 -1000
Regulation of p38-alpha and p38-beta 21 1181 54 -0.44 0.051 1000 -1000 -0.039 -1000
Regulation of Androgen receptor activity 21 1504 70 -0.59 0.06 1000 -1000 -0.058 -1000
Aurora B signaling 21 1447 67 -0.52 0.074 1000 -1000 -0.043 -1000
IL12-mediated signaling events 20 1799 87 -0.88 0.027 1000 -1000 -0.078 -1000
Insulin-mediated glucose transport 19 613 32 -0.11 0.049 1000 -1000 -0.04 -1000
Coregulation of Androgen receptor activity 18 1414 76 -0.25 0.026 1000 -1000 -0.033 -1000
Signaling events mediated by PRL 18 633 34 -0.43 0.025 1000 -1000 -0.033 -1000
Syndecan-4-mediated signaling events 17 1155 67 -0.55 0.049 1000 -1000 -0.073 -1000
Syndecan-1-mediated signaling events 15 537 34 -0.1 0.016 1000 -1000 -0.042 -1000
PLK2 and PLK4 events 15 46 3 -0.019 -0.01 1000 -1000 -0.005 -1000
Noncanonical Wnt signaling pathway 15 409 26 -0.041 0.033 1000 -1000 -0.06 -1000
E-cadherin signaling in the nascent adherens junction 15 1145 76 -0.056 0.046 1000 -1000 -0.058 -1000
IL2 signaling events mediated by PI3K 14 842 58 -0.11 0.039 1000 -1000 -0.065 -1000
Arf6 trafficking events 14 1035 71 -0.41 0.054 1000 -1000 -0.057 -1000
BCR signaling pathway 14 1453 99 -0.24 0.076 1000 -1000 -0.071 -1000
Caspase cascade in apoptosis 13 998 74 -0.22 0.074 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 12 827 65 -0.25 0.079 1000 -1000 -0.053 -1000
Class I PI3K signaling events mediated by Akt 12 848 68 -0.24 0.069 1000 -1000 -0.04 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 12 555 45 -0.048 0.07 1000 -1000 -0.062 -1000
VEGFR1 specific signals 12 689 56 -0.52 0.07 1000 -1000 -0.053 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 11 620 54 -0.1 0.043 1000 -1000 -0.07 -1000
TRAIL signaling pathway 11 545 48 -0.024 0.046 1000 -1000 -0.046 -1000
JNK signaling in the CD4+ TCR pathway 10 177 17 -0.082 0.057 1000 -1000 -0.036 -1000
Signaling mediated by p38-gamma and p38-delta 10 155 15 0 0.029 1000 -1000 -0.014 -1000
Cellular roles of Anthrax toxin 9 363 39 -0.14 0.023 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class III 9 373 40 -0.1 0.029 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class II 8 605 75 -0.18 0.043 1000 -1000 -0.041 -1000
EPO signaling pathway 8 494 55 -0.13 0.063 1000 -1000 -0.066 -1000
ceramide signaling pathway 8 428 49 -0.13 0.061 1000 -1000 -0.036 -1000
FoxO family signaling 8 542 64 -0.027 0.11 1000 -1000 -0.048 -1000
Retinoic acid receptors-mediated signaling 8 490 58 -0.1 0.042 1000 -1000 -0.052 -1000
IFN-gamma pathway 7 514 68 -0.056 0.086 1000 -1000 -0.063 -1000
TCR signaling in naïve CD8+ T cells 7 680 93 -0.082 0.089 1000 -1000 -0.047 -1000
p38 MAPK signaling pathway 7 314 44 -0.036 0.039 1000 -1000 -0.043 -1000
Visual signal transduction: Cones 6 231 38 -0.029 0.026 1000 -1000 -0.032 -1000
Paxillin-independent events mediated by a4b1 and a4b7 6 258 37 -0.056 0.051 1000 -1000 -0.038 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 566 83 -0.13 0.065 1000 -1000 -0.055 -1000
Paxillin-dependent events mediated by a4b1 6 240 36 -0.056 0.029 1000 -1000 -0.049 -1000
HIF-2-alpha transcription factor network 5 251 43 -0.21 0.22 1000 -1000 -0.11 -1000
Atypical NF-kappaB pathway 5 157 31 -0.056 0.062 1000 -1000 -0.035 -1000
IL2 signaling events mediated by STAT5 4 93 22 -0.055 0.086 1000 -1000 -0.015 -1000
Class I PI3K signaling events 4 316 73 -0.027 0.089 1000 -1000 -0.043 -1000
PDGFR-beta signaling pathway 4 439 97 -0.19 0.045 1000 -1000 -0.073 -1000
Aurora A signaling 3 208 60 -0.088 0.048 1000 -1000 -0.035 -1000
Arf6 downstream pathway 3 132 43 -0.039 0.04 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class I 3 415 104 -0.24 0.074 1000 -1000 -0.042 -1000
LPA4-mediated signaling events 1 13 12 0 0.042 1000 -1000 -0.013 -1000
Nephrin/Neph1 signaling in the kidney podocyte 1 56 34 -0.004 0.056 1000 -1000 -0.043 -1000
Ephrin A reverse signaling 1 7 7 0 0.03 1000 -1000 -0.021 -1000
Effects of Botulinum toxin 1 29 26 -0.047 0.024 1000 -1000 -0.047 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 20 23 -0.029 0.063 1000 -1000 -0.043 -1000
Canonical NF-kappaB pathway 0 5 39 -0.018 0.1 1000 -1000 -0.055 -1000
BARD1 signaling events 0 9 57 -0.079 0.052 1000 -1000 -0.049 -1000
Circadian rhythm pathway 0 16 22 -0.054 0.065 1000 -1000 -0.044 -1000
a4b1 and a4b7 Integrin signaling 0 0 5 -0.003 0.016 1000 -1000 -0.036 -1000
Aurora C signaling 0 1 7 -0.014 0.021 1000 -1000 -0.023 -1000
PLK1 signaling events 0 42 85 -0.091 0.067 1000 -1000 -0.043 -1000
TCGA08_p53 0 0 7 -0.004 0.015 1000 -1000 -0.009 -1000
Glypican 2 network 0 0 4 -0.007 -1000 1000 -1000 -0.015 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 0 0.039 1000 -1000 -0.037 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0 6 33 -0.018 0.05 1000 -1000 -0.047 -1000
Rapid glucocorticoid signaling 0 16 20 -0.003 0.016 1000 -1000 -0.034 -1000
Arf1 pathway 0 6 54 -0.001 0.045 1000 -1000 -0.035 -1000
Alternative NF-kappaB pathway 0 3 13 -0.002 0.016 1000 -1000 -0.039 -1000
Total 4611 280427 7203 -40 -2000 131000 -131000 -6.3 -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 -0.72 0.63 -9999 0 -1.2 317 317
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 -0.18 0.16 -9999 0 -0.31 317 317
ATF2/c-Jun -0.26 0.38 -9999 0 -1 97 97
MAPK11 -0.18 0.16 -9999 0 -0.31 317 317
MITF -0.21 0.21 -9999 0 -0.37 320 320
MAPKAPK5 -0.2 0.2 -9999 0 -0.37 317 317
KRT8 -0.21 0.21 -9999 0 -0.37 317 317
MAPKAPK3 0.015 0.012 -9999 0 -10000 0 0
MAPKAPK2 0.016 0.01 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.27 0.25 -9999 0 -0.47 317 317
CEBPB -0.2 0.21 -9999 0 -0.37 317 317
SLC9A1 -0.2 0.2 -9999 0 -0.37 317 317
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.22 0.23 -9999 0 -0.38 317 317
p38alpha-beta/MNK1 -0.22 0.18 -9999 0 -0.37 317 317
JUN -0.26 0.38 -9999 0 -1 97 97
PPARGC1A -0.26 0.29 -9999 0 -0.45 328 328
USF1 -0.21 0.2 -9999 0 -0.37 317 317
RAB5/GDP/GDI1 -0.16 0.13 -9999 0 -0.33 82 82
NOS2 -0.22 0.2 -9999 0 -0.38 317 317
DDIT3 -0.2 0.2 -9999 0 -0.37 317 317
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 -0.17 0.18 -9999 0 -0.3 317 317
p38alpha-beta/HBP1 -0.22 0.18 -9999 0 -0.37 317 317
CREB1 -0.22 0.21 -9999 0 -0.38 319 319
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.17 0.18 -9999 0 -0.4 78 78
RPS6KA4 -0.2 0.2 -9999 0 -0.37 317 317
PLA2G4A -0.42 0.34 -9999 0 -0.66 327 327
GDI1 -0.2 0.2 -9999 0 -0.37 317 317
TP53 -0.26 0.25 -9999 0 -0.46 317 317
RPS6KA5 -0.22 0.22 -9999 0 -0.38 329 329
ESR1 -0.32 0.27 -9999 0 -0.45 392 392
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C -0.24 0.26 -9999 0 -0.41 325 325
MEF2A -0.2 0.2 -9999 0 -0.37 317 317
EIF4EBP1 -0.22 0.21 -9999 0 -0.38 319 319
KRT19 -0.22 0.22 -9999 0 -0.39 320 320
ELK4 -0.2 0.2 -9999 0 -0.37 317 317
ATF6 -0.2 0.2 -9999 0 -0.37 317 317
ATF1 -0.22 0.21 -9999 0 -0.38 319 319
p38alpha-beta/MAPKAPK2 -0.22 0.18 -9999 0 -0.37 317 317
p38alpha-beta/MAPKAPK3 -0.22 0.18 -9999 0 -0.37 317 317
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 -0.39 417 417
CRKL -0.33 0.18 -10000 0 -0.42 417 417
HRAS -0.25 0.15 -10000 0 -0.34 158 158
mol:PIP3 -0.33 0.18 -10000 0 -0.42 414 414
SPRED1 0.013 0.045 -10000 0 -0.72 2 2
SPRED2 0.016 0 -10000 0 -10000 0 0
GAB1 -0.36 0.18 -10000 0 -0.45 417 417
FOXO3 -0.3 0.16 -10000 0 -0.38 415 415
AKT1 -0.33 0.18 -10000 0 -0.41 416 416
BAD -0.3 0.16 -10000 0 -0.38 416 416
megakaryocyte differentiation -0.35 0.18 -10000 0 -0.44 417 417
GSK3B -0.3 0.16 -10000 0 -0.38 416 416
RAF1 -0.2 0.13 -10000 0 -0.31 16 16
SHC1 0.016 0 -10000 0 -10000 0 0
STAT3 -0.36 0.18 -10000 0 -0.44 417 417
STAT1 -0.87 0.45 -10000 0 -1.1 445 445
HRAS/SPRED1 -0.21 0.11 -10000 0 -0.34 18 18
cell proliferation -0.35 0.18 -10000 0 -0.44 417 417
PIK3CA 0.015 0.007 -10000 0 -10000 0 0
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 -0.35 0.18 -10000 0 -0.44 417 417
HRAS/SPRED2 -0.21 0.1 -10000 0 -0.31 16 16
LYN/TEC/p62DOK -0.33 0.16 -10000 0 -0.41 416 416
MAPK3 -0.14 0.098 -10000 0 -0.29 2 2
STAP1 -0.36 0.18 -10000 0 -0.45 422 422
GRAP2 0.014 0.019 -10000 0 -10000 0 0
JAK2 -0.72 0.34 -10000 0 -0.88 424 424
STAT1 (dimer) -0.85 0.43 -10000 0 -1 445 445
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.33 0.16 -10000 0 -0.41 416 416
actin filament polymerization -0.36 0.18 -10000 0 -0.44 419 419
LYN 0.016 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.49 0.25 -10000 0 -0.61 421 421
PIK3R1 -0.057 0.22 -10000 0 -0.72 52 52
CBL/CRKL/GRB2 -0.3 0.15 -10000 0 -0.37 417 417
PI3K -0.36 0.21 -10000 0 -0.45 419 419
PTEN -0.002 0.11 -10000 0 -0.72 13 13
SCF/KIT/EPO/EPOR -1.1 0.55 -10000 0 -1.3 416 416
MAPK8 -0.36 0.18 -10000 0 -0.45 417 417
STAT3 (dimer) -0.35 0.18 -10000 0 -0.44 417 417
positive regulation of transcription -0.11 0.084 -10000 0 -0.23 2 2
mol:GDP -0.28 0.13 -10000 0 -0.34 414 414
PIK3C2B -0.36 0.18 -10000 0 -0.45 417 417
CBL/CRKL -0.3 0.17 -10000 0 -0.38 417 417
FER -0.36 0.18 -10000 0 -0.44 417 417
SH2B3 -0.36 0.18 -10000 0 -0.44 417 417
PDPK1 -0.3 0.16 -10000 0 -0.38 413 413
SNAI2 -0.41 0.23 -10000 0 -0.5 430 430
positive regulation of cell proliferation -0.61 0.31 -10000 0 -0.74 445 445
KITLG -0.019 0.078 -10000 0 -0.75 3 3
cell motility -0.61 0.31 -10000 0 -0.74 445 445
PTPN6 0.032 0.019 -10000 0 -10000 0 0
EPOR -0.22 0.14 -10000 0 -0.62 1 1
STAT5A (dimer) -0.5 0.26 -10000 0 -0.62 422 422
SOCS1 0.015 0.012 -10000 0 -10000 0 0
cell migration 0.35 0.18 0.44 419 -10000 0 419
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.02 0.058 -10000 0 -10000 0 0
VAV1 0.012 0.027 -10000 0 -10000 0 0
GRB10 -0.36 0.19 -10000 0 -0.45 417 417
PTPN11 0.029 0.007 -10000 0 -10000 0 0
SCF/KIT -0.38 0.19 -10000 0 -0.48 419 419
GO:0007205 0.018 0.01 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.32 2 2
CBL 0.016 0 -10000 0 -10000 0 0
KIT -1.1 0.58 -10000 0 -1.4 417 417
MAP2K2 -0.15 0.11 -10000 0 -0.32 2 2
SHC/Grb2/SOS1 -0.33 0.16 -10000 0 -0.41 416 416
STAT5A -0.52 0.26 -10000 0 -0.64 422 422
GRB2 0.013 0.022 -10000 0 -10000 0 0
response to radiation -0.4 0.22 -10000 0 -0.49 430 430
SHC/GRAP2 -0.001 0.009 -10000 0 -10000 0 0
PTPRO -0.36 0.18 -10000 0 -0.45 417 417
SH2B2 -0.37 0.18 -10000 0 -0.45 419 419
DOK1 0.014 0.019 -10000 0 -10000 0 0
MATK -0.36 0.18 -10000 0 -0.45 419 419
CREBBP 0.006 0.036 -10000 0 -0.72 1 1
BCL2 -0.45 0.55 -10000 0 -1.5 108 108
EGFR-dependent Endothelin signaling events

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
HRAS 0.015 0.012 -9999 0 -10000 0 0
EGFR -0.37 0.37 -9999 0 -0.72 274 274
EGF/EGFR -0.45 0.34 -9999 0 -0.6 392 392
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.33 0.26 -9999 0 -0.47 370 370
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.013 0.046 -9999 0 -0.72 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.24 0.35 -9999 0 -0.72 179 179
EGF/EGFR dimer/SHC -0.39 0.3 -9999 0 -0.55 370 370
mol:GDP -0.32 0.25 -9999 0 -0.46 370 370
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.22 0.34 -9999 0 -0.72 170 170
GRB2/SOS1 -0.001 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.3 0.24 -9999 0 -0.43 370 370
SHC1 0.016 0 -9999 0 -10000 0 0
HRAS/GDP -0.3 0.24 -9999 0 -0.43 370 370
FRAP1 -0.29 0.26 -9999 0 -0.44 370 370
EGF/EGFR dimer -0.45 0.33 -9999 0 -0.64 370 370
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.18 0.25 -9999 0 -0.54 172 172
Endothelins

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
AKT1 -0.11 0.24 -9999 0 -0.45 174 174
PTK2B 0.016 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.14 0.3 -9999 0 -0.71 84 84
EDN1 -0.21 0.35 -9999 0 -0.72 170 170
EDN3 -0.6 0.28 -9999 0 -0.72 439 439
EDN2 -0.061 0.091 -9999 0 -0.72 2 2
HRAS/GDP -0.24 0.25 -9999 0 -0.5 209 209
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.12 0.19 -9999 0 -0.35 168 168
ADCY4 -0.097 0.21 -9999 0 -0.38 175 175
ADCY5 -0.094 0.2 -9999 0 -0.38 174 174
ADCY6 -0.093 0.2 -9999 0 -0.38 173 173
ADCY7 -0.092 0.2 -9999 0 -0.38 173 173
ADCY1 -0.093 0.2 -9999 0 -0.38 173 173
ADCY2 -0.098 0.21 -9999 0 -0.39 177 177
ADCY3 -0.093 0.2 -9999 0 -0.38 173 173
ADCY8 -0.093 0.2 -9999 0 -0.38 173 173
ADCY9 -0.093 0.2 -9999 0 -0.38 173 173
arachidonic acid secretion -0.53 0.37 -9999 0 -0.69 406 406
ETB receptor/Endothelin-1/Gq/GTP -0.26 0.25 -9999 0 -0.43 322 322
GNAO1 0.016 0.007 -9999 0 -10000 0 0
HRAS 0.009 0.014 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.094 0.24 -9999 0 -0.42 172 172
ETA receptor/Endothelin-1/Gs/GTP -0.092 0.23 -9999 0 -0.41 173 173
mol:GTP -0.007 0.009 -9999 0 -10000 0 0
COL3A1 -0.11 0.24 -9999 0 -0.45 172 172
EDNRB -0.35 0.37 -9999 0 -0.72 260 260
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.11 0.24 -9999 0 -0.45 172 172
CYSLTR1 -0.11 0.25 -9999 0 -0.46 174 174
SLC9A1 -0.063 0.14 -9999 0 -0.26 172 172
mol:GDP -0.27 0.27 -9999 0 -0.51 238 238
SLC9A3 -0.4 0.41 -9999 0 -0.67 331 331
RAF1 -0.36 0.29 -9999 0 -0.56 309 309
JUN -0.24 0.46 -9999 0 -1.1 116 116
JAK2 -0.11 0.25 -9999 0 -0.46 174 174
mol:IP3 -0.23 0.25 -9999 0 -0.46 222 222
ETA receptor/Endothelin-1 -0.12 0.29 -9999 0 -0.54 174 174
PLCB1 -0.1 0.25 -9999 0 -0.73 74 74
PLCB2 0.005 0.008 -9999 0 -10000 0 0
ETA receptor/Endothelin-3 -0.44 0.21 -9999 0 -0.54 439 439
FOS -0.71 0.47 -9999 0 -1 378 378
Gai/GDP -0.1 0.16 -9999 0 -0.79 2 2
CRK 0.014 0.032 -9999 0 -0.72 1 1
mol:Ca ++ -0.3 0.33 -9999 0 -0.63 226 226
BCAR1 0.017 0.001 -9999 0 -10000 0 0
PRKCB1 -0.22 0.24 -9999 0 -0.46 212 212
GNAQ -0.008 0.01 -9999 0 -10000 0 0
GNAZ 0.006 0.084 -9999 0 -0.72 7 7
GNAL 0.012 0.056 -9999 0 -0.72 3 3
Gs family/GDP -0.25 0.22 -9999 0 -0.48 208 208
ETA receptor/Endothelin-1/Gq/GTP -0.086 0.17 -9999 0 -0.31 166 166
MAPK14 -0.24 0.26 -9999 0 -0.44 270 270
TRPC6 -0.15 0.32 -9999 0 -0.8 77 77
GNAI2 0.016 0.007 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.27 0.27 -9999 0 -0.46 300 300
ETB receptor/Endothelin-2 -0.29 0.29 -9999 0 -0.58 262 262
ETB receptor/Endothelin-3 -0.67 0.34 -9999 0 -0.78 458 458
ETB receptor/Endothelin-1 -0.41 0.38 -9999 0 -0.68 329 329
MAPK3 -0.62 0.42 -9999 0 -0.86 382 382
MAPK1 -0.62 0.42 -9999 0 -0.86 382 382
Rac1/GDP -0.24 0.25 -9999 0 -0.5 208 208
cAMP biosynthetic process -0.039 0.19 -9999 0 -0.34 89 89
MAPK8 -0.16 0.29 -9999 0 -0.62 120 120
SRC 0.016 0.007 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.3 0.32 -9999 0 -0.51 309 309
p130Cas/CRK/Src/PYK2 -0.24 0.29 -9999 0 -0.56 191 191
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.24 0.25 -9999 0 -0.5 205 205
COL1A2 -0.32 0.35 -9999 0 -0.69 193 193
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 0.029 0.078 -9999 0 -0.53 4 4
mol:DAG -0.23 0.25 -9999 0 -0.46 222 222
MAP2K2 -0.47 0.34 -9999 0 -0.66 384 384
MAP2K1 -0.47 0.34 -9999 0 -0.66 384 384
EDNRA 0.024 0.053 -9999 0 -0.71 2 2
positive regulation of muscle contraction -0.089 0.21 -9999 0 -0.39 173 173
Gq family/GDP -0.22 0.21 -9999 0 -0.48 158 158
HRAS/GTP -0.28 0.26 -9999 0 -0.44 323 323
PRKCH -0.22 0.24 -9999 0 -0.46 211 211
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.22 0.24 -9999 0 -0.47 197 197
PRKCB -0.23 0.24 -9999 0 -0.44 243 243
PRKCE -0.22 0.24 -9999 0 -0.47 195 195
PRKCD -0.22 0.24 -9999 0 -0.47 198 198
PRKCG -0.22 0.24 -9999 0 -0.45 217 217
regulation of vascular smooth muscle contraction -0.82 0.55 -9999 0 -1.2 378 378
PRKCQ -0.23 0.24 -9999 0 -0.46 214 214
PLA2G4A -0.6 0.44 -9999 0 -0.79 406 406
GNA14 -0.019 0.095 -9999 0 -0.73 7 7
GNA15 0.005 0.022 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA11 0.008 0.008 -9999 0 -10000 0 0
Rac1/GTP -0.094 0.24 -9999 0 -0.42 172 172
MMP1 0.026 0.14 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.022 0.012 -10000 0 -10000 0 0
NFATC2 -0.066 0.22 -10000 0 -0.54 81 81
NFATC3 -0.17 0.14 -10000 0 -0.31 147 147
CD40LG -0.79 0.56 -10000 0 -1.1 366 366
ITCH -0.055 0.15 -10000 0 -0.59 1 1
CBLB -0.056 0.15 -10000 0 -1.1 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.33 0.24 -10000 0 -0.67 85 85
JUNB 0.012 0.055 -10000 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.12 0.15 -10000 0 -0.31 197 197
T cell anergy -0.13 0.24 -10000 0 -0.43 197 197
TLE4 -0.048 0.23 -10000 0 -0.97 22 22
Jun/NFAT1-c-4/p21SNFT -0.7 0.53 -10000 0 -1 365 365
AP-1/NFAT1-c-4 -1 0.74 -10000 0 -1.4 372 372
IKZF1 -0.03 0.16 -10000 0 -0.52 20 20
T-helper 2 cell differentiation -0.15 0.3 -10000 0 -0.7 76 76
AP-1/NFAT1 -0.46 0.35 -10000 0 -0.65 378 378
CALM1 -0.039 0.094 -10000 0 -0.3 1 1
EGR2 -0.89 0.85 -10000 0 -1.4 362 362
EGR3 -0.98 0.85 -10000 0 -1.6 331 331
NFAT1/FOXP3 -0.036 0.16 -10000 0 -0.49 24 24
EGR1 -0.59 0.28 -10000 0 -0.72 437 437
JUN -0.12 0.29 -10000 0 -0.72 97 97
EGR4 0.001 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.061 0.1 -10000 0 -0.34 1 1
GBP3 -0.074 0.28 -10000 0 -0.82 52 52
FOSL1 0.016 0.01 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.64 0.51 -10000 0 -0.94 365 365
DGKA -0.029 0.16 -10000 0 -0.5 25 25
CREM 0.016 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.92 0.57 -10000 0 -1.3 366 366
CTLA4 -0.02 0.14 -10000 0 -0.53 11 11
NFAT1-c-4 (dimer)/EGR1 -0.95 0.59 -10000 0 -1.3 367 367
NFAT1-c-4 (dimer)/EGR4 -0.64 0.52 -10000 0 -0.96 365 365
FOS -0.51 0.34 -10000 0 -0.72 375 375
IFNG -0.2 0.26 -10000 0 -0.89 43 43
T cell activation -0.48 0.39 -10000 0 -0.79 276 276
MAF -0.049 0.21 -10000 0 -0.72 47 47
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.48 0.43 0.74 365 -10000 0 365
TNF -0.76 0.52 -10000 0 -1.1 366 366
FASLG -0.96 0.82 -10000 0 -1.4 365 365
TBX21 -0.034 0.18 -10000 0 -0.72 35 35
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.009 0.047 -10000 0 -0.72 1 1
PTPN1 -0.031 0.16 -10000 0 -0.56 19 19
NFAT1-c-4/ICER1 -0.65 0.51 -10000 0 -0.96 365 365
GATA3 -0.077 0.2 -10000 0 -0.72 39 39
T-helper 1 cell differentiation -0.19 0.25 -10000 0 -0.87 43 43
IL2RA -0.34 0.24 -10000 0 -0.54 234 234
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.028 0.16 -10000 0 -0.58 14 14
E2F1 0.004 0.055 -10000 0 -10000 0 0
PPARG -0.53 0.32 -10000 0 -0.72 390 390
SLC3A2 -0.028 0.16 -10000 0 -0.53 20 20
IRF4 0.011 0.03 -10000 0 -10000 0 0
PTGS2 -0.96 0.63 -10000 0 -1.3 396 396
CSF2 -0.79 0.56 -10000 0 -1.1 369 369
JunB/Fra1/NFAT1-c-4 -0.61 0.49 -10000 0 -0.91 365 365
IL4 -0.16 0.31 -10000 0 -0.78 66 66
IL5 -0.79 0.56 -10000 0 -1.1 369 369
IL2 -0.48 0.4 -10000 0 -0.82 262 262
IL3 -0.085 0.051 -10000 0 -10000 0 0
RNF128 -0.26 0.4 -10000 0 -0.78 197 197
NFATC1 -0.48 0.43 -10000 0 -0.75 365 365
CDK4 0.28 0.26 0.52 176 -10000 0 176
PTPRK -0.081 0.3 -10000 0 -0.98 47 47
IL8 -0.8 0.56 -10000 0 -1.1 371 371
POU2F1 0.026 0 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.016 0.01 -10000 0 -10000 0 0
PTK2 0.015 0.014 -10000 0 -10000 0 0
CRKL -0.23 0.29 -10000 0 -0.46 282 282
GRB2/SOS1/SHC 0.002 0.011 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
IRS1/Crk -0.23 0.29 -10000 0 -0.47 282 282
IGF-1R heterotetramer/IGF1/PTP1B -0.25 0.26 -10000 0 -0.49 267 267
AKT1 -0.21 0.28 -10000 0 -0.62 119 119
BAD -0.18 0.26 -10000 0 -0.61 101 101
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.23 0.29 -10000 0 -0.46 282 282
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.23 0.29 -10000 0 -0.47 282 282
RAF1 -0.17 0.24 -10000 0 -0.58 96 96
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.23 0.26 -10000 0 -0.45 268 268
YWHAZ 0.014 0.017 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.26 0.31 -10000 0 -0.51 282 282
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.21 0.28 -10000 0 -0.62 120 120
GNB2L1 0.016 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.14 0.21 -10000 0 -0.48 96 96
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.2 0.23 -10000 0 -0.62 78 78
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.19 0.21 -10000 0 -0.38 267 267
IGF-1R heterotetramer -0.074 0.18 -10000 0 -0.62 37 37
IGF-1R heterotetramer/IGF1/IRS/Nck -0.25 0.28 -10000 0 -0.47 282 282
Crk/p130 Cas/Paxillin -0.22 0.25 -10000 0 -0.42 267 267
IGF1R -0.074 0.18 -10000 0 -0.62 37 37
IGF1 -0.37 0.38 -10000 0 -0.75 264 264
IRS2/Crk -0.31 0.37 -10000 0 -0.57 303 303
PI3K -0.27 0.3 -10000 0 -0.5 278 278
apoptosis 0.15 0.22 0.52 96 -10000 0 96
HRAS/GDP -0.001 0.007 -10000 0 -10000 0 0
PRKCD -0.23 0.3 -10000 0 -0.51 267 267
RAF1/14-3-3 E -0.14 0.21 -10000 0 -0.48 96 96
BAD/14-3-3 -0.16 0.24 -10000 0 -0.56 96 96
PRKCZ -0.22 0.28 -10000 0 -0.44 278 278
Crk/p130 Cas/Paxillin/FAK1 -0.19 0.21 -10000 0 -0.57 96 96
PTPN1 0.008 0.036 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.26 0.31 -10000 0 -0.54 267 267
BCAR1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.22 0.24 -10000 0 -0.43 267 267
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.23 0.29 -10000 0 -0.46 282 282
GRB10 0.011 0.064 -10000 0 -0.72 4 4
PTPN11 -0.23 0.29 -10000 0 -0.46 282 282
IRS1 -0.26 0.31 -10000 0 -0.5 282 282
IRS2 -0.34 0.38 -10000 0 -0.6 309 309
IGF-1R heterotetramer/IGF1 -0.31 0.32 -10000 0 -0.62 267 267
GRB2 0.013 0.022 -10000 0 -10000 0 0
PDPK1 -0.23 0.3 -10000 0 -0.46 278 278
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
PRKD1 -0.3 0.36 -10000 0 -0.6 284 284
SHC1 0.016 0 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.17 0.32 0.72 136 -10000 0 136
PI3K Class IB/PDE3B -0.17 0.32 -10000 0 -0.72 136 136
PDE3B -0.17 0.32 -10000 0 -0.72 136 136
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.001 0.021 -10000 0 -0.48 1 1
ARNO/beta Arrestin1-2 -0.19 0.18 -10000 0 -0.35 288 288
EGFR -0.37 0.37 -10000 0 -0.72 274 274
EPHA2 0.005 0.09 -10000 0 -0.72 8 8
USP6 0.015 0.016 -10000 0 -10000 0 0
IQSEC1 0.016 0 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.45 0.33 -10000 0 -0.64 370 370
ARRB2 0.018 0.037 -10000 0 -0.41 4 4
mol:GTP 0.008 0.005 0.081 1 -10000 0 1
ARRB1 0.011 0.057 -10000 0 -0.72 3 3
FBXO8 0.016 0 -10000 0 -10000 0 0
TSHR 0.01 0.064 -10000 0 -0.72 4 4
EGF -0.24 0.35 -10000 0 -0.72 179 179
somatostatin receptor activity 0 0 -10000 0 -0.001 318 318
ARAP2 0 0 -10000 0 0 316 316
mol:GDP -0.16 0.14 -10000 0 -0.29 235 235
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 319 319
ITGA2B 0.015 0.012 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.053 -10000 0 -0.41 8 8
ADAP1 0 0 -10000 0 0 314 314
KIF13B 0.015 0.032 -10000 0 -0.72 1 1
HGF/MET -0.053 0.16 -10000 0 -0.54 52 52
PXN 0.016 0 -10000 0 -10000 0 0
ARF6/GTP -0.18 0.13 -10000 0 -0.27 317 317
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.39 0.3 -10000 0 -0.56 370 370
ADRB2 -0.38 0.37 -10000 0 -0.72 286 286
receptor agonist activity 0 0 -10000 0 0 317 317
actin filament binding 0 0 -10000 0 -0.001 318 318
SRC 0.016 0.007 -10000 0 -10000 0 0
ITGB3 0.014 0.02 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -0.001 315 315
EFA6/PI-4-5-P2 -0.001 0 -10000 0 -0.001 316 316
ARF6/GDP -0.029 0.057 -10000 0 -0.25 4 4
ARF6/GDP/GULP/ACAP1 -0.2 0.2 -10000 0 -0.42 196 196
alphaIIb/beta3 Integrin/paxillin/GIT1 0.003 0.015 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 0 34 34
ACAP2 0 0 -10000 0 0 317 317
LHCGR/beta Arrestin2 0.015 0.054 -10000 0 -0.6 4 4
EFNA1 0.013 0.022 -10000 0 -10000 0 0
HGF 0.015 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 319 319
CYTH2 -0.003 0.002 -10000 0 -0.004 319 319
NCK1 0.016 0 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 279 279
endosomal lumen acidification 0 0 -10000 0 0 192 192
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.12 0.29 -10000 0 -0.72 98 98
GNAQ/ARNO -0.004 0.003 -10000 0 -0.006 315 315
mol:Phosphatidic acid 0 0 -10000 0 0 317 317
PIP3-E 0.011 0.049 -10000 0 -0.72 2 2
MET -0.057 0.22 -10000 0 -0.72 52 52
GNA14 -0.009 0.095 -10000 0 -0.72 7 7
GNA15 0.013 0.021 -10000 0 -10000 0 0
GIT1 0.015 0.016 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -0.001 316 316
GNA11 0.016 0 -10000 0 -10000 0 0
LHCGR 0.009 0.065 -10000 0 -0.72 4 4
AGTR1 -0.32 0.35 -10000 0 -0.72 227 227
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.053 -10000 0 -0.59 4 4
IPCEF1/ARNO -0.31 0.25 -10000 0 -0.44 371 371
alphaIIb/beta3 Integrin -0.002 0.011 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.096 0.17 -9999 0 -0.36 146 146
PDGFRB 0.007 0.008 -9999 0 -10000 0 0
SPHK1 -0.048 0.098 -9999 0 -1.1 4 4
mol:S1P -0.059 0.095 -9999 0 -1 4 4
S1P1/S1P/Gi -0.34 0.34 -9999 0 -0.55 325 325
GNAO1 0.007 0.011 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.28 0.29 -9999 0 -0.59 205 205
PLCG1 -0.31 0.31 -9999 0 -0.63 214 214
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.007 0.008 -9999 0 -10000 0 0
GNAI2 0.007 0.012 -9999 0 -10000 0 0
GNAI3 0.007 0.009 -9999 0 -10000 0 0
GNAI1 -0.26 0.36 -9999 0 -0.73 189 189
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.22 0.38 -9999 0 -0.83 146 146
S1P1/S1P -0.24 0.31 -9999 0 -0.73 146 146
negative regulation of cAMP metabolic process -0.33 0.33 -9999 0 -0.53 325 325
MAPK3 -0.43 0.4 -9999 0 -0.71 323 323
calcium-dependent phospholipase C activity -0.005 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.036 0.089 -9999 0 -10000 0 0
PLCB2 -0.18 0.28 -9999 0 -0.62 146 146
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.19 0.25 -9999 0 -0.58 146 146
receptor internalization -0.22 0.28 -9999 0 -0.66 146 146
PTGS2 -0.67 0.57 -9999 0 -1.1 323 323
Rac1/GTP -0.19 0.25 -9999 0 -0.58 146 146
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.06 0.12 -9999 0 -0.36 30 30
negative regulation of T cell proliferation -0.33 0.33 -9999 0 -0.53 325 325
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.003 0.085 -9999 0 -0.73 7 7
MAPK1 -0.43 0.4 -9999 0 -0.71 323 323
S1P1/S1P/PDGFB-D/PDGFRB -0.24 0.34 -9999 0 -0.77 146 146
ABCC1 0.008 0.027 -9999 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 0.013 0.009 -10000 0 -10000 0 0
GNB1/GNG2 -0.049 0.15 -10000 0 -0.43 71 71
regulation of S phase of mitotic cell cycle -0.045 0.15 -10000 0 -0.33 113 113
GNAO1 0.015 0.007 -10000 0 -10000 0 0
HRAS 0.013 0.012 -10000 0 -10000 0 0
SHBG/T-DHT 0.006 0.005 -10000 0 -10000 0 0
PELP1 0.014 0.002 -10000 0 -10000 0 0
AKT1 0.014 0.013 -10000 0 -10000 0 0
MAP2K1 -0.08 0.15 -10000 0 -0.43 70 70
T-DHT/AR -0.07 0.19 -10000 0 -0.56 70 70
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.004 -10000 0 -0.007 375 375
GNAI2 0.015 0.007 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.25 0.35 -10000 0 -0.72 189 189
mol:GDP -0.099 0.21 -10000 0 -0.6 70 70
cell proliferation -0.26 0.23 -10000 0 -0.4 375 375
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
FOS -0.58 0.42 -10000 0 -0.85 375 375
mol:Ca2+ -0.036 0.039 -10000 0 -0.076 245 245
MAPK3 -0.18 0.19 -10000 0 -0.56 63 63
MAPK1 -0.13 0.12 -10000 0 -0.29 62 62
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
mol:IP3 -0.003 0.002 -10000 0 -0.005 375 375
cAMP biosynthetic process 0.03 0.032 -10000 0 -10000 0 0
GNG2 0.015 0.032 -10000 0 -0.72 1 1
potassium channel inhibitor activity -0.003 0.002 -10000 0 -0.005 375 375
HRAS/GTP -0.067 0.14 -10000 0 -0.42 70 70
actin cytoskeleton reorganization -0.036 0.11 -10000 0 -0.37 52 52
SRC 0.013 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.003 0.002 -10000 0 -0.005 375 375
PI3K -0.046 0.14 -10000 0 -0.47 52 52
apoptosis 0.28 0.23 0.41 375 -10000 0 375
T-DHT/AR/PELP1 -0.057 0.17 -10000 0 -0.48 70 70
HRAS/GDP -0.084 0.21 -10000 0 -0.57 70 70
CREB1 -0.3 0.24 -10000 0 -0.44 375 375
RAC1-CDC42/GTP -0.037 0.11 -10000 0 -0.38 52 52
AR -0.086 0.25 -10000 0 -0.73 70 70
GNB1 0.016 0.01 -10000 0 -10000 0 0
RAF1 -0.067 0.15 -10000 0 -0.43 70 70
RAC1-CDC42/GDP -0.087 0.19 -10000 0 -0.54 70 70
T-DHT/AR/PELP1/Src -0.052 0.15 -10000 0 -0.44 70 70
MAP2K2 -0.08 0.15 -10000 0 -0.43 70 70
T-DHT/AR/PELP1/Src/PI3K -0.045 0.15 -10000 0 -0.33 113 113
GNAZ 0.006 0.084 -10000 0 -0.72 7 7
SHBG 0.016 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.061 0.13 -10000 0 -0.37 15 15
mol:T-DHT -0.002 0.002 0.002 11 -0.003 313 324
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.013 0.12 -10000 0 -0.55 25 25
Gi family/GTP -0.11 0.13 -10000 0 -0.26 194 194
CDC42 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.016 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.34 0.22 -10000 0 -0.5 343 343
PTP1B/AKT1 -0.17 0.13 -10000 0 -0.28 295 295
FYN 0.013 0.045 -10000 0 -0.72 2 2
p210 bcr-abl/PTP1B -0.2 0.15 -10000 0 -0.32 297 297
EGFR -0.38 0.37 -10000 0 -0.74 274 274
EGF/EGFR -0.47 0.32 -10000 0 -0.66 370 370
CSF1 0.016 0.007 -10000 0 -10000 0 0
AKT1 0.013 0.02 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.19 0.15 -10000 0 -0.31 307 307
Insulin Receptor/Insulin -0.12 0.084 -10000 0 -0.3 1 1
HCK 0.013 0.024 -10000 0 -10000 0 0
CRK 0.015 0.032 -10000 0 -0.72 1 1
TYK2 -0.19 0.14 -10000 0 -0.3 295 295
EGF -0.25 0.35 -10000 0 -0.74 179 179
YES1 0.015 0.032 -10000 0 -0.72 1 1
CAV1 -0.43 0.26 -10000 0 -0.57 386 386
TXN 0.004 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.22 0.19 -10000 0 -0.34 329 329
cell migration 0.2 0.15 0.32 297 -10000 0 297
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.022 0.077 -10000 0 -0.72 1 1
ITGA2B 0.013 0.012 -10000 0 -10000 0 0
CSF1R 0.016 0 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.049 0.035 -10000 0 -0.53 1 1
FGR 0.016 0 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.19 0.14 -10000 0 -0.3 296 296
Crk/p130 Cas -0.17 0.14 -10000 0 -0.28 295 295
DOK1 -0.15 0.12 -10000 0 -0.26 191 191
JAK2 -0.094 0.09 -10000 0 -0.65 2 2
Jak2/Leptin Receptor/Leptin -0.36 0.23 -10000 0 -0.5 344 344
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
PTPN1 -0.21 0.15 -10000 0 -0.33 298 298
LYN 0.016 0.01 -10000 0 -10000 0 0
CDH2 -0.013 0.063 -10000 0 -10000 0 0
SRC -0.057 0.055 -10000 0 -10000 0 0
ITGB3 0.011 0.02 -10000 0 -10000 0 0
CAT1/PTP1B -0.14 0.14 -10000 0 -0.33 57 57
CAPN1 0.003 0.016 -10000 0 -10000 0 0
CSK 0.016 0.01 -10000 0 -10000 0 0
PI3K -0.14 0.14 -10000 0 -0.5 52 52
mol:H2O2 -0.007 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.32 0.21 -10000 0 -0.44 339 339
negative regulation of transcription -0.093 0.09 -10000 0 -0.64 2 2
FCGR2A 0.013 0.023 -10000 0 -10000 0 0
FER 0.004 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.002 0.012 -10000 0 -10000 0 0
BLK 0.003 0.045 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.005 0.007 -10000 0 -10000 0 0
LEPR -0.47 0.35 -10000 0 -0.72 345 345
BCAR1 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0.022 -10000 0 -10000 0 0
mol:NADPH -0.007 0.004 -10000 0 -10000 0 0
TRPV6 0.026 0.06 -10000 0 -0.37 3 3
PRL 0.021 0.003 -10000 0 -10000 0 0
SOCS3 0.003 0.25 -10000 0 -1.4 15 15
SPRY2 -0.48 0.35 -10000 0 -0.73 351 351
Insulin Receptor/Insulin/IRS1 -0.06 0.16 -10000 0 -0.46 69 69
CSF1/CSF1R -0.17 0.14 -10000 0 -0.28 292 292
Ras protein signal transduction 0.075 0.044 -10000 0 -10000 0 0
IRS1 -0.08 0.25 -10000 0 -0.72 69 69
INS 0.016 0.001 -10000 0 -10000 0 0
LEP -0.35 0.37 -10000 0 -0.72 259 259
STAT5B -0.16 0.12 -10000 0 -0.25 294 294
STAT5A -0.16 0.12 -10000 0 -0.26 294 294
GRB2 0.013 0.022 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.19 0.14 -10000 0 -0.3 295 295
CSN2 0.071 0.032 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
LAT -0.056 0.056 -10000 0 -10000 0 0
YBX1 0.018 0.017 -10000 0 -10000 0 0
LCK 0 0.049 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
NOX4 -0.019 0.069 -10000 0 -0.74 1 1
HIF-1-alpha transcription factor network

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
PKM2 -0.11 0.48 -10000 0 -0.78 123 123
HDAC7 0.002 0.005 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.14 0.3 0.52 12 -0.63 91 103
SMAD4 0.015 0.045 -10000 0 -0.72 2 2
ID2 -0.11 0.48 -10000 0 -0.78 123 123
AP1 -0.47 0.35 -10000 0 -0.67 376 376
ABCG2 -0.12 0.51 -10000 0 -0.83 128 128
HIF1A 0.001 0.12 -10000 0 -0.48 9 9
TFF3 -0.18 0.54 -10000 0 -0.88 151 151
GATA2 0.003 0.043 -10000 0 -10000 0 0
AKT1 0.006 0.1 -10000 0 -0.25 7 7
response to hypoxia -0.014 0.11 -10000 0 -0.16 56 56
MCL1 -0.11 0.48 -10000 0 -0.78 120 120
NDRG1 -0.11 0.48 -10000 0 -0.78 123 123
SERPINE1 -0.11 0.48 -10000 0 -0.77 124 124
FECH -0.11 0.48 -10000 0 -0.78 124 124
FURIN -0.11 0.48 -10000 0 -0.78 120 120
NCOA2 0.017 0.014 -10000 0 -10000 0 0
EP300 0.032 0.15 -10000 0 -0.2 5 5
HMOX1 -0.11 0.48 -10000 0 -0.77 124 124
BHLHE40 -0.12 0.47 -10000 0 -0.75 135 135
BHLHE41 -0.12 0.47 -10000 0 -0.75 135 135
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.029 0.083 0.29 1 -0.5 7 8
ENG 0.052 0.14 -10000 0 -0.45 7 7
JUN -0.12 0.29 -10000 0 -0.73 97 97
RORA -0.12 0.49 -10000 0 -0.81 123 123
ABCB1 -0.41 0.57 -10000 0 -1.2 168 168
TFRC -0.11 0.48 -10000 0 -0.79 124 124
CXCR4 -0.11 0.48 -10000 0 -0.78 125 125
TF -0.12 0.5 -10000 0 -0.81 128 128
CITED2 -0.11 0.48 -10000 0 -0.79 123 123
HIF1A/ARNT -0.23 0.45 0.64 24 -0.88 123 147
LDHA -0.022 0.038 -10000 0 -10000 0 0
ETS1 -0.11 0.48 -10000 0 -0.77 125 125
PGK1 -0.11 0.48 -10000 0 -0.78 123 123
NOS2 -0.12 0.47 -10000 0 -0.75 135 135
ITGB2 -0.11 0.48 -10000 0 -0.77 127 127
ALDOA -0.11 0.48 -10000 0 -0.78 120 120
Cbp/p300/CITED2 -0.12 0.47 -10000 0 -0.81 112 112
FOS -0.51 0.34 -10000 0 -0.73 375 375
HK2 -0.11 0.48 -10000 0 -0.77 123 123
SP1 0.004 0.049 -10000 0 -10000 0 0
GCK 0.054 0.2 -10000 0 -10000 0 0
HK1 -0.11 0.48 -10000 0 -0.78 120 120
NPM1 -0.11 0.48 -10000 0 -0.77 123 123
EGLN1 -0.11 0.48 -10000 0 -0.78 123 123
CREB1 0.026 0.002 -10000 0 -10000 0 0
PGM1 -0.11 0.48 -10000 0 -0.78 126 126
SMAD3 0.017 0.033 -10000 0 -0.72 1 1
EDN1 -0.46 0.64 -10000 0 -1.3 182 182
IGFBP1 -0.11 0.48 -10000 0 -0.78 120 120
VEGFA -0.036 0.37 -10000 0 -0.58 93 93
HIF1A/JAB1 -0.013 0.061 0.2 1 -0.6 4 5
CP -0.22 0.56 -10000 0 -0.87 175 175
CXCL12 -0.23 0.6 -10000 0 -0.96 176 176
COPS5 0.018 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.003 0.04 -10000 0 -0.54 3 3
BNIP3 -0.11 0.48 -10000 0 -0.78 125 125
EGLN3 -0.11 0.49 -10000 0 -0.79 122 122
CA9 -0.11 0.48 -10000 0 -0.78 129 129
TERT -0.11 0.48 -10000 0 -0.77 125 125
ENO1 -0.11 0.48 -10000 0 -0.78 123 123
PFKL -0.11 0.48 -10000 0 -0.78 123 123
NCOA1 0.015 0.032 -10000 0 -0.72 1 1
ADM -0.26 0.55 -10000 0 -0.85 190 190
ARNT 0.008 0.09 -10000 0 -10000 0 0
HNF4A 0.022 0 -10000 0 -10000 0 0
ADFP -0.13 0.51 -10000 0 -0.82 132 132
SLC2A1 -0.034 0.37 -10000 0 -0.59 83 83
LEP -0.3 0.6 -10000 0 -0.9 222 222
HIF1A/ARNT/Cbp/p300 -0.13 0.34 -10000 0 -0.66 91 91
EPO 0.003 0.32 -10000 0 -0.55 22 22
CREBBP 0.031 0.15 -10000 0 -0.25 6 6
HIF1A/ARNT/Cbp/p300/HDAC7 -0.15 0.31 0.52 13 -0.64 93 106
PFKFB3 -0.11 0.48 -10000 0 -0.78 123 123
NT5E -0.11 0.49 -10000 0 -0.81 121 121
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.015 0.042 -9999 0 -0.47 3 3
NFATC2 0.017 0.029 -9999 0 -0.47 1 1
NFATC3 0.018 0.02 -9999 0 -10000 0 0
CD40LG -0.34 0.32 -9999 0 -0.57 299 299
PTGS2 -0.53 0.44 -9999 0 -0.82 344 344
JUNB 0.012 0.055 -9999 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.006 -9999 0 -10000 0 0
CaM/Ca2+ 0.002 0.006 -9999 0 -10000 0 0
CALM1 0.015 0.005 -9999 0 -10000 0 0
JUN -0.12 0.29 -9999 0 -0.73 97 97
mol:Ca2+ -0.006 0.006 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.005 -9999 0 -10000 0 0
FOSL1 0.016 0.01 -9999 0 -10000 0 0
CREM 0.015 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.084 0.16 -9999 0 -0.4 99 99
FOS -0.51 0.34 -9999 0 -0.73 375 375
IFNG -0.34 0.32 -9999 0 -0.59 304 304
AP-1/NFAT1-c-4 -0.41 0.39 -9999 0 -0.7 304 304
FASLG -0.34 0.32 -9999 0 -0.58 300 300
NFAT1-c-4/ICER1 0 0.038 -9999 0 -0.36 4 4
IL2RA -0.34 0.32 -9999 0 -0.58 300 300
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.34 0.32 -9999 0 -0.58 298 298
JunB/Fra1/NFAT1-c-4 0.009 0.048 -9999 0 -0.36 5 5
IL4 -0.34 0.32 -9999 0 -0.57 298 298
IL2 -0.011 0.067 -9999 0 -1.5 1 1
IL3 -0.009 0.019 -9999 0 -10000 0 0
FKBP1A 0.016 0.01 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.026 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.3 0.46 -10000 0 -0.91 108 108
PLK1 0.01 0.055 -10000 0 -10000 0 0
BIRC5 -0.026 0.071 -10000 0 -10000 0 0
HSPA1B -0.31 0.46 -10000 0 -0.81 187 187
MAP2K1 0.011 0.036 -10000 0 -10000 0 0
BRCA2 -0.3 0.47 -10000 0 -0.87 138 138
FOXM1 -0.36 0.55 -10000 0 -0.99 167 167
XRCC1 -0.3 0.46 -10000 0 -0.91 109 109
FOXM1B/p19 -0.42 0.42 0.5 1 -0.89 195 196
Cyclin D1/CDK4 -0.29 0.45 -10000 0 -0.86 131 131
CDC2 -0.32 0.49 -10000 0 -0.9 154 154
TGFA -0.32 0.5 -10000 0 -0.99 123 123
SKP2 -0.3 0.46 -10000 0 -0.92 103 103
CCNE1 -0.024 0.071 -10000 0 -10000 0 0
CKS1B -0.3 0.46 -10000 0 -0.87 131 131
RB1 -0.13 0.14 -10000 0 -1.2 2 2
FOXM1C/SP1 -0.34 0.51 -10000 0 -0.92 169 169
AURKB 0.002 0.062 -10000 0 -10000 0 0
CENPF -0.32 0.47 -10000 0 -0.89 136 136
CDK4 0.009 0.024 -10000 0 -10000 0 0
MYC -0.28 0.45 -10000 0 -0.83 141 141
CHEK2 0.008 0.044 -10000 0 -10000 0 0
ONECUT1 -0.3 0.47 -10000 0 -0.85 158 158
CDKN2A -0.015 0.06 -10000 0 -10000 0 0
LAMA4 -0.3 0.47 -10000 0 -0.99 87 87
FOXM1B/HNF6 -0.36 0.55 -10000 0 -1 158 158
FOS -0.84 0.7 -10000 0 -1.3 381 381
SP1 0.017 0.003 -10000 0 -10000 0 0
CDC25B -0.3 0.46 -10000 0 -0.98 84 84
response to radiation -0.01 0.036 -10000 0 -10000 0 0
CENPB -0.3 0.46 -10000 0 -0.92 103 103
CENPA -0.31 0.47 -10000 0 -0.97 94 94
NEK2 -0.32 0.47 -10000 0 -0.89 136 136
HIST1H2BA -0.3 0.46 -10000 0 -0.91 108 108
CCNA2 -0.046 0.083 -10000 0 -10000 0 0
EP300 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.35 0.52 -10000 0 -1.1 92 92
CCNB2 -0.31 0.47 -10000 0 -0.87 150 150
CCNB1 -0.32 0.49 -10000 0 -0.94 127 127
ETV5 -0.31 0.49 -10000 0 -0.98 112 112
ESR1 -0.45 0.63 -10000 0 -1.2 180 180
CCND1 -0.3 0.47 -10000 0 -0.88 133 133
GSK3A 0.015 0.029 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.024 0.089 -10000 0 -10000 0 0
CDK2 0.007 0.029 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.013 0.042 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.39 0.39 -10000 0 -0.84 187 187
GAS1 -0.51 0.67 -10000 0 -1.3 184 184
MMP2 -0.3 0.47 -10000 0 -0.94 102 102
RB1/FOXM1C -0.3 0.47 -10000 0 -0.87 138 138
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
Glucocorticoid receptor regulatory network

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
PCK2 0.016 0.071 0.32 7 -10000 0 7
SMARCC2 0.016 0 -10000 0 -10000 0 0
SMARCC1 0.014 0.02 -10000 0 -10000 0 0
TBX21 -0.091 0.27 -10000 0 -0.96 40 40
SUMO2 0.003 0.009 -10000 0 -10000 0 0
STAT1 (dimer) -0.001 0.064 -10000 0 -10000 0 0
FKBP4 0.01 0.031 -10000 0 -10000 0 0
FKBP5 -0.002 0.11 -10000 0 -0.72 11 11
GR alpha/HSP90/FKBP51/HSP90 0.089 0.15 0.32 34 -0.36 15 49
PRL -0.037 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.26 0.25 0.48 278 -10000 0 278
RELA -0.1 0.082 -10000 0 -0.3 9 9
FGG 0.26 0.21 0.45 241 -10000 0 241
GR beta/TIF2 0.11 0.15 0.3 72 -0.44 7 79
IFNG -0.51 0.32 -10000 0 -0.73 314 314
apoptosis -0.25 0.15 0.56 1 -0.53 19 20
CREB1 0.026 0.004 -10000 0 -10000 0 0
histone acetylation 0.049 0.15 0.45 45 -0.35 9 54
BGLAP -0.05 0.13 -10000 0 -0.47 7 7
GR/PKAc 0.1 0.14 0.32 28 -0.38 9 37
NF kappa B1 p50/RelA -0.17 0.15 -10000 0 -0.43 39 39
SMARCD1 0.016 0 -10000 0 -10000 0 0
MDM2 0.13 0.091 0.23 147 -10000 0 147
GATA3 -0.064 0.2 -10000 0 -0.71 39 39
AKT1 -0.002 0.02 -10000 0 -10000 0 0
CSF2 0.001 0.11 -10000 0 -10000 0 0
GSK3B 0.002 0.012 -10000 0 -10000 0 0
NR1I3 -0.2 0.16 0.54 1 -0.54 3 4
CSN2 0.22 0.18 0.39 228 -10000 0 228
BRG1/BAF155/BAF170/BAF60A 0.002 0.013 -10000 0 -10000 0 0
NFATC1 0.023 0.056 -10000 0 -0.71 3 3
POU2F1 0.026 0 -10000 0 -10000 0 0
CDKN1A 0.058 0.098 -10000 0 -1.5 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.012 0.006 -10000 0 -10000 0 0
SFN 0.011 0.05 -10000 0 -0.72 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.33 29 -0.38 6 35
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.7 0.37 0.52 1 -0.87 437 438
JUN -0.24 0.27 -10000 0 -0.56 188 188
IL4 -0.053 0.13 -10000 0 -0.43 22 22
CDK5R1 0.001 0.019 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.64 0.36 -10000 0 -0.75 441 441
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.14 0.32 30 -0.37 8 38
cortisol/GR alpha (monomer) 0.3 0.3 0.55 284 -0.46 4 288
NCOA2 0.015 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.58 0.34 -10000 0 -0.8 375 375
AP-1/NFAT1-c-4 -0.86 0.49 -10000 0 -1.1 415 415
AFP -0.18 0.22 -10000 0 -0.58 76 76
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.19 0.16 0.5 25 -10000 0 25
TP53 0.043 0.032 -10000 0 -0.47 2 2
PPP5C 0.014 0.02 -10000 0 -10000 0 0
KRT17 -1.1 0.75 -10000 0 -1.7 339 339
KRT14 -0.94 0.72 -10000 0 -1.5 335 335
TBP 0.028 0.001 -10000 0 -10000 0 0
CREBBP 0.17 0.14 0.28 285 -0.46 1 286
HDAC1 0.003 0.005 -10000 0 -10000 0 0
HDAC2 0.011 0.017 -10000 0 -10000 0 0
AP-1 -0.87 0.5 -10000 0 -1.1 415 415
MAPK14 0.003 0.007 -10000 0 -10000 0 0
MAPK10 -0.016 0.11 -10000 0 -0.73 12 12
MAPK11 0.003 0.007 -10000 0 -10000 0 0
KRT5 -1.2 0.73 -10000 0 -1.6 368 368
interleukin-1 receptor activity -0.003 0.002 -10000 0 -10000 0 0
NCOA1 0.019 0.032 -10000 0 -0.71 1 1
STAT1 -0.001 0.064 -10000 0 -10000 0 0
CGA -0.068 0.14 -10000 0 -0.5 9 9
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.17 0.18 0.33 259 -0.37 4 263
MAPK3 0.003 0.007 -10000 0 -10000 0 0
MAPK1 0.003 0.007 -10000 0 -10000 0 0
ICAM1 -0.28 0.23 -10000 0 -0.57 109 109
NFKB1 -0.1 0.082 -10000 0 -0.3 9 9
MAPK8 -0.13 0.18 -10000 0 -0.36 132 132
MAPK9 0.003 0.01 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.15 0.56 1 -0.56 19 20
BAX 0.063 0.035 -10000 0 -10000 0 0
POMC -0.13 0.2 -10000 0 -0.76 15 15
EP300 0.17 0.14 0.31 123 -10000 0 123
cortisol/GR alpha (dimer)/p53 0.28 0.26 0.5 283 -10000 0 283
proteasomal ubiquitin-dependent protein catabolic process 0.086 0.078 0.23 24 -10000 0 24
SGK1 0.25 0.16 0.37 334 -10000 0 334
IL13 -0.36 0.24 -10000 0 -0.74 74 74
IL6 -0.88 0.54 -10000 0 -1.2 391 391
PRKACG 0.015 0.032 -10000 0 -0.72 1 1
IL5 -0.31 0.2 -10000 0 -0.64 54 54
IL2 -0.5 0.32 -10000 0 -0.77 263 263
CDK5 -0.001 0.025 -10000 0 -10000 0 0
PRKACB -0.007 0.098 -10000 0 -0.72 8 8
HSP90AA1 0.015 0.012 -10000 0 -10000 0 0
IL8 -0.28 0.23 -10000 0 -0.62 83 83
CDK5R1/CDK5 -0.003 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.1 0.13 -10000 0 -0.52 17 17
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.26 0.24 0.46 274 -0.41 1 275
SMARCA4 0.015 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.16 0.34 240 -10000 0 240
NF kappa B1 p50/RelA/Cbp -0.013 0.16 0.39 5 -0.52 1 6
JUN (dimer) -0.24 0.27 -10000 0 -0.56 188 188
YWHAH 0.015 0.012 -10000 0 -10000 0 0
VIPR1 -0.055 0.18 -10000 0 -0.53 41 41
NR3C1 0.18 0.2 0.35 232 -0.5 12 244
NR4A1 -0.007 0.16 -10000 0 -0.72 24 24
TIF2/SUV420H1 -0.001 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.25 0.15 0.56 1 -0.53 19 20
cortisol/GR alpha (dimer)/Src-1 0.26 0.26 0.48 280 -10000 0 280
PBX1 0.008 0.065 -10000 0 -0.72 2 2
POU1F1 0.025 0.032 -10000 0 -0.72 1 1
SELE -0.34 0.38 -10000 0 -0.99 87 87
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.34 236 -10000 0 236
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.26 0.24 0.46 274 -0.41 1 275
mol:cortisol 0.19 0.17 0.32 288 -10000 0 288
MMP1 -0.17 0.08 -10000 0 -10000 0 0
Ras 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
ERK1-2/ELK1 -0.23 0.2 -9999 0 -0.36 375 375
MAP3K8 -0.093 0.25 -9999 0 -0.73 70 70
FOS -0.12 0.12 -9999 0 -0.3 58 58
PRKCA 0.005 0.013 -9999 0 -10000 0 0
PTPN7 -0.003 0.038 -9999 0 -10000 0 0
HRAS 0.013 0.012 -9999 0 -10000 0 0
PRKCB -0.013 0.01 -9999 0 -0.019 375 375
NRAS 0.012 0.019 -9999 0 -10000 0 0
RAS family/GTP -0.002 0.014 -9999 0 -10000 0 0
MAPK3 -0.052 0.065 -9999 0 -10000 0 0
MAP2K1 -0.055 0.091 -9999 0 -0.27 58 58
ELK1 0 0.018 -9999 0 -10000 0 0
BRAF -0.018 0.015 -9999 0 -10000 0 0
mol:GTP -0.004 0.003 -9999 0 -0.006 375 375
MAPK1 -0.052 0.065 -9999 0 -10000 0 0
RAF1 -0.018 0.015 -9999 0 -10000 0 0
KRAS 0.01 0.025 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.1 0.25 -9999 0 -0.76 65 65
PDGF/PDGFRA/CRKL -0.069 0.18 -9999 0 -0.56 65 65
positive regulation of JUN kinase activity -0.05 0.14 -9999 0 -0.42 65 65
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.071 0.19 -9999 0 -0.56 66 66
AP1 -0.84 0.54 -9999 0 -1.2 376 376
mol:IP3 -0.084 0.19 -9999 0 -0.59 65 65
PLCG1 -0.085 0.19 -9999 0 -0.6 65 65
PDGF/PDGFRA/alphaV Integrin -0.07 0.18 -9999 0 -0.56 66 66
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
mol:Ca2+ -0.084 0.19 -9999 0 -0.59 65 65
CAV3 0.013 0.046 -9999 0 -0.72 2 2
CAV1 -0.52 0.33 -9999 0 -0.72 385 385
SHC/Grb2/SOS1 -0.05 0.14 -9999 0 -0.42 65 65
PDGF/PDGFRA/Shf -0.069 0.18 -9999 0 -0.56 65 65
FOS -0.8 0.54 -9999 0 -1.1 377 377
JUN -0.15 0.23 -9999 0 -0.62 97 97
oligodendrocyte development -0.07 0.18 -9999 0 -0.56 66 66
GRB2 0.013 0.022 -9999 0 -10000 0 0
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
mol:DAG -0.084 0.19 -9999 0 -0.59 65 65
PDGF/PDGFRA -0.1 0.25 -9999 0 -0.76 65 65
actin cytoskeleton reorganization -0.071 0.18 -9999 0 -0.56 66 66
SRF 0.046 0.012 -9999 0 -10000 0 0
SHC1 0.016 0 -9999 0 -10000 0 0
PI3K -0.1 0.23 -9999 0 -0.56 97 97
PDGF/PDGFRA/Crk/C3G -0.059 0.16 -9999 0 -0.48 65 65
JAK1 -0.059 0.19 -9999 0 -0.56 67 67
ELK1/SRF -0.024 0.16 -9999 0 -0.45 65 65
SHB 0.013 0.037 -9999 0 -0.72 1 1
SHF 0.015 0.012 -9999 0 -10000 0 0
CSNK2A1 0.046 0.028 -9999 0 -10000 0 0
GO:0007205 -0.091 0.2 -9999 0 -0.62 65 65
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.05 0.14 -9999 0 -0.42 65 65
PDGF/PDGFRA/SHB -0.071 0.18 -9999 0 -0.56 66 66
PDGF/PDGFRA/Caveolin-1 -0.46 0.31 -9999 0 -0.63 388 388
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
ELK1 -0.099 0.18 -9999 0 -0.57 65 65
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.07 0.19 -9999 0 -0.56 65 65
JAK-STAT cascade -0.059 0.19 -9999 0 -0.56 67 67
cell proliferation -0.069 0.18 -9999 0 -0.56 65 65
BMP receptor signaling

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.036 0.077 -9999 0 -0.42 9 9
SMAD6-7/SMURF1 0 0.004 -9999 0 -10000 0 0
NOG 0.014 0.035 -9999 0 -0.72 1 1
SMAD9 -0.084 0.18 -9999 0 -0.91 20 20
SMAD4 0.013 0.045 -9999 0 -0.72 2 2
SMAD5 -0.15 0.21 -9999 0 -0.41 169 169
BMP7/USAG1 -0.39 0.24 -9999 0 -0.55 377 377
SMAD5/SKI -0.13 0.2 -9999 0 -0.52 70 70
SMAD1 0.025 0.045 -9999 0 -10000 0 0
BMP2 -0.33 0.37 -9999 0 -0.72 251 251
SMAD1/SMAD1/SMAD4 -0.002 0.021 -9999 0 -10000 0 0
BMPR1A 0.009 0.071 -9999 0 -0.72 5 5
BMPR1B -0.046 0.079 -9999 0 -10000 0 0
BMPR1A-1B/BAMBI -0.014 0.16 -9999 0 -0.51 43 43
AHSG 0.016 0 -9999 0 -10000 0 0
CER1 0.016 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.28 0.28 -9999 0 -0.51 289 289
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.21 -9999 0 -0.5 97 97
BMP2-4 (homodimer) -0.33 0.32 -9999 0 -0.6 289 289
RGMB 0.016 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.14 0.23 -9999 0 -0.45 183 183
RGMA -0.097 0.27 -9999 0 -0.72 81 81
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.16 0.22 -9999 0 -0.54 96 96
BMP2-4/USAG1 -0.59 0.34 -9999 0 -0.7 445 445
SMAD6/SMURF1/SMAD5 -0.13 0.2 -9999 0 -0.53 69 69
SOSTDC1 -0.51 0.33 -9999 0 -0.72 377 377
BMP7/BMPR2/BMPR1A-1B 0.038 0.065 -9999 0 -0.44 5 5
SKI 0.016 0.007 -9999 0 -10000 0 0
BMP6 (homodimer) -0.24 0.35 -9999 0 -0.72 181 181
HFE2 0.011 0.056 -9999 0 -0.72 3 3
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0.007 -9999 0 -10000 0 0
BMP2-4/CHRD -0.28 0.28 -9999 0 -0.51 289 289
SMAD5/SMAD5/SMAD4 -0.13 0.2 -9999 0 -0.53 71 71
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.13 0.16 -9999 0 -0.44 95 95
BMP7 (homodimer) -0.003 0.052 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.18 0.26 -9999 0 -0.54 181 181
SMAD1/SKI 0.033 0.043 -9999 0 -10000 0 0
SMAD6 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.28 0.28 -9999 0 -0.51 289 289
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
GREM1 -0.002 0.052 -9999 0 -10000 0 0
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.001 0.032 -9999 0 -0.46 2 2
BMPR1A-1B (homodimer) -0.035 0.065 -9999 0 -0.57 5 5
CHRDL1 -0.42 0.36 -9999 0 -0.72 310 310
ENDOFIN/SMAD1 0.033 0.043 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0 0.014 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI -0.067 0.2 -9999 0 -0.72 39 39
SMURF2 0.015 0.012 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.53 0.4 -9999 0 -0.74 379 379
BMP2-4/GREM1 -0.28 0.28 -9999 0 -0.52 289 289
SMAD7 0.016 0.007 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.06 0.18 -9999 0 -0.85 21 21
SMAD1/SMAD6 0.033 0.043 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.003 -9999 0 -10000 0 0
BMP7 -0.003 0.052 -9999 0 -10000 0 0
BMP6 -0.24 0.35 -9999 0 -0.72 181 181
MAP3K7IP2 0.015 0.032 -9999 0 -0.72 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.14 0.21 -9999 0 -0.51 95 95
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.033 0.043 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0.003 -9999 0 -10000 0 0
CTDSPL 0.013 0.045 -9999 0 -0.72 2 2
PPP1CA 0.01 0.032 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0.045 -9999 0 -0.72 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.15 0.22 -9999 0 -0.51 97 97
CHRD 0.013 0.022 -9999 0 -10000 0 0
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.19 0.25 -9999 0 -0.64 95 95
BMP4 -0.089 0.26 -9999 0 -0.72 74 74
FST 0.009 0.066 -9999 0 -0.72 4 4
BMP2-4/NOG -0.28 0.28 -9999 0 -0.51 290 290
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.039 0.064 -9999 0 -0.4 5 5
Ephrin B reverse signaling

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
EFNB2 0.008 0.078 -10000 0 -0.72 6 6
EPHB2 0.006 0.04 -10000 0 -10000 0 0
EFNB1 0.026 0.035 -10000 0 -0.54 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.18 -10000 0 -0.35 196 196
Ephrin B2/EPHB1-2 -0.15 0.22 -10000 0 -0.43 197 197
neuron projection morphogenesis -0.12 0.17 -10000 0 -0.33 196 196
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.19 -10000 0 -0.38 196 196
DNM1 0.016 0.007 -10000 0 -10000 0 0
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.045 0.21 -10000 0 -0.65 58 58
YES1 -0.083 0.27 -10000 0 -0.91 52 52
Ephrin B1/EPHB1-2/NCK2 -0.13 0.19 -10000 0 -0.38 196 196
PI3K -0.082 0.25 -10000 0 -0.58 96 96
mol:GDP -0.13 0.19 -10000 0 -0.38 196 196
ITGA2B 0.015 0.012 -10000 0 -10000 0 0
endothelial cell proliferation -0.005 0.055 -10000 0 -0.47 7 7
FYN -0.084 0.27 -10000 0 -0.91 52 52
MAP3K7 -0.064 0.22 -10000 0 -0.72 52 52
FGR -0.084 0.27 -10000 0 -0.91 52 52
TIAM1 0.015 0.012 -10000 0 -10000 0 0
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion -0.057 0.23 -10000 0 -0.52 96 96
LYN -0.083 0.27 -10000 0 -0.91 52 52
Ephrin B1/EPHB1-2/Src Family Kinases -0.081 0.26 -10000 0 -0.85 52 52
Ephrin B1/EPHB1-2 -0.076 0.23 -10000 0 -0.78 52 52
SRC -0.084 0.27 -10000 0 -0.91 52 52
ITGB3 0.014 0.02 -10000 0 -10000 0 0
EPHB1 -0.26 0.36 -10000 0 -0.72 196 196
EPHB4 0.011 0.039 -10000 0 -0.72 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.005 0.055 -10000 0 -0.47 7 7
alphaIIb/beta3 Integrin -0.002 0.011 -10000 0 -10000 0 0
BLK -0.083 0.27 -10000 0 -0.91 52 52
HCK -0.084 0.27 -10000 0 -0.91 52 52
regulation of stress fiber formation 0.13 0.19 0.38 196 -10000 0 196
MAPK8 -0.034 0.21 -10000 0 -0.61 58 58
Ephrin B1/EPHB1-2/RGS3 -0.13 0.19 -10000 0 -0.38 196 196
endothelial cell migration -0.057 0.19 -10000 0 -0.6 57 57
NCK2 0.016 0.01 -10000 0 -10000 0 0
PTPN13 -0.072 0.25 -10000 0 -0.83 52 52
regulation of focal adhesion formation 0.13 0.19 0.38 196 -10000 0 196
chemotaxis 0.13 0.19 0.38 196 -10000 0 196
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.12 0.17 -10000 0 -0.34 196 196
angiogenesis -0.075 0.23 -10000 0 -0.77 52 52
LCK -0.083 0.27 -10000 0 -0.91 52 52
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 0.056 0.11 0.28 107 -10000 0 107
RFC1 0.056 0.11 0.28 107 -10000 0 107
PRKDC 0.053 0.11 0.27 101 -10000 0 101
RIPK1 0.023 0.004 -10000 0 -10000 0 0
CASP7 -0.047 0.054 -10000 0 -0.99 1 1
FASLG/FAS/FADD/FAF1 -0.033 0.1 0.25 11 -0.37 25 36
MAP2K4 -0.16 0.16 -10000 0 -0.47 39 39
mol:ceramide -0.1 0.13 -10000 0 -0.46 32 32
GSN -0.072 0.23 0.28 77 -0.46 114 191
FASLG/FAS/FADD/FAF1/Caspase 8 -0.047 0.097 -10000 0 -0.35 22 22
FAS -0.045 0.18 -10000 0 -0.74 35 35
BID -0.002 0.008 -10000 0 -10000 0 0
MAP3K1 -0.073 0.11 -10000 0 -0.44 9 9
MAP3K7 0.004 0.01 -10000 0 -10000 0 0
RB1 0.054 0.11 0.28 106 -0.45 1 107
CFLAR 0.02 0.044 -10000 0 -0.69 2 2
HGF/MET -0.089 0.2 -10000 0 -0.49 97 97
ARHGDIB 0.054 0.11 0.28 105 -0.45 1 106
FADD -0.01 0.049 -10000 0 -10000 0 0
actin filament polymerization 0.071 0.23 0.45 114 -0.27 77 191
NFKB1 -0.15 0.093 -10000 0 -10000 0 0
MAPK8 -0.28 0.23 -10000 0 -0.42 391 391
DFFA 0.056 0.11 0.28 107 -10000 0 107
DNA fragmentation during apoptosis 0.056 0.11 0.27 107 -10000 0 107
FAS/FADD/MET -0.082 0.19 -10000 0 -0.52 80 80
CFLAR/RIP1 -0.002 0.03 -10000 0 -0.5 2 2
FAIM3 0.015 0.031 -10000 0 -10000 0 0
FAF1 0.005 0.008 -10000 0 -10000 0 0
PARP1 0.049 0.11 0.28 90 -10000 0 90
DFFB 0.056 0.11 0.28 107 -10000 0 107
CHUK -0.13 0.084 -10000 0 -0.59 1 1
FASLG -0.011 0.056 -10000 0 -0.73 1 1
FAS/FADD -0.044 0.14 -10000 0 -0.57 35 35
HGF 0.016 0.01 -10000 0 -10000 0 0
LMNA 0.051 0.1 0.25 104 -10000 0 104
CASP6 0.055 0.11 0.28 105 -10000 0 105
CASP10 0.004 0.011 -10000 0 -10000 0 0
CASP3 0.066 0.13 0.33 107 -10000 0 107
PTPN13 -0.057 0.22 -10000 0 -0.72 52 52
CASP8 -0.002 0.009 -10000 0 -10000 0 0
IL6 -0.96 0.61 -10000 0 -1.3 391 391
MET -0.057 0.22 -10000 0 -0.72 52 52
ICAD/CAD 0.053 0.1 0.26 107 -10000 0 107
FASLG/FAS/FADD/FAF1/Caspase 10 -0.1 0.13 -10000 0 -0.47 32 32
activation of caspase activity by cytochrome c -0.002 0.008 -10000 0 -10000 0 0
PAK2 0.055 0.11 0.27 107 -10000 0 107
BCL2 -0.13 0.3 -10000 0 -0.72 107 107
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.08 0.26 -9999 0 -0.78 26 26
CRP -0.08 0.26 -9999 0 -0.64 48 48
cell cycle arrest -0.096 0.3 -9999 0 -0.62 104 104
TIMP1 -0.097 0.23 -9999 0 -0.58 48 48
IL6ST -0.008 0.14 -9999 0 -0.72 20 20
Rac1/GDP -0.16 0.22 -9999 0 -0.48 115 115
AP1 -0.29 0.26 -9999 0 -0.58 161 161
GAB2 0.019 0.018 -9999 0 -10000 0 0
TNFSF11 -0.087 0.26 -9999 0 -0.72 34 34
HSP90B1 0.02 0.065 -9999 0 -0.96 1 1
GAB1 0.017 0.034 -9999 0 -0.72 1 1
MAPK14 -0.2 0.24 -9999 0 -0.76 56 56
AKT1 0.043 0.079 -9999 0 -10000 0 0
FOXO1 -0.003 0.17 -9999 0 -0.53 18 18
MAP2K6 -0.21 0.24 -9999 0 -0.53 118 118
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
MAP2K4 -0.12 0.23 -9999 0 -0.48 113 113
MITF -0.19 0.24 -9999 0 -0.51 117 117
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.016 0 -9999 0 -10000 0 0
A2M -0.15 0.49 -9999 0 -1.5 65 65
CEBPB 0.025 0.033 -9999 0 -0.72 1 1
GRB2/SOS1/GAB family/SHP2 -0.024 0.093 -9999 0 -10000 0 0
STAT3 -0.11 0.32 -9999 0 -0.67 105 105
STAT1 -0.001 0.034 -9999 0 -10000 0 0
CEBPD -0.16 0.42 -9999 0 -1.1 71 71
PIK3CA 0.018 0.007 -9999 0 -10000 0 0
PI3K -0.029 0.17 -9999 0 -0.54 52 52
JUN -0.12 0.29 -9999 0 -0.72 97 97
PIAS3/MITF -0.17 0.23 -9999 0 -0.49 111 111
MAPK11 -0.2 0.24 -9999 0 -0.76 56 56
STAT3 (dimer)/FOXO1 -0.12 0.32 -9999 0 -0.69 87 87
GRB2/SOS1/GAB family -0.17 0.17 -9999 0 -0.65 41 41
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.21 0.23 -9999 0 -0.51 111 111
GRB2 0.016 0.023 -9999 0 -10000 0 0
JAK2 0.015 0.033 -9999 0 -0.72 1 1
LBP -0.086 0.22 -9999 0 -0.62 30 30
PIK3R1 -0.055 0.22 -9999 0 -0.72 52 52
JAK1 0.017 0.046 -9999 0 -0.73 2 2
MYC -0.11 0.33 -9999 0 -1 40 40
FGG -0.081 0.26 -9999 0 -0.76 28 28
macrophage differentiation -0.096 0.3 -9999 0 -0.62 104 104
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.3 0.22 -9999 0 -0.4 395 395
JUNB -0.09 0.26 -9999 0 -0.72 34 34
FOS -0.51 0.34 -9999 0 -0.72 375 375
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.21 0.25 -9999 0 -0.53 118 118
STAT1/PIAS1 -0.16 0.23 -9999 0 -0.51 107 107
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.082 -9999 0 -10000 0 0
STAT3 (dimer) -0.1 0.31 -9999 0 -0.65 104 104
PRKCD -0.089 0.24 -9999 0 -0.49 107 107
IL6R 0.018 0.033 -9999 0 -0.72 1 1
SOCS3 -0.2 0.27 -9999 0 -0.86 55 55
gp130 (dimer)/JAK1/JAK1/LMO4 0.018 0.15 -9999 0 -0.47 43 43
Rac1/GTP -0.15 0.23 -9999 0 -0.49 110 110
HCK 0.013 0.024 -9999 0 -10000 0 0
MAPKKK cascade 0.006 0.083 -9999 0 -10000 0 0
bone resorption -0.091 0.24 -9999 0 -0.68 34 34
IRF1 -0.081 0.26 -9999 0 -0.77 27 27
mol:GDP -0.18 0.23 -9999 0 -0.5 116 116
SOS1 0.02 0.008 -9999 0 -10000 0 0
VAV1 -0.18 0.24 -9999 0 -0.51 116 116
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.22 0.24 -9999 0 -0.78 56 56
PTPN11 -0.009 0.02 -9999 0 -10000 0 0
IL6/IL6RA -0.38 0.25 -9999 0 -0.53 391 391
gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.14 -9999 0 -0.46 42 42
gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.15 -9999 0 -0.48 42 42
IL6 -0.52 0.33 -9999 0 -0.72 391 391
PIAS3 0.016 0 -9999 0 -10000 0 0
PTPRE 0.002 0.045 -9999 0 -0.72 2 2
PIAS1 0.016 0.007 -9999 0 -10000 0 0
RAC1 0.017 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.23 0.21 -9999 0 -0.37 231 231
LMO4 -0.017 0.15 -9999 0 -0.72 22 22
STAT3 (dimer)/PIAS3 -0.17 0.26 -9999 0 -0.64 104 104
MCL1 0.052 0.073 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.01 0.026 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.35 0.2 -9999 0 -0.46 405 405
PTK2 -0.096 0.11 -9999 0 -0.56 1 1
IGF1R -0.023 0.15 -9999 0 -0.72 23 23
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 -0.021 0.16 -9999 0 -0.72 25 25
SRC 0.016 0.007 -9999 0 -10000 0 0
CDKN1B -0.14 0.12 -9999 0 -0.93 9 9
VEGFA -0.005 0.055 -9999 0 -10000 0 0
ILK -0.12 0.068 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.095 0.078 -9999 0 -10000 0 0
PTK2B 0.039 0.032 -9999 0 -0.38 1 1
alphaV/beta3 Integrin/JAM-A -0.29 0.16 -9999 0 -0.38 405 405
CBL 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.001 0.023 -9999 0 -0.46 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.28 0.31 -9999 0 -0.52 282 282
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.053 0.013 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Syndecan-1 0.021 0.043 -9999 0 -0.46 1 1
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.54 0.34 -9999 0 -0.64 452 452
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.028 0.062 -9999 0 -0.46 4 4
RPS6KB1 -0.49 0.3 -9999 0 -0.61 413 413
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.57 0.33 -9999 0 -0.73 405 405
GPR124 -0.014 0.15 -9999 0 -0.72 22 22
MAPK1 -0.57 0.33 -9999 0 -0.73 405 405
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
alphaV/beta3 Integrin/Tumstatin 0.001 0.023 -9999 0 -0.46 1 1
cell adhesion -0.023 0.095 -9999 0 -0.36 36 36
ANGPTL3 0.016 0.001 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.011 0.027 -9999 0 -10000 0 0
IGF-1R heterotetramer -0.023 0.15 -9999 0 -0.72 23 23
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.037 0.19 -9999 0 -0.72 38 38
ITGB3 0.014 0.02 -9999 0 -10000 0 0
IGF1 -0.35 0.37 -9999 0 -0.72 264 264
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.094 -9999 0 -0.46 23 23
apoptosis 0.014 0.033 -9999 0 -0.72 1 1
CD47 0.001 0.1 -9999 0 -0.72 11 11
alphaV/beta3 Integrin/CD47 -0.009 0.069 -9999 0 -0.46 12 12
VCL 0.016 0.007 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.012 0.1 -9999 0 -0.46 25 25
CSF1 0.016 0.007 -9999 0 -10000 0 0
PIK3C2A -0.12 0.068 -9999 0 -10000 0 0
PI4 Kinase/Pyk2 -0.24 0.14 -9999 0 -0.37 56 56
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.012 0.036 -9999 0 -0.41 1 1
FAK1/Vinculin -0.073 0.091 -9999 0 -0.43 1 1
alphaV beta3/Integrin/ppsTEM5 -0.018 0.094 -9999 0 -0.46 23 23
RHOA 0.016 0 -9999 0 -10000 0 0
VTN 0.015 0.012 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
FGF2 -0.55 0.31 -9999 0 -0.72 405 405
F11R -0.41 0.24 -9999 0 -0.54 405 405
alphaV/beta3 Integrin/Lactadherin -0.02 0.1 -9999 0 -0.46 26 26
alphaV/beta3 Integrin/TGFBR2 -0.033 0.12 -9999 0 -0.46 39 39
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0 0.019 -9999 0 -0.41 1 1
HSP90AA1 0.015 0.012 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.001 0.021 -9999 0 -0.42 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.098 0.075 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.003 0.022 -9999 0 -0.38 1 1
SDC1 -0.028 0.072 -9999 0 -10000 0 0
VAV3 0.036 0.09 -9999 0 -0.38 23 23
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 -0.08 0.25 -9999 0 -0.72 69 69
FAK1/Paxillin -0.073 0.091 -9999 0 -0.43 1 1
cell migration -0.06 0.087 -9999 0 -0.39 1 1
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
PI3K -0.29 0.19 -9999 0 -0.38 410 410
SPP1 -0.058 0.095 -9999 0 -0.72 3 3
KDR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.014 0.034 -9999 0 -0.72 1 1
COL4A3 0.016 0 -9999 0 -10000 0 0
angiogenesis -0.55 0.33 -9999 0 -0.71 405 405
Rac1/GTP -0.005 0.078 -9999 0 -0.34 23 23
EDIL3 -0.036 0.16 -9999 0 -0.72 24 24
cell proliferation -0.032 0.12 -9999 0 -0.46 39 39
Plasma membrane estrogen receptor signaling

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.071 0.18 -10000 0 -0.39 120 120
ER alpha/Gai/GDP/Gbeta gamma -0.14 0.2 -10000 0 -0.42 122 122
AKT1 -0.18 0.36 -10000 0 -0.82 119 119
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.18 0.36 -10000 0 -0.83 119 119
mol:Ca2+ -0.052 0.16 -10000 0 -0.4 78 78
IGF1R -0.023 0.15 -10000 0 -0.72 23 23
E2/ER alpha (dimer)/Striatin -0.092 0.21 -10000 0 -0.47 120 120
SHC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.17 0.34 0.78 119 -10000 0 119
RhoA/GTP -0.07 0.15 -10000 0 -0.34 119 119
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.15 0.2 -10000 0 -0.48 122 122
regulation of stress fiber formation 0.02 0.13 0.31 15 -10000 0 15
E2/ERA-ERB (dimer) -0.09 0.2 -10000 0 -0.47 119 119
KRAS 0.013 0.024 -10000 0 -10000 0 0
G13/GTP -0.082 0.19 -10000 0 -0.43 119 119
pseudopodium formation -0.02 0.13 -10000 0 -0.31 15 15
E2/ER alpha (dimer)/PELP1 -0.09 0.2 -10000 0 -0.47 119 119
GRB2 0.013 0.022 -10000 0 -10000 0 0
GNG2 0.015 0.032 -10000 0 -0.72 1 1
GNAO1 0.016 0.007 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.12 0.23 -10000 0 -0.5 122 122
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.094 0.21 -10000 0 -0.49 119 119
mol:NADP -0.12 0.23 -10000 0 -0.5 122 122
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
mol:IP3 -0.054 0.17 -10000 0 -0.41 78 78
IGF-1R heterotetramer -0.023 0.15 -10000 0 -0.72 23 23
PLCB1 -0.065 0.17 -10000 0 -0.43 78 78
PLCB2 -0.008 0.1 -10000 0 -0.66 7 7
IGF1 -0.35 0.37 -10000 0 -0.72 264 264
mol:L-citrulline -0.12 0.23 -10000 0 -0.5 122 122
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.096 0.13 -10000 0 -0.77 2 2
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.016 0 -10000 0 -10000 0 0
ESR2 0.016 0 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.72 119 119
Gq family/GDP/Gbeta gamma 0.032 0.054 -10000 0 -0.78 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.044 0.14 -10000 0 -0.29 119 119
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.15 0.2 -10000 0 -0.48 122 122
GNAZ 0.006 0.084 -10000 0 -0.72 7 7
E2/ER alpha (dimer) -0.14 0.22 -10000 0 -0.55 119 119
STRN 0.014 0.034 -10000 0 -0.72 1 1
GNAL 0.012 0.056 -10000 0 -0.72 3 3
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.024 0 -10000 0 -10000 0 0
GNAI2 0.016 0.007 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.25 0.35 -10000 0 -0.72 189 189
HBEGF -0.12 0.18 -10000 0 -0.38 125 125
cAMP biosynthetic process -0.077 0.17 -10000 0 -0.38 121 121
SRC -0.12 0.19 -10000 0 -0.39 122 122
PI3K -0.053 0.16 -10000 0 -0.54 52 52
GNB1 0.016 0.01 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.078 0.19 -10000 0 -0.42 120 120
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.27 0.24 -10000 0 -0.49 253 253
Gs family/GTP -0.076 0.17 -10000 0 -0.38 121 121
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.003 0.016 -10000 0 -10000 0 0
vasodilation -0.12 0.22 -10000 0 -0.48 122 122
mol:DAG -0.054 0.17 -10000 0 -0.41 78 78
Gs family/GDP/Gbeta gamma -0.08 0.17 -10000 0 -0.39 121 121
MSN -0.023 0.14 -10000 0 -0.33 15 15
Gq family/GTP -0.034 0.1 -10000 0 -0.7 7 7
mol:PI-3-4-5-P3 -0.18 0.34 -10000 0 -0.79 119 119
NRAS 0.014 0.019 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.12 0.22 0.48 122 -10000 0 122
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.084 0.2 -10000 0 -0.45 119 119
NOS3 -0.13 0.24 -10000 0 -0.53 122 122
GNA11 0.016 0 -10000 0 -10000 0 0
MAPKKK cascade -0.12 0.27 -10000 0 -0.6 120 120
E2/ER alpha (dimer)/PELP1/Src -0.16 0.21 -10000 0 -0.51 122 122
ruffle organization -0.02 0.13 -10000 0 -0.31 15 15
ROCK2 -0.036 0.15 -10000 0 -0.37 15 15
GNA14 -0.009 0.095 -10000 0 -0.72 7 7
GNA15 0.013 0.021 -10000 0 -10000 0 0
GNA13 0.015 0.014 -10000 0 -10000 0 0
MMP9 -0.13 0.18 -10000 0 -0.4 122 122
MMP2 -0.11 0.18 -10000 0 -0.37 126 126
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.21 0.48 -10000 0 -0.97 102 102
STAT6 (cleaved dimer) -0.3 0.38 -10000 0 -0.87 131 131
IGHG1 -0.047 0.22 -10000 0 -0.32 103 103
IGHG3 -0.22 0.46 -10000 0 -0.8 151 151
AKT1 -0.069 0.28 -10000 0 -0.5 63 63
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.01 0.2 -10000 0 -0.47 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.084 0.3 -10000 0 -0.55 76 76
THY1 -0.21 0.48 -10000 0 -0.97 102 102
MYB -0.052 0.2 -10000 0 -0.72 43 43
HMGA1 0.011 0.029 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.083 0.3 -10000 0 -0.5 97 97
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.058 0.26 -10000 0 -0.45 62 62
SP1 0.023 0.01 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.018 0.036 -10000 0 -0.72 1 1
STAT6 (dimer)/ETS1 -0.28 0.38 -10000 0 -0.88 119 119
SOCS1 -0.099 0.34 -10000 0 -0.62 100 100
SOCS3 -0.071 0.33 -10000 0 -1.3 16 16
FCER2 -0.21 0.42 -10000 0 -0.76 96 96
PARP14 0.011 0.033 -10000 0 -10000 0 0
CCL17 -0.21 0.48 -10000 0 -0.97 103 103
GRB2 0.013 0.022 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.033 0.22 -10000 0 -0.41 26 26
T cell proliferation -0.24 0.49 -10000 0 -0.9 142 142
IL4R/JAK1 -0.22 0.48 -10000 0 -0.98 104 104
EGR2 -0.63 0.81 -10000 0 -1.4 267 267
JAK2 0.014 0.053 -10000 0 -0.76 1 1
JAK3 0.021 0.008 -10000 0 -10000 0 0
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
JAK1 0.016 0.05 -10000 0 -0.72 2 2
COL1A2 -0.042 0.22 -10000 0 -1.6 3 3
CCL26 -0.21 0.48 -10000 0 -0.97 102 102
IL4R -0.23 0.52 -10000 0 -1 104 104
PTPN6 0.02 0.021 -10000 0 -10000 0 0
IL13RA2 -0.22 0.5 -10000 0 -0.99 109 109
IL13RA1 0.016 0.043 -10000 0 -10000 0 0
IRF4 0.017 0.13 -10000 0 -10000 0 0
ARG1 -0.008 0.2 -10000 0 -1.3 4 4
CBL -0.069 0.28 -10000 0 -0.47 97 97
GTF3A 0.012 0.015 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 0.02 0.072 -10000 0 -0.58 1 1
IRF4/BCL6 -0.038 0.16 -10000 0 -0.55 13 13
CD40LG 0.025 0.023 -10000 0 -10000 0 0
MAPK14 -0.069 0.29 -10000 0 -0.5 90 90
mitosis -0.065 0.27 -10000 0 -0.48 63 63
STAT6 -0.24 0.55 -10000 0 -1 122 122
SPI1 0.019 0.031 -10000 0 -10000 0 0
RPS6KB1 -0.055 0.26 -10000 0 -0.48 52 52
STAT6 (dimer) -0.24 0.55 -10000 0 -1 122 122
STAT6 (dimer)/PARP14 -0.23 0.49 -10000 0 -0.94 123 123
mast cell activation 0.001 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.042 0.25 -10000 0 -0.47 27 27
FRAP1 -0.069 0.28 -10000 0 -0.5 63 63
LTA -0.21 0.48 -10000 0 -0.96 104 104
FES 0.013 0.045 -10000 0 -0.72 2 2
T-helper 1 cell differentiation 0.24 0.54 1 122 -10000 0 122
CCL11 -0.22 0.46 -10000 0 -0.94 104 104
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.042 0.24 -10000 0 -0.47 26 26
IL2RG 0.011 0.041 -10000 0 -10000 0 0
IL10 -0.21 0.48 -10000 0 -0.97 102 102
IRS1 -0.08 0.25 -10000 0 -0.72 69 69
IRS2 -0.17 0.32 -10000 0 -0.72 136 136
IL4 -0.007 0.16 -10000 0 -10000 0 0
IL5 -0.21 0.48 -10000 0 -0.97 103 103
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.16 0.41 -10000 0 -0.75 109 109
COL1A1 -0.053 0.21 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.22 0.49 -10000 0 -1 103 103
IL2R gamma/JAK3 0.033 0.021 -10000 0 -10000 0 0
TFF3 -0.36 0.68 -10000 0 -1.3 153 153
ALOX15 -0.21 0.49 -10000 0 -0.97 104 104
MYBL1 -0.022 0.069 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.17 0.42 -10000 0 -0.72 130 130
SHC1 0.016 0 -10000 0 -10000 0 0
CEBPB 0.022 0.035 -10000 0 -0.72 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.1 0.29 -10000 0 -0.51 94 94
mol:PI-3-4-5-P3 -0.069 0.28 -10000 0 -0.5 63 63
PI3K -0.074 0.29 -10000 0 -0.53 62 62
DOK2 0.013 0.046 -10000 0 -0.72 2 2
ETS1 0.017 0.038 -10000 0 -0.68 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.024 0.21 -10000 0 -0.38 25 25
ITGB3 -0.21 0.48 -10000 0 -0.96 104 104
PIGR -0.57 0.8 -10000 0 -1.4 225 225
IGHE 0.002 0.064 -10000 0 -10000 0 0
MAPKKK cascade -0.023 0.21 -10000 0 -0.38 25 25
BCL6 -0.058 0.22 -10000 0 -0.72 52 52
OPRM1 -0.21 0.48 -10000 0 -0.97 103 103
RETNLB -0.21 0.48 -10000 0 -0.97 102 102
SELP -0.44 0.78 -10000 0 -1.5 161 161
AICDA -0.21 0.46 -10000 0 -0.93 107 107
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.088 0.26 -9999 0 -0.72 75 75
LAT2 -0.048 0.18 -9999 0 -0.49 52 52
AP1 -0.32 0.25 -9999 0 -0.58 215 215
mol:PIP3 -0.047 0.23 -9999 0 -0.54 61 61
IKBKB -0.016 0.14 -9999 0 -0.28 69 69
AKT1 -0.07 0.24 -9999 0 -0.62 57 57
IKBKG -0.015 0.14 -9999 0 -0.28 68 68
MS4A2 -0.12 0.28 -9999 0 -0.72 92 92
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.007 -9999 0 -10000 0 0
MAP3K1 -0.013 0.16 -9999 0 -0.42 47 47
mol:Ca2+ -0.026 0.18 -9999 0 -0.39 61 61
LYN 0.014 0.012 -9999 0 -10000 0 0
CBLB -0.047 0.18 -9999 0 -0.48 53 53
SHC1 0.016 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.18 0.21 -9999 0 -0.42 225 225
positive regulation of cell migration -0.14 0.25 -9999 0 -0.55 146 146
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.085 0.24 -9999 0 -0.46 139 139
PTPN13 -0.071 0.22 -9999 0 -0.58 54 54
PTPN11 0.015 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.017 0.18 -9999 0 -0.39 57 57
SYK 0.008 0.033 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.2 -9999 0 -0.56 62 62
LAT -0.048 0.18 -9999 0 -0.39 92 92
PAK2 -0.021 0.17 -9999 0 -0.44 49 49
NFATC2 -0.041 0.073 -9999 0 -0.61 1 1
HRAS -0.034 0.18 -9999 0 -0.49 49 49
GAB2 0.015 0.016 -9999 0 -10000 0 0
PLA2G1B 0.039 0.021 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.27 -9999 0 -0.58 138 138
Antigen/IgE/Fc epsilon R1 -0.14 0.25 -9999 0 -0.53 138 138
mol:GDP -0.042 0.19 -9999 0 -0.5 49 49
JUN -0.12 0.29 -9999 0 -0.72 97 97
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.057 0.22 -9999 0 -0.72 52 52
FOS -0.51 0.34 -9999 0 -0.72 375 375
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.091 0.17 -9999 0 -0.42 92 92
CHUK -0.016 0.14 -9999 0 -0.29 67 67
KLRG1 -0.047 0.17 -9999 0 -0.46 51 51
VAV1 -0.051 0.18 -9999 0 -0.49 52 52
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.046 0.18 -9999 0 -0.39 92 92
negative regulation of mast cell degranulation -0.076 0.14 -9999 0 -0.44 49 49
BTK -0.085 0.17 -9999 0 -0.51 48 48
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.087 0.26 -9999 0 -0.46 138 138
GAB2/PI3K/SHP2 -0.14 0.23 -9999 0 -0.7 57 57
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.064 0.21 -9999 0 -0.55 57 57
RAF1 0.023 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.24 -9999 0 -0.5 138 138
FCER1G 0.016 0.017 -9999 0 -10000 0 0
FCER1A -0.11 0.28 -9999 0 -0.74 88 88
Antigen/IgE/Fc epsilon R1/Fyn -0.13 0.24 -9999 0 -0.5 138 138
MAPK3 0.037 0.021 -9999 0 -10000 0 0
MAPK1 0.037 0.021 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.011 0.076 -9999 0 -0.42 8 8
DUSP1 -0.3 0.36 -9999 0 -0.72 225 225
NF-kappa-B/RelA -0.036 0.06 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.045 0.18 -9999 0 -0.52 42 42
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.1 0.18 -9999 0 -0.53 58 58
FER -0.046 0.18 -9999 0 -0.48 52 52
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.021 0.049 -9999 0 -0.56 2 2
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.039 0.2 -9999 0 -0.52 49 49
cytokine secretion -0.027 0.044 -9999 0 -10000 0 0
SPHK1 -0.052 0.19 -9999 0 -0.47 64 64
PTK2 -0.048 0.19 -9999 0 -0.54 42 42
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.21 -9999 0 -0.58 62 62
EDG1 -0.14 0.25 -9999 0 -0.55 146 146
mol:DAG -0.081 0.26 -9999 0 -0.58 83 83
MAP2K2 0.032 0.022 -9999 0 -10000 0 0
MAP2K1 0.032 0.022 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.074 0.14 -9999 0 -0.46 42 42
MAP2K4 0.011 0.11 -9999 0 -0.92 7 7
Fc epsilon R1/FcgammaRIIB -0.14 0.26 -9999 0 -0.53 138 138
mol:Choline -0.083 0.24 -9999 0 -0.45 139 139
SHC/Grb2/SOS1 -0.07 0.15 -9999 0 -0.48 42 42
FYN 0.013 0.045 -9999 0 -0.72 2 2
DOK1 0.014 0.019 -9999 0 -10000 0 0
PXN -0.035 0.18 -9999 0 -0.49 42 42
HCLS1 -0.047 0.18 -9999 0 -0.39 92 92
PRKCB -0.041 0.18 -9999 0 -0.39 82 82
FCGR2B 0.01 0.065 -9999 0 -0.72 4 4
IGHE -0.001 0.007 -9999 0 -10000 0 0
KLRG1/SHIP -0.077 0.14 -9999 0 -0.44 49 49
LCP2 0.012 0.024 -9999 0 -10000 0 0
PLA2G4A -0.29 0.26 -9999 0 -0.45 341 341
RASA1 0.015 0.012 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.083 0.24 -9999 0 -0.45 139 139
IKK complex 0.008 0.11 -9999 0 -0.22 45 45
WIPF1 0.013 0.024 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.008 0.13 -10000 0 -0.37 52 52
adherens junction organization 0.012 0.096 -10000 0 -0.28 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.17 0.22 -10000 0 -0.55 63 63
FMN1 0.011 0.089 -10000 0 -0.28 38 38
mol:IP3 -0.042 0.1 -10000 0 -0.34 52 52
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.011 0.094 -10000 0 -0.29 38 38
CTNNB1 0.01 0.065 -10000 0 -0.72 4 4
AKT1 0.008 0.12 -10000 0 -0.33 52 52
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.016 0.13 -10000 0 -0.45 37 37
CTNND1 0.015 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.089 -10000 0 -0.26 38 38
VASP 0.016 0.091 -10000 0 -0.37 4 4
ZYX 0.02 0.091 -10000 0 -0.38 3 3
JUB 0.006 0.12 -10000 0 -0.42 21 21
EGFR(dimer) -0.19 0.23 -10000 0 -0.39 274 274
E-cadherin/beta catenin-gamma catenin -0.026 0.12 -10000 0 -0.44 38 38
mol:PI-3-4-5-P3 -0.046 0.11 -10000 0 -0.35 52 52
PIK3CA 0.015 0.009 -10000 0 -10000 0 0
PI3K -0.047 0.11 -10000 0 -0.36 52 52
FYN 0.022 0.12 -10000 0 -0.48 3 3
mol:Ca2+ 0.002 0.12 -10000 0 -0.33 52 52
JUP 0.013 0.036 -10000 0 -0.72 1 1
PIK3R1 -0.055 0.22 -10000 0 -0.72 52 52
mol:DAG -0.042 0.1 -10000 0 -0.34 52 52
CDH1 -0.033 0.18 -10000 0 -0.72 33 33
RhoA/GDP -0.17 0.22 -10000 0 -0.56 59 59
establishment of polarity of embryonic epithelium 0.016 0.09 -10000 0 -0.36 4 4
SRC 0.016 0.007 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR -0.37 0.37 -10000 0 -0.72 274 274
CASR 0.013 0.12 -10000 0 -0.39 2 2
RhoA/GTP -0.036 0.092 -10000 0 -0.38 2 2
AKT2 0.008 0.12 -10000 0 -0.33 52 52
actin cable formation 0.015 0.089 -10000 0 -0.36 4 4
apoptosis 0.044 0.11 0.35 52 -10000 0 52
CTNNA1 0.016 0.005 -10000 0 -10000 0 0
mol:GDP -0.19 0.24 -10000 0 -0.39 291 291
PIP5K1A 0.019 0.09 -10000 0 -0.27 38 38
PLCG1 -0.043 0.11 -10000 0 -0.34 52 52
Rac1/GTP -0.19 0.18 -10000 0 -0.35 274 274
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0 0.003 -9999 0 -10000 0 0
Necdin/E2F1 -0.15 0.24 -9999 0 -0.56 136 136
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.087 0.18 -9999 0 -0.41 112 112
NGF (dimer)/p75(NTR)/BEX1 -0.078 0.19 -9999 0 -0.48 95 95
NT-4/5 (dimer)/p75(NTR) -0.099 0.21 -9999 0 -0.55 95 95
IKBKB 0.014 0.02 -9999 0 -10000 0 0
AKT1 -0.077 0.21 -9999 0 -0.43 132 132
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF 0.006 0.057 -9999 0 -0.72 2 2
MGDIs/NGR/p75(NTR)/LINGO1 -0.072 0.19 -9999 0 -0.47 95 95
FURIN 0.013 0.024 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.081 0.18 -9999 0 -0.46 97 97
LINGO1 -0.01 0.06 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.002 0.016 -9999 0 -10000 0 0
proBDNF (dimer) 0.006 0.057 -9999 0 -0.72 2 2
NTRK1 0.014 0.019 -9999 0 -10000 0 0
RTN4R 0.007 0.038 -9999 0 -10000 0 0
neuron apoptosis -0.015 0.17 -9999 0 -0.38 95 95
IRAK1 0.014 0.02 -9999 0 -10000 0 0
SHC1 -0.064 0.19 -9999 0 -0.47 95 95
ARHGDIA 0.015 0.014 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0.004 0.027 -9999 0 -0.38 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.087 0.18 -9999 0 -0.44 104 104
MAGEH1 -0.005 0.12 -9999 0 -0.72 15 15
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.18 0.27 -9999 0 -0.52 187 187
Mammalian IAPs/DIABLO -0.024 0.1 -9999 0 -0.42 34 34
proNGF (dimer) 0 0 -9999 0 -10000 0 0
MAGED1 0.006 0.04 -9999 0 -10000 0 0
APP 0.006 0.074 -9999 0 -0.72 5 5
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.015 0.014 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.045 0.16 -9999 0 -0.4 95 95
NGF 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.062 0.15 -9999 0 -0.38 95 95
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.021 0.13 -9999 0 -0.3 95 95
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.084 0.18 -9999 0 -0.47 95 95
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.087 0.2 -9999 0 -0.5 97 97
PSENEN 0.014 0.019 -9999 0 -10000 0 0
mol:ceramide -0.048 0.17 -9999 0 -0.42 95 95
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.009 0.11 -9999 0 -0.24 95 95
p75(NTR)/beta APP -0.1 0.22 -9999 0 -0.55 98 98
BEX1 -0.006 0.056 -9999 0 -10000 0 0
mol:GDP -0.076 0.19 -9999 0 -0.48 95 95
NGF (dimer) -0.067 0.16 -9999 0 -0.42 86 86
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.059 0.17 -9999 0 -0.42 95 95
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
RAC1/GTP -0.073 0.16 -9999 0 -0.41 95 95
MYD88 0.016 0.01 -9999 0 -10000 0 0
CHUK 0.015 0.032 -9999 0 -0.72 1 1
NGF (dimer)/p75(NTR)/PKA -0.087 0.2 -9999 0 -0.5 97 97
RHOB 0.013 0.046 -9999 0 -0.72 2 2
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.011 0.027 -9999 0 -10000 0 0
NT3 (dimer) -0.2 0.33 -9999 0 -0.72 150 150
TP53 -0.02 0.16 -9999 0 -0.36 97 97
PRDM4 -0.049 0.17 -9999 0 -0.42 95 95
BDNF (dimer) -0.032 0.2 -9999 0 -0.46 89 89
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
SORT1 0.016 0.007 -9999 0 -10000 0 0
activation of caspase activity -0.086 0.17 -9999 0 -0.41 112 112
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.075 0.16 -9999 0 -0.42 95 95
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.015 0.17 -9999 0 -0.36 95 95
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.048 0.17 -9999 0 -0.42 95 95
APH1B 0.015 0.033 -9999 0 -0.72 1 1
APH1A 0.009 0.033 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.084 0.18 -9999 0 -0.47 95 95
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.003 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.25 0.31 -9999 0 -0.6 216 216
MAPK8 -0.008 0.17 -9999 0 -0.36 95 95
MAPK9 -0.008 0.17 -9999 0 -0.36 95 95
APAF1 0.016 0.007 -9999 0 -10000 0 0
NTF3 -0.2 0.33 -9999 0 -0.72 150 150
NTF4 0 0 -9999 0 -10000 0 0
NDN -0.17 0.32 -9999 0 -0.72 136 136
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.067 0.16 -9999 0 -0.39 98 98
p75 CTF/Sortilin/TRAF6/NRIF 0.001 0.009 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.086 0.2 -9999 0 -0.5 97 97
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.066 0.15 -9999 0 -0.38 97 97
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.072 0.16 -9999 0 -0.41 97 97
PRKACB -0.007 0.098 -9999 0 -0.72 8 8
proBDNF (dimer)/p75 ECD -0.006 0.037 -9999 0 -0.54 2 2
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.037 0.18 -9999 0 -0.72 34 34
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.14 0.23 -9999 0 -0.55 106 106
BAD -0.003 0.17 -9999 0 -0.35 95 95
RIPK2 0.014 0.02 -9999 0 -10000 0 0
NGFR -0.12 0.28 -9999 0 -0.72 95 95
CYCS -0.04 0.16 -9999 0 -0.39 95 95
ADAM17 0.016 0.007 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.075 0.16 -9999 0 -0.42 95 95
BCL2L11 -0.003 0.17 -9999 0 -0.36 95 95
BDNF (dimer)/p75(NTR) -0.1 0.21 -9999 0 -0.54 97 97
PI3K -0.12 0.21 -9999 0 -0.47 132 132
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.075 0.16 -9999 0 -0.42 95 95
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.015 0.032 -9999 0 -0.72 1 1
PRKCI 0.013 0.023 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.099 0.21 -9999 0 -0.55 95 95
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.072 0.17 -9999 0 -0.42 95 95
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG 0.015 0.032 -9999 0 -0.72 1 1
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.048 0.18 -9999 0 -0.43 97 97
SQSTM1 0.016 0.007 -9999 0 -10000 0 0
NGFRAP1 -0.016 0.15 -9999 0 -0.72 23 23
CASP3 0 0.16 -9999 0 -0.33 95 95
E2F1 -0.006 0.056 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.03 0.07 -9999 0 -0.37 1 1
NGF (dimer)/TRKA -0.001 0.011 -9999 0 -10000 0 0
MMP7 -0.1 0.27 -9999 0 -0.72 85 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.069 0.15 -9999 0 -0.39 95 95
MMP3 -0.078 0.11 -9999 0 -0.72 8 8
APAF-1/Caspase 9 -0.068 0.14 -9999 0 -0.45 21 21
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.36 0.21 -9999 0 -0.47 409 409
fibroblast growth factor receptor signaling pathway -0.36 0.21 -9999 0 -0.47 409 409
LAMA1 0.016 0.01 -9999 0 -10000 0 0
PRNP -0.002 0.11 -9999 0 -0.72 13 13
GPC1/SLIT2 -0.073 0.18 -9999 0 -0.54 71 71
SMAD2 0.009 0.12 -9999 0 -0.41 38 38
GPC1/PrPc/Cu2+ -0.011 0.073 -9999 0 -0.47 13 13
GPC1/Laminin alpha1 -0.001 0.008 -9999 0 -10000 0 0
TDGF1 0.016 0.007 -9999 0 -10000 0 0
CRIPTO/GPC1 -0.001 0.008 -9999 0 -10000 0 0
APP/GPC1 -0.007 0.053 -9999 0 -0.54 5 5
mol:NO 0 0 -9999 0 -10000 0 0
YES1 0.034 0.023 -9999 0 -0.46 1 1
FLT1 0.015 0.012 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.031 0.12 -9999 0 -0.46 38 38
SERPINC1 0.012 0.025 -9999 0 -10000 0 0
FYN 0.033 0.031 -9999 0 -0.46 2 2
FGR 0.035 0.008 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.061 0.021 -9999 0 -10000 0 0
SLIT2 -0.083 0.25 -9999 0 -0.72 71 71
GPC1/NRG -0.069 0.18 -9999 0 -0.54 67 67
NRG1 -0.078 0.24 -9999 0 -0.72 67 67
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.01 0.03 -9999 0 -10000 0 0
LYN 0.035 0.01 -9999 0 -10000 0 0
mol:Spermine 0.014 0.009 -9999 0 -10000 0 0
cell growth -0.36 0.21 -9999 0 -0.47 409 409
BMP signaling pathway -0.015 0.014 -9999 0 -10000 0 0
SRC 0.035 0.009 -9999 0 -10000 0 0
TGFBR1 0.014 0.017 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.1 0.26 -9999 0 -0.72 78 78
GPC1 0.015 0.014 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.014 0.017 -9999 0 -10000 0 0
VEGFA -0.005 0.055 -9999 0 -10000 0 0
BLK 0.028 0.025 -9999 0 -10000 0 0
HCK 0.033 0.015 -9999 0 -10000 0 0
FGF2 -0.55 0.31 -9999 0 -0.72 405 405
FGFR1 -0.007 0.12 -9999 0 -0.72 15 15
VEGFR1 homodimer 0.015 0.012 -9999 0 -10000 0 0
TGFBR2 -0.037 0.19 -9999 0 -0.72 38 38
cell death -0.007 0.053 -9999 0 -0.54 5 5
ATIII/GPC1 -0.003 0.014 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.085 0.19 -9999 0 -0.54 78 78
LCK 0.026 0.027 -9999 0 -10000 0 0
neuron differentiation -0.069 0.18 -9999 0 -0.54 67 67
PrPc/Cu2+ -0.014 0.085 -9999 0 -0.55 13 13
APP 0.006 0.074 -9999 0 -0.72 5 5
TGFBR2 (dimer) -0.037 0.19 -9999 0 -0.72 38 38
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.35 0.46 -10000 0 -1.4 48 48
IL23A -0.31 0.38 -10000 0 -1 40 40
NF kappa B1 p50/RelA/I kappa B alpha -0.35 0.3 -10000 0 -0.96 47 47
positive regulation of T cell mediated cytotoxicity -0.35 0.41 -10000 0 -0.92 75 75
ITGA3 -0.31 0.38 -10000 0 -1 41 41
IL17F -0.22 0.3 -10000 0 -0.64 71 71
IL12B 0.012 0.035 -10000 0 -10000 0 0
STAT1 (dimer) -0.34 0.4 -10000 0 -0.88 80 80
CD4 -0.31 0.37 -10000 0 -0.98 40 40
IL23 -0.3 0.37 -10000 0 -0.98 40 40
IL23R -0.039 0.13 -10000 0 -1.6 2 2
IL1B -0.32 0.39 -10000 0 -1.1 40 40
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.31 0.37 -10000 0 -0.98 40 40
TYK2 0.009 0.019 -10000 0 -10000 0 0
STAT4 0.005 0.086 -10000 0 -0.72 7 7
STAT3 0.017 0.001 -10000 0 -10000 0 0
IL18RAP -0.046 0.2 -10000 0 -0.72 45 45
IL12RB1 0.009 0.019 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.006 0.026 -10000 0 -10000 0 0
IL23R/JAK2 -0.047 0.14 -10000 0 -1.2 3 3
positive regulation of chronic inflammatory response -0.35 0.41 -10000 0 -0.92 75 75
natural killer cell activation 0.003 0.009 0.079 2 -10000 0 2
JAK2 0.011 0.043 -10000 0 -0.76 1 1
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
NFKB1 0.014 0.004 -10000 0 -10000 0 0
RELA 0.014 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.29 0.36 -10000 0 -0.94 40 40
ALOX12B -0.31 0.37 -10000 0 -0.98 40 40
CXCL1 -0.76 0.7 -10000 0 -1.3 303 303
T cell proliferation -0.35 0.41 -10000 0 -0.92 75 75
NFKBIA 0.013 0.033 -10000 0 -0.73 1 1
IL17A -0.15 0.25 -10000 0 -0.5 51 51
PI3K -0.39 0.34 -10000 0 -0.97 79 79
IFNG -0.012 0.03 0.15 2 -0.094 17 19
STAT3 (dimer) -0.36 0.32 -10000 0 -0.94 73 73
IL18R1 0.015 0.035 -10000 0 -0.72 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.25 -10000 0 -0.55 50 50
IL18/IL18R -0.01 0.15 -10000 0 -0.47 45 45
macrophage activation -0.021 0.016 -10000 0 -0.042 40 40
TNF -0.32 0.38 -10000 0 -1 40 40
STAT3/STAT4 -0.36 0.32 -10000 0 -0.86 79 79
STAT4 (dimer) -0.34 0.4 -10000 0 -0.9 79 79
IL18 0.003 0.055 -10000 0 -0.72 1 1
IL19 -0.31 0.38 -10000 0 -0.99 40 40
STAT5A (dimer) -0.33 0.39 -10000 0 -0.88 77 77
STAT1 -0.011 0.06 -10000 0 -10000 0 0
SOCS3 -0.005 0.12 -10000 0 -0.72 15 15
CXCL9 -0.32 0.39 -10000 0 -1.1 43 43
MPO -0.31 0.37 -10000 0 -0.98 40 40
positive regulation of humoral immune response -0.35 0.41 -10000 0 -0.92 75 75
IL23/IL23R/JAK2/TYK2 -0.36 0.43 -10000 0 -0.96 75 75
IL6 -0.92 0.66 -10000 0 -1.3 391 391
STAT5A 0.013 0.045 -10000 0 -0.72 2 2
IL2 0.019 0.034 -10000 0 -0.72 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.009 0.079 2 -10000 0 2
CD3E -0.31 0.37 -10000 0 -0.98 40 40
keratinocyte proliferation -0.35 0.41 -10000 0 -0.92 75 75
NOS2 -0.32 0.37 -10000 0 -0.77 96 96
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.023 0.013 -9999 0 -10000 0 0
RAS family/GTP -0.021 0.1 -9999 0 -0.33 20 20
NFATC4 -0.018 0.098 -9999 0 -0.3 15 15
ERBB2IP 0.017 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.015 0.012 -9999 0 -10000 0 0
mammary gland morphogenesis -0.034 0.13 -9999 0 -0.35 68 68
JUN -0.035 0.082 -9999 0 -10000 0 0
HRAS 0.014 0.012 -9999 0 -10000 0 0
DOCK7 -0.029 0.12 -9999 0 -0.33 68 68
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.055 0.14 -9999 0 -0.41 68 68
AKT1 0.012 0.014 -9999 0 -10000 0 0
BAD 0.024 0.011 -9999 0 -10000 0 0
MAPK10 -0.025 0.07 -9999 0 -0.28 15 15
mol:GTP -0.002 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.036 0.14 -9999 0 -0.38 68 68
RAF1 -0.021 0.11 -9999 0 -0.34 20 20
ErbB2/ErbB3/neuregulin 2 -0.3 0.21 -9999 0 -0.44 356 356
STAT3 0.004 0.009 -9999 0 -10000 0 0
cell migration 0.017 0.078 -9999 0 -0.26 6 6
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.24 0.28 -9999 0 -0.62 133 133
FOS -0.34 0.29 -9999 0 -0.52 376 376
NRAS 0.013 0.019 -9999 0 -10000 0 0
mol:Ca2+ -0.034 0.13 -9999 0 -0.35 68 68
MAPK3 -0.14 0.21 -9999 0 -0.48 101 101
MAPK1 -0.14 0.21 -9999 0 -0.48 101 101
JAK2 -0.029 0.12 -9999 0 -0.33 69 69
NF2 0.001 0.008 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.014 0.12 -9999 0 -0.33 67 67
NRG1 -0.08 0.25 -9999 0 -0.72 67 67
GRB2/SOS1 -0.002 0.011 -9999 0 -10000 0 0
MAPK8 -0.023 0.11 -9999 0 -0.3 68 68
MAPK9 -0.02 0.056 -9999 0 -0.2 2 2
ERBB2 -0.013 0.041 -9999 0 -0.56 1 1
ERBB3 0.008 0.03 -9999 0 -10000 0 0
SHC1 0.015 0.001 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
apoptosis 0.013 0.014 -9999 0 -10000 0 0
STAT3 (dimer) 0.004 0.009 -9999 0 -10000 0 0
RNF41 0.03 0.013 -9999 0 -10000 0 0
FRAP1 0.024 0.011 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.031 0.078 -9999 0 -0.26 15 15
ErbB2/ErbB2/HSP90 (dimer) -0.009 0.031 -9999 0 -0.47 1 1
CHRNA1 -0.11 0.17 -9999 0 -0.36 96 96
myelination 0.012 0.1 -9999 0 -0.32 2 2
PPP3CB -0.026 0.11 -9999 0 -0.31 68 68
KRAS 0.011 0.024 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.006 0.1 -9999 0 -0.27 52 52
NRG2 -0.48 0.35 -9999 0 -0.72 355 355
mol:GDP -0.014 0.12 -9999 0 -0.32 67 67
SOS1 0.015 0.001 -9999 0 -10000 0 0
MAP2K2 -0.025 0.12 -9999 0 -0.36 20 20
SRC 0.016 0.007 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.028 0.12 -9999 0 -0.34 52 52
MAP2K1 -0.15 0.2 -9999 0 -0.42 132 132
heart morphogenesis -0.034 0.13 -9999 0 -0.35 68 68
RAS family/GDP -0.015 0.1 -9999 0 -0.32 10 10
GRB2 0.012 0.022 -9999 0 -10000 0 0
PRKACA -0.002 0.008 -9999 0 -10000 0 0
CHRNE 0.007 0.02 -9999 0 -10000 0 0
HSP90AA1 0.015 0.012 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.014 -9999 0 -10000 0 0
nervous system development -0.034 0.13 -9999 0 -0.35 68 68
CDC42 0.016 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.003 0.026 -9999 0 -0.54 1 1
PTK2 -0.082 0.19 -9999 0 -0.49 88 88
positive regulation of JNK cascade -0.053 0.12 -9999 0 -0.32 88 88
CDC42/GDP -0.007 0.19 -9999 0 -0.43 88 88
Rac1/GDP -0.004 0.19 -9999 0 -0.42 88 88
RAP1B 0.016 0.01 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.064 -9999 0 -0.72 4 4
CDC42/GTP -0.065 0.15 -9999 0 -0.39 88 88
nectin-3/I-afadin -0.094 0.21 -9999 0 -0.56 88 88
RAPGEF1 -0.02 0.21 -9999 0 -0.48 88 88
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.038 0.24 -9999 0 -0.56 88 88
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
TLN1 -0.019 0.16 -9999 0 -0.64 23 23
Rap1/GTP -0.055 0.13 -9999 0 -0.34 88 88
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.007 0.058 -9999 0 -0.42 10 10
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.094 0.21 -9999 0 -0.56 88 88
PVR 0.014 0.017 -9999 0 -10000 0 0
Necl-5(dimer) 0.014 0.017 -9999 0 -10000 0 0
mol:GDP -0.023 0.23 -9999 0 -0.53 88 88
MLLT4 0.002 0.1 -9999 0 -0.72 10 10
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PI3K -0.1 0.2 -9999 0 -0.44 125 125
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.011 0.074 -9999 0 -0.54 10 10
positive regulation of lamellipodium assembly -0.055 0.12 -9999 0 -0.33 88 88
PVRL1 0.015 0.012 -9999 0 -10000 0 0
PVRL3 -0.099 0.27 -9999 0 -0.72 82 82
PVRL2 0.01 0.031 -9999 0 -10000 0 0
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
CDH1 -0.032 0.18 -9999 0 -0.72 33 33
CLDN1 -0.055 0.2 -9999 0 -0.72 42 42
JAM-A/CLDN1 -0.098 0.22 -9999 0 -0.48 115 115
SRC -0.1 0.24 -9999 0 -0.63 88 88
ITGB3 0.014 0.02 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin -0.011 0.074 -9999 0 -0.54 10 10
FARP2 -0.029 0.22 -9999 0 -0.52 88 88
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.079 0.18 -9999 0 -0.48 88 88
nectin-1/I-afadin -0.011 0.074 -9999 0 -0.54 10 10
nectin-2/I-afadin -0.013 0.075 -9999 0 -0.54 10 10
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.079 0.18 -9999 0 -0.48 88 88
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.011 0.029 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.053 0.12 -9999 0 -0.32 88 88
alphaV/beta3 Integrin/Talin 0 0.15 -9999 0 -0.61 21 21
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.013 0.075 -9999 0 -0.54 10 10
nectin-2(dimer)/I-afadin/I-afadin -0.013 0.075 -9999 0 -0.54 10 10
PIP5K1C -0.031 0.17 -9999 0 -0.68 23 23
VAV2 -0.031 0.22 -9999 0 -0.53 88 88
RAP1/GDP -0.065 0.15 -9999 0 -0.39 88 88
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.077 0.18 -9999 0 -0.48 88 88
nectin-3(dimer)/I-afadin/I-afadin -0.094 0.21 -9999 0 -0.56 88 88
Rac1/GTP -0.067 0.15 -9999 0 -0.4 88 88
PTPRM -0.047 0.19 -9999 0 -0.38 95 95
E-cadherin/beta catenin/alpha catenin -0.027 0.11 -9999 0 -0.37 46 46
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.002 0.1 -10000 0 -0.29 60 60
epithelial cell differentiation -0.026 0.099 -10000 0 -0.39 37 37
CYFIP2 -0.002 0.052 -10000 0 -10000 0 0
ENAH 0.058 0.084 -10000 0 -0.43 2 2
EGFR -0.37 0.37 -10000 0 -0.72 274 274
EPHA2 0.005 0.09 -10000 0 -0.72 8 8
MYO6 0.019 0.11 -10000 0 -0.37 38 38
CTNNB1 0.01 0.064 -10000 0 -0.72 4 4
ABI1/Sra1/Nap1 0.009 0.026 -10000 0 -10000 0 0
AQP5 -0.18 0.26 -10000 0 -0.55 157 157
CTNND1 0.016 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.1 -10000 0 -0.36 37 37
regulation of calcium-dependent cell-cell adhesion -0.015 0.15 -10000 0 -0.37 80 80
EGF -0.24 0.35 -10000 0 -0.72 179 179
NCKAP1 0.016 0 -10000 0 -10000 0 0
AQP3 -0.08 0.2 -10000 0 -0.56 66 66
cortical microtubule organization -0.026 0.099 -10000 0 -0.39 37 37
GO:0000145 0.019 0.099 -10000 0 -0.34 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.026 0.1 -10000 0 -0.39 37 37
MLLT4 0.002 0.1 -10000 0 -0.72 10 10
ARF6/GDP -0.025 0.085 -10000 0 -0.64 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.053 -10000 0 -0.41 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.034 0.1 -10000 0 -0.33 37 37
PVRL2 0.01 0.031 -10000 0 -10000 0 0
ZYX 0.018 0.11 -10000 0 -0.36 38 38
ARF6/GTP -0.003 0.048 -10000 0 -0.37 8 8
CDH1 -0.032 0.18 -10000 0 -0.72 33 33
EGFR/EGFR/EGF/EGF -0.33 0.26 -10000 0 -0.46 380 380
RhoA/GDP -0.024 0.092 -10000 0 -0.36 37 37
actin cytoskeleton organization 0.026 0.1 -10000 0 -0.34 38 38
IGF-1R heterotetramer -0.023 0.15 -10000 0 -0.72 23 23
GIT1 0.015 0.016 -10000 0 -10000 0 0
IGF1R -0.023 0.15 -10000 0 -0.72 23 23
IGF1 -0.35 0.37 -10000 0 -0.72 264 264
DIAPH1 0.012 0.026 -10000 0 -10000 0 0
Wnt receptor signaling pathway 0.026 0.099 0.39 37 -10000 0 37
RHOA 0.016 0 -10000 0 -10000 0 0
RhoA/GTP -0.025 0.086 -10000 0 -0.64 2 2
CTNNA1 0.016 0 -10000 0 -10000 0 0
VCL 0.026 0.1 -10000 0 -0.35 38 38
EFNA1 0.013 0.022 -10000 0 -10000 0 0
LPP 0.029 0.1 -10000 0 -0.34 37 37
Ephrin A1/EPHA2 -0.027 0.1 -10000 0 -0.36 43 43
SEC6/SEC8 -0.027 0.091 -10000 0 -0.44 4 4
MGAT3 -0.016 0.15 -10000 0 -0.38 80 80
HGF/MET -0.057 0.14 -10000 0 -0.37 84 84
HGF 0.016 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.002 0.11 -10000 0 -0.3 60 60
actin cable formation 0.08 0.081 -10000 0 -0.35 2 2
KIAA1543 0.029 0.1 -10000 0 -0.34 37 37
KIFC3 0.019 0.1 -10000 0 -0.36 37 37
NCK1 0.016 0 -10000 0 -10000 0 0
EXOC3 0.016 0 -10000 0 -10000 0 0
ACTN1 0.019 0.1 -10000 0 -0.36 37 37
NCK1/GIT1 -0.001 0.008 -10000 0 -10000 0 0
mol:GDP -0.026 0.099 -10000 0 -0.39 37 37
EXOC4 0.016 0 -10000 0 -10000 0 0
STX4 0.019 0.1 -10000 0 -0.36 37 37
PIP5K1C 0.019 0.1 -10000 0 -0.36 37 37
LIMA1 -0.016 0.15 -10000 0 -0.72 23 23
ABI1 0.016 0 -10000 0 -10000 0 0
ROCK1 -0.02 0.074 -10000 0 -0.54 2 2
adherens junction assembly 0.05 0.096 -10000 0 -0.37 1 1
IGF-1R heterotetramer/IGF1 -0.21 0.22 -10000 0 -0.39 292 292
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.013 0.075 -10000 0 -0.54 10 10
MET -0.057 0.22 -10000 0 -0.72 52 52
PLEKHA7 0.019 0.1 -10000 0 -0.36 37 37
mol:GTP -0.004 0.052 -10000 0 -0.41 8 8
establishment of epithelial cell apical/basal polarity 0.044 0.11 -10000 0 -0.62 1 1
cortical actin cytoskeleton stabilization 0.002 0.1 -10000 0 -0.29 60 60
regulation of cell-cell adhesion 0.026 0.1 -10000 0 -0.34 38 38
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.002 0.11 -10000 0 -0.3 60 60
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.011 0.038 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.13 0.17 -9999 0 -0.47 81 81
JUN -0.074 0.19 -9999 0 -0.42 98 98
HRAS 0.015 0.012 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.01 0.18 -9999 0 -0.43 72 72
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.011 0.039 -9999 0 -0.72 1 1
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.014 0.18 -9999 0 -0.42 68 68
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
RET9/GFRalpha1/GDNF/Enigma -0.017 0.16 -9999 0 -0.42 68 68
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP 0.01 0.15 -9999 0 -0.37 68 68
GRB7 0 0.048 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.015 0.18 -9999 0 -0.42 68 68
MAPKKK cascade -0.003 0.13 -9999 0 -0.34 68 68
BCAR1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.074 0.25 -9999 0 -0.53 109 109
lamellipodium assembly -0.12 0.17 -9999 0 -0.4 103 103
RET51/GFRalpha1/GDNF/SHC 0.015 0.18 -9999 0 -0.42 68 68
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.017 0.16 -9999 0 -0.42 68 68
RET9/GFRalpha1/GDNF/Shank3 -0.017 0.16 -9999 0 -0.42 68 68
MAPK3 -0.057 0.12 -9999 0 -0.35 68 68
DOK1 0.014 0.019 -9999 0 -10000 0 0
DOK6 0.009 0.059 -9999 0 -0.72 3 3
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.034 0.12 -9999 0 -0.38 14 14
DOK5 -0.02 0.16 -9999 0 -0.72 25 25
GFRA1 -0.16 0.23 -9999 0 -0.72 68 68
MAPK8 -0.005 0.1 -9999 0 -0.27 69 69
HRAS/GTP 0.01 0.16 -9999 0 -0.39 68 68
tube development -0.013 0.15 -9999 0 -0.39 68 68
MAPK1 -0.057 0.12 -9999 0 -0.35 68 68
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.01 0.11 -9999 0 -0.29 69 69
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
PDLIM7 0.016 0.007 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.018 0.17 -9999 0 -0.41 69 69
SHC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.015 0.18 -9999 0 -0.42 68 68
RET51/GFRalpha1/GDNF/Dok5 -0.01 0.21 -9999 0 -0.46 89 89
PRKCA 0.016 0.01 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.007 -9999 0 -10000 0 0
CREB1 -0.011 0.12 -9999 0 -0.32 68 68
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.01 0.11 -9999 0 -0.29 69 69
RET51/GFRalpha1/GDNF/Grb7 0.011 0.18 -9999 0 -0.44 68 68
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.062 0.081 -9999 0 -10000 0 0
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade -0.072 0.19 -9999 0 -0.41 98 98
RET9/GFRalpha1/GDNF/FRS2 -0.017 0.16 -9999 0 -0.42 69 69
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.01 0.11 -9999 0 -0.3 68 68
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.009 0.11 -9999 0 -0.29 69 69
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.007 0.11 -9999 0 -0.29 68 68
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.006 0.11 -9999 0 -0.29 68 68
PI3K -0.16 0.3 -9999 0 -0.66 106 106
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.01 0.15 -9999 0 -0.39 68 68
GRB10 0.011 0.064 -9999 0 -0.72 4 4
activation of MAPKK activity -0.012 0.1 -9999 0 -0.3 12 12
RET51/GFRalpha1/GDNF/FRS2 0.012 0.18 -9999 0 -0.42 69 69
GAB1 0.014 0.034 -9999 0 -0.72 1 1
IRS1 -0.08 0.25 -9999 0 -0.72 69 69
IRS2 -0.17 0.32 -9999 0 -0.72 136 136
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.007 0.11 -9999 0 -0.29 69 69
RET51/GFRalpha1/GDNF/PKC alpha 0.015 0.18 -9999 0 -0.42 68 68
GRB2 0.013 0.022 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.016 0.007 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.044 0.27 -9999 0 -0.54 109 109
Rac1/GTP -0.14 0.21 -9999 0 -0.5 103 103
RET9/GFRalpha1/GDNF -0.027 0.17 -9999 0 -0.47 68 68
GFRalpha1/GDNF -0.11 0.17 -9999 0 -0.54 68 68
Insulin 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
CBL/APS/CAP -0.25 0.23 -9999 0 -0.42 313 313
TC10/GTP -0.2 0.18 -9999 0 -0.35 294 294
Insulin Receptor/Insulin/IRS1/Shp2 -0.053 0.14 -9999 0 -0.42 69 69
HRAS 0.015 0.012 -9999 0 -10000 0 0
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.091 0.23 -9999 0 -0.72 57 57
FOXO3 -0.016 0.031 -9999 0 -10000 0 0
AKT1 -0.06 0.2 -9999 0 -0.52 40 40
INSR 0.018 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.046 0.036 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.011 0.064 -9999 0 -0.72 4 4
SORBS1 -0.39 0.37 -9999 0 -0.72 294 294
CRK 0.015 0.032 -9999 0 -0.72 1 1
PTPN1 0.046 0.035 -9999 0 -10000 0 0
CAV1 -0.33 0.25 -9999 0 -0.46 394 394
CBL/APS/CAP/Crk-II/C3G -0.22 0.19 -9999 0 -0.39 294 294
Insulin Receptor/Insulin/IRS1/NCK2 -0.053 0.14 -9999 0 -0.42 69 69
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.083 0.16 -9999 0 -0.38 114 114
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.017 0.098 -9999 0 -10000 0 0
RPS6KB1 -0.046 0.19 -9999 0 -0.54 27 27
PARD6A 0.015 0.016 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.002 0.012 -9999 0 -10000 0 0
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.093 0.16 -9999 0 -0.57 25 25
HRAS/GTP -0.04 0.1 -9999 0 -0.36 4 4
Insulin Receptor 0.018 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.047 0.13 -9999 0 -0.38 69 69
PRKCI -0.02 0.058 -9999 0 -0.63 2 2
Insulin Receptor/Insulin/GRB14/PDK1 -0.11 0.19 -9999 0 -0.56 42 42
SHC1 0.016 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.002 0.013 -9999 0 -10000 0 0
PI3K -0.084 0.17 -9999 0 -0.39 114 114
NCK2 0.016 0.01 -9999 0 -10000 0 0
RHOQ 0.015 0.032 -9999 0 -0.72 1 1
mol:H2O2 -0.001 0.004 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.007 -9999 0 -10000 0 0
AKT2 -0.06 0.2 -9999 0 -0.53 38 38
PRKCZ -0.026 0.059 -9999 0 -0.64 2 2
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.014 0.14 -9999 0 -0.37 69 69
F2RL2 -0.007 0.075 -9999 0 -0.72 3 3
TRIP10 0.015 0.032 -9999 0 -0.72 1 1
Insulin Receptor/Insulin/Shc 0.001 0.005 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst -0.002 0.029 -9999 0 -0.47 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.004 0.015 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.23 0.21 -9999 0 -0.42 294 294
TC10/GDP -0.001 0.024 -9999 0 -0.55 1 1
Insulin Receptor/Insulin/SHC/GRB10 -0.002 0.037 -9999 0 -0.42 4 4
INPP5D -0.025 0.14 -9999 0 -0.4 69 69
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.01 0.016 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 -0.08 0.25 -9999 0 -0.72 69 69
p62DOK/RasGAP 0.002 0.013 -9999 0 -10000 0 0
INS 0.018 0.002 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.025 0.14 -9999 0 -0.4 69 69
GRB2 0.013 0.022 -9999 0 -10000 0 0
EIF4EBP1 -0.05 0.19 -9999 0 -0.47 41 41
PTPRA 0.018 0.002 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
TC10/GTP/CIP4 -0.002 0.029 -9999 0 -0.47 2 2
PDPK1 0.016 0.007 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.007 0.11 -9999 0 -0.28 69 69
Insulin Receptor/Insulin/IRS1 -0.055 0.14 -9999 0 -0.43 69 69
Insulin Receptor/Insulin/IRS3 0.001 0.003 -9999 0 -10000 0 0
Par3/Par6 0.007 0.047 -9999 0 -0.39 5 5
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.002 0.09 -10000 0 -0.42 8 8
epithelial cell differentiation 0.024 0.084 -10000 0 -0.56 1 1
ITCH 0.025 0.02 -10000 0 -10000 0 0
WWP1 0.007 0.077 -10000 0 -10000 0 0
FYN 0.013 0.045 -10000 0 -0.72 2 2
EGFR -0.37 0.37 -10000 0 -0.72 274 274
PRL 0.016 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.012 0.14 -10000 0 -0.41 10 10
PTPRZ1 -0.5 0.34 -10000 0 -0.72 370 370
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.12 -10000 0 -0.41 24 24
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.04 0.16 -10000 0 -0.43 70 70
ADAM17 0.024 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.001 0.097 -10000 0 -0.46 4 4
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.005 0.087 -10000 0 -0.41 6 6
NCOR1 0.015 0.032 -10000 0 -0.72 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.066 0.14 -10000 0 -0.41 67 67
GRIN2B -0.028 0.16 -10000 0 -0.38 79 79
ErbB4/ErbB2/betacellulin -0.034 0.1 -10000 0 -0.42 26 26
STAT1 -0.011 0.06 -10000 0 -10000 0 0
HBEGF 0.01 0.064 -10000 0 -0.72 4 4
PRLR -0.028 0.078 -10000 0 -0.72 1 1
E4ICDs/ETO2 -0.056 0.19 -10000 0 -0.5 73 73
axon guidance 0.11 0.12 -10000 0 -10000 0 0
NEDD4 0.017 0.073 -10000 0 -0.7 5 5
Prolactin receptor/Prolactin receptor/Prolactin -0.022 0.041 -10000 0 -0.54 1 1
CBFA2T3 -0.086 0.25 -10000 0 -0.72 72 72
ErbB4/ErbB2/HBEGF -0.019 0.061 -10000 0 -0.4 5 5
MAPK3 0.002 0.14 -10000 0 -0.43 11 11
STAT1 (dimer) 0.006 0.095 -10000 0 -0.4 4 4
MAPK1 0.002 0.14 -10000 0 -0.42 13 13
JAK2 0.015 0.033 -10000 0 -0.72 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.038 0.16 -10000 0 -0.41 69 69
NRG1 -0.039 0.19 -10000 0 -0.55 67 67
NRG3 0.009 0.052 -10000 0 -0.72 2 2
NRG2 -0.48 0.35 -10000 0 -0.72 355 355
NRG4 0.014 0.017 -10000 0 -10000 0 0
heart development 0.11 0.12 -10000 0 -10000 0 0
neural crest cell migration -0.037 0.16 -10000 0 -0.4 69 69
ERBB2 0.021 0.044 -10000 0 -0.53 1 1
WWOX/E4ICDs 0.007 0.084 -10000 0 -0.4 4 4
SHC1 0.016 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.23 0.18 -10000 0 -0.4 278 278
apoptosis 0.017 0.066 0.36 6 -10000 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.31 0.22 -10000 0 -0.45 356 356
ErbB4/ErbB2/epiregulin -0.013 0.065 -10000 0 -0.42 4 4
ErbB4/ErbB4/betacellulin/betacellulin -0.016 0.13 -10000 0 -0.45 28 28
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.002 0.086 -10000 0 -0.44 5 5
MDM2 0.008 0.084 -10000 0 -0.4 4 4
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.061 0.14 -10000 0 -0.41 67 67
STAT5A 0.11 0.11 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.26 0.25 -10000 0 -0.46 287 287
DLG4 0.016 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.062 -10000 0 -0.38 6 6
STAT5A (dimer) 0.031 0.097 -10000 0 -0.61 1 1
MAP3K7IP2 0.015 0.032 -10000 0 -0.72 1 1
STAT5B (dimer) 0.11 0.1 -10000 0 -10000 0 0
LRIG1 -0.02 0.16 -10000 0 -0.72 26 26
EREG -0.002 0.065 -10000 0 -0.72 2 2
BTC -0.019 0.15 -10000 0 -0.72 24 24
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.11 0.12 -10000 0 -10000 0 0
ERBB4 -0.001 0.097 -10000 0 -0.47 4 4
STAT5B 0.016 0.007 -10000 0 -10000 0 0
YAP1 -0.011 0.058 -10000 0 -0.63 4 4
GRB2 0.013 0.022 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.016 0.054 -10000 0 -0.46 2 2
glial cell differentiation 0.024 0.061 0.38 6 -10000 0 6
WWOX 0.009 0.033 -10000 0 -10000 0 0
cell proliferation 0.021 0.16 -10000 0 -0.47 13 13
Visual signal transduction: Rods

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:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0.004 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0.009 0.039 -9999 0 -0.47 2 2
PDE6G/GNAT1/GTP 0.001 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.016 0.007 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.16 0.18 -9999 0 -0.36 239 239
mol:Na + -0.15 0.18 -9999 0 -0.57 11 11
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.018 0.12 -9999 0 -0.47 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.16 0.18 -9999 0 -0.6 11 11
CNGB1 0.016 0 -9999 0 -10000 0 0
RDH5 -0.58 0.29 -9999 0 -0.72 431 431
SAG -0.013 0.074 -9999 0 -0.72 2 2
mol:Ca2+ -0.11 0.2 -9999 0 -0.65 7 7
Na + (4 Units) -0.14 0.16 -9999 0 -0.63 7 7
RGS9 -0.029 0.18 -9999 0 -0.72 32 32
GNB1/GNGT1 -0.019 0.034 -9999 0 -10000 0 0
GNAT1/GDP -0.013 0.11 -9999 0 -0.4 35 35
GUCY2D 0.016 0 -9999 0 -10000 0 0
GNGT1 -0.023 0.069 -9999 0 -10000 0 0
GUCY2F 0.012 0.047 -9999 0 -0.72 2 2
GNB5 0.015 0.032 -9999 0 -0.72 1 1
mol:GMP (4 units) 0.028 0.071 -9999 0 -0.39 15 15
mol:11-cis-retinal -0.58 0.29 -9999 0 -0.72 431 431
mol:cGMP -0.01 0.074 -9999 0 -0.44 14 14
GNB1 0.016 0.01 -9999 0 -10000 0 0
Rhodopsin -0.44 0.21 -9999 0 -0.54 431 431
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.31 0.36 -9999 0 -0.72 230 230
Metarhodopsin II 0 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.01 0.071 -9999 0 -0.44 13 13
RGS9BP -0.015 0.076 -9999 0 -0.72 2 2
Metarhodopsin II/Transducin 0.029 0.005 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.01 0.073 -9999 0 -0.45 13 13
PDE6A/B -0.016 0.09 -9999 0 -0.54 15 15
mol:Pi -0.018 0.12 -9999 0 -0.47 35 35
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.019 0.033 -9999 0 -10000 0 0
PDE6B -0.006 0.12 -9999 0 -0.72 15 15
PDE6A 0.016 0.01 -9999 0 -10000 0 0
PDE6G 0.015 0.012 -9999 0 -10000 0 0
RHO 0.016 0 -9999 0 -10000 0 0
PDE6 -0.02 0.12 -9999 0 -0.39 48 48
GUCA1A 0.002 0.1 -9999 0 -0.72 10 10
GC2/GCAP Family -0.011 0.08 -9999 0 -0.47 14 14
GUCA1C 0.011 0.057 -9999 0 -0.72 3 3
GUCA1B 0.015 0.033 -9999 0 -0.72 1 1
EPHB forward signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.003 0.028 -10000 0 -0.47 1 1
cell-cell adhesion 0.12 0.16 0.45 21 -10000 0 21
Ephrin B/EPHB2/RasGAP 0.001 0.053 -10000 0 -0.38 8 8
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.001 0.03 -10000 0 -0.47 2 2
Ephrin B1/EPHB1 -0.17 0.23 -10000 0 -0.47 196 196
HRAS/GDP -0.11 0.16 -10000 0 -0.52 15 15
Ephrin B/EPHB1/GRB7 -0.14 0.2 -10000 0 -0.4 197 197
Endophilin/SYNJ1 0.038 0.052 -10000 0 -0.36 8 8
KRAS 0.013 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.14 0.2 -10000 0 -0.39 197 197
endothelial cell migration -0.041 0.13 -10000 0 -0.4 57 57
GRB2 0.013 0.022 -10000 0 -10000 0 0
GRB7 0 0.048 -10000 0 -10000 0 0
PAK1 0.053 0.059 -10000 0 -0.38 8 8
HRAS 0.015 0.012 -10000 0 -10000 0 0
RRAS 0.038 0.052 -10000 0 -0.36 8 8
DNM1 0.016 0.007 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.11 0.21 -10000 0 -0.37 198 198
lamellipodium assembly -0.12 0.16 -10000 0 -0.45 21 21
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.079 0.18 -10000 0 -0.3 197 197
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
EPHB2 0.006 0.04 -10000 0 -10000 0 0
EPHB3 0.014 0.017 -10000 0 -10000 0 0
EPHB1 -0.26 0.36 -10000 0 -0.72 196 196
EPHB4 0.011 0.039 -10000 0 -0.72 1 1
mol:GDP -0.099 0.14 -10000 0 -0.62 10 10
Ephrin B/EPHB2 -0.001 0.052 -10000 0 -0.39 8 8
Ephrin B/EPHB3 -0.005 0.048 -10000 0 -0.39 8 8
JNK cascade -0.11 0.21 -10000 0 -0.38 196 196
Ephrin B/EPHB1 -0.15 0.2 -10000 0 -0.4 197 197
RAP1/GDP -0.082 0.12 -10000 0 -0.52 10 10
EFNB2 0.008 0.078 -10000 0 -0.72 6 6
EFNB3 0.016 0 -10000 0 -10000 0 0
EFNB1 0.013 0.045 -10000 0 -0.72 2 2
Ephrin B2/EPHB1-2 -0.16 0.22 -10000 0 -0.43 197 197
RAP1B 0.016 0.01 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.11 0.16 -10000 0 -0.62 9 9
Rap1/GTP -0.11 0.15 -10000 0 -0.47 16 16
axon guidance 0.003 0.028 -10000 0 -0.47 1 1
MAPK3 -0.052 0.16 -10000 0 -0.66 7 7
MAPK1 -0.052 0.16 -10000 0 -0.66 7 7
Rac1/GDP -0.053 0.16 -10000 0 -0.55 10 10
actin cytoskeleton reorganization -0.087 0.12 -10000 0 -0.46 9 9
CDC42/GDP -0.053 0.16 -10000 0 -0.55 10 10
PI3K -0.042 0.13 -10000 0 -0.4 57 57
EFNA5 0.014 0.034 -10000 0 -0.72 1 1
Ephrin B2/EPHB4 -0.005 0.055 -10000 0 -0.47 7 7
Ephrin B/EPHB2/Intersectin/N-WASP 0.041 0.043 -10000 0 -0.29 9 9
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.15 -10000 0 -0.57 8 8
PTK2 0.038 0.051 -10000 0 -10000 0 0
MAP4K4 -0.11 0.21 -10000 0 -0.38 196 196
SRC 0.016 0.007 -10000 0 -10000 0 0
KALRN 0.016 0 -10000 0 -10000 0 0
Intersectin/N-WASP -0.001 0.023 -10000 0 -0.54 1 1
neuron projection morphogenesis -0.03 0.16 -10000 0 -0.46 9 9
MAP2K1 -0.065 0.17 -10000 0 -0.51 13 13
WASL 0.015 0.032 -10000 0 -0.72 1 1
Ephrin B1/EPHB1-2/NCK1 -0.15 0.21 -10000 0 -0.42 196 196
cell migration -0.068 0.18 -10000 0 -0.52 13 13
NRAS 0.014 0.019 -10000 0 -10000 0 0
SYNJ1 0.038 0.052 -10000 0 -0.36 8 8
PXN 0.016 0 -10000 0 -10000 0 0
TF 0.032 0.089 -10000 0 -0.35 27 27
HRAS/GTP -0.12 0.17 -10000 0 -0.5 16 16
Ephrin B1/EPHB1-2 -0.15 0.21 -10000 0 -0.43 196 196
cell adhesion mediated by integrin -0.028 0.063 0.36 8 -10000 0 8
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.13 0.18 -10000 0 -0.36 197 197
RAC1-CDC42/GTP -0.11 0.15 -10000 0 -0.47 15 15
RASA1 0.015 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.082 0.12 -10000 0 -0.52 10 10
ruffle organization -0.07 0.19 -10000 0 -0.45 21 21
NCK1 0.016 0 -10000 0 -10000 0 0
receptor internalization 0.047 0.05 -10000 0 -0.34 8 8
Ephrin B/EPHB2/KALRN 0 0.052 -10000 0 -0.38 8 8
ROCK1 0.03 0.029 -10000 0 -0.42 2 2
RAS family/GDP -0.073 0.1 -10000 0 -0.47 8 8
Rac1/GTP -0.12 0.16 -10000 0 -0.48 21 21
Ephrin B/EPHB1/Src/Paxillin -0.083 0.18 -10000 0 -0.3 197 197
Presenilin action in Notch and Wnt signaling

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.002 0.01 -10000 0 -10000 0 0
HDAC1 0.006 0.014 -10000 0 -10000 0 0
AES 0.016 0.003 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 0.012 0.055 -10000 0 -0.72 3 3
LRP6/FZD1 -0.001 0.024 -10000 0 -0.54 1 1
TLE1 -0.009 0.13 -10000 0 -0.72 18 18
AP1 -0.26 0.2 -10000 0 -0.38 375 375
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.015 0.012 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.015 0.093 -10000 0 -0.58 2 2
NICD/RBPSUH 0.002 0.009 -10000 0 -10000 0 0
WIF1 -0.53 0.32 -10000 0 -0.72 394 394
NOTCH1 0.002 0.008 -10000 0 -10000 0 0
PSENEN 0.014 0.019 -10000 0 -10000 0 0
KREMEN2 -0.078 0.081 -10000 0 -10000 0 0
DKK1 -0.075 0.21 -10000 0 -0.72 46 46
beta catenin/beta TrCP1 -0.004 0.053 -10000 0 -0.48 4 4
APH1B 0.015 0.033 -10000 0 -0.72 1 1
APH1A 0.009 0.033 -10000 0 -10000 0 0
AXIN1 0.006 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.027 0.073 0.3 1 -0.3 18 19
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.51 0.34 -10000 0 -0.72 375 375
JUN -0.12 0.29 -10000 0 -0.72 97 97
MAP3K7 0.015 0.009 -10000 0 -10000 0 0
CTNNB1 -0.015 0.055 -10000 0 -0.51 4 4
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.04 0.068 -10000 0 -0.5 5 5
HNF1A 0.014 0.014 -10000 0 -10000 0 0
CTBP1 0.015 0.008 -10000 0 -10000 0 0
MYC -0.052 0.34 -10000 0 -1.5 28 28
NKD1 0.014 0.019 -10000 0 -10000 0 0
FZD1 0.015 0.032 -10000 0 -0.72 1 1
NOTCH1 precursor/Deltex homolog 1 0 0.03 -10000 0 -0.38 3 3
apoptosis -0.26 0.2 -10000 0 -0.38 375 375
Delta 1/NOTCHprecursor 0.002 0.009 -10000 0 -10000 0 0
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.022 0.027 -10000 0 -10000 0 0
Gamma Secretase 0.004 0.027 -10000 0 -0.38 1 1
APC 0.006 0.006 -10000 0 -10000 0 0
DVL1 -0.041 0.025 -10000 0 -10000 0 0
CSNK2A1 0.016 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0.015 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.027 0.16 -10000 0 -0.5 46 46
LRP6 0.015 0.012 -10000 0 -10000 0 0
CSNK1A1 0.016 0.004 -10000 0 -10000 0 0
NLK 0.029 0.015 -10000 0 -10000 0 0
CCND1 -0.019 0.22 -10000 0 -1.5 12 12
WNT1 0.016 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.006 0.044 -10000 0 -0.33 1 1
DKK2 0.007 0.074 -10000 0 -0.72 5 5
NOTCH1 precursor/DVL1 -0.008 0.012 -10000 0 -10000 0 0
GSK3B 0.015 0.01 -10000 0 -10000 0 0
FRAT1 0.015 0.01 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0 0.03 -10000 0 -0.39 1 1
PPP2R5D -0.021 0.016 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.31 0.18 -10000 0 -0.41 394 394
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.018 0.033 -10000 0 -0.73 1 1
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.007 0.06 -10000 0 -0.69 3 3
CDKN2C -0.045 0.2 -10000 0 -0.7 46 46
CDKN2A -0.008 0.067 -10000 0 -10000 0 0
CCND2 0.016 0.06 0.2 44 -0.17 7 51
RB1 -0.019 0.064 0.18 3 -0.22 44 47
CDK4 0.022 0.068 0.23 47 -10000 0 47
CDK6 0.018 0.068 0.22 44 -0.26 4 48
G1/S progression 0.003 0.069 0.22 44 -0.18 3 47
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.053 0.16 -10000 0 -0.54 52 52
CRKL 0.018 0.1 -10000 0 -0.4 1 1
mol:PIP3 -0.014 0.1 0.62 13 -10000 0 13
AKT1 0.007 0.068 0.42 13 -10000 0 13
PTK2B 0.016 0 -10000 0 -10000 0 0
RAPGEF1 0.027 0.098 -10000 0 -0.37 1 1
RANBP10 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.044 0.14 -10000 0 -0.46 52 52
MAP3K5 0.013 0.14 -10000 0 -0.38 35 35
HGF/MET/CIN85/CBL/ENDOPHILINS -0.04 0.12 -10000 0 -0.41 53 53
AP1 -0.42 0.32 -10000 0 -0.6 376 376
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
apoptosis -0.54 0.37 -10000 0 -0.76 376 376
STAT3 (dimer) 0.023 0.097 -10000 0 -0.27 52 52
GAB1/CRKL/SHP2/PI3K -0.054 0.12 -10000 0 -0.59 7 7
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.026 0.099 -10000 0 -0.35 2 2
PTPN11 0.016 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.007 -10000 0 -10000 0 0
PTEN -0.002 0.11 -10000 0 -0.72 13 13
ELK1 -0.022 0.076 -10000 0 -0.25 52 52
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.017 0.052 -10000 0 -10000 0 0
PAK1 0.005 0.067 0.39 13 -10000 0 13
HGF/MET/RANBP10 -0.045 0.14 -10000 0 -0.46 52 52
HRAS -0.022 0.22 -10000 0 -0.68 52 52
DOCK1 0.024 0.1 -10000 0 -0.35 5 5
GAB1 0.008 0.11 -10000 0 -0.31 53 53
CRK 0.017 0.1 -10000 0 -0.38 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.061 0.19 -10000 0 -0.64 52 52
JUN -0.12 0.29 -10000 0 -0.72 97 97
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.032 0.098 -10000 0 -0.33 52 52
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
cell morphogenesis 0.021 0.15 -10000 0 -0.57 7 7
GRB2/SHC 0.007 0.094 -10000 0 -0.28 52 52
FOS -0.51 0.34 -10000 0 -0.72 375 375
GLMN 0 0.002 -10000 0 -10000 0 0
cell motility -0.022 0.076 -10000 0 -0.25 52 52
HGF/MET/MUC20 -0.046 0.14 -10000 0 -0.47 52 52
cell migration 0.007 0.093 -10000 0 -0.27 52 52
GRB2 0.013 0.022 -10000 0 -10000 0 0
CBL 0.016 0 -10000 0 -10000 0 0
MET/RANBP10 -0.053 0.16 -10000 0 -0.54 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.1 -10000 0 -0.29 52 52
MET/MUC20 -0.054 0.16 -10000 0 -0.55 52 52
RAP1B 0.035 0.093 -10000 0 -0.34 1 1
RAP1A 0.035 0.093 -10000 0 -0.34 1 1
HGF/MET/RANBP9 -0.044 0.14 -10000 0 -0.46 52 52
RAF1 -0.01 0.2 -10000 0 -0.63 52 52
STAT3 0.023 0.098 -10000 0 -0.27 52 52
cell proliferation 0.023 0.14 -10000 0 -0.41 52 52
RPS6KB1 0.005 0.04 -10000 0 -10000 0 0
MAPK3 -0.027 0.069 -10000 0 -10000 0 0
MAPK1 -0.027 0.069 -10000 0 -10000 0 0
RANBP9 0.016 0.007 -10000 0 -10000 0 0
MAPK8 0.027 0.12 -10000 0 -0.39 14 14
SRC 0.025 0.095 -10000 0 -0.29 1 1
PI3K -0.034 0.16 -10000 0 -0.35 97 97
MET/Glomulin -0.034 0.15 -10000 0 -0.49 52 52
SOS1 0.016 0 -10000 0 -10000 0 0
MAP2K1 0.002 0.19 -10000 0 -0.57 52 52
MET -0.057 0.22 -10000 0 -0.72 52 52
MAP4K1 0.03 0.098 -10000 0 -0.37 1 1
PTK2 0.015 0.014 -10000 0 -10000 0 0
MAP2K2 0.002 0.19 -10000 0 -0.57 52 52
BAD 0.016 0.062 0.4 13 -10000 0 13
MAP2K4 0.019 0.14 -10000 0 -0.52 9 9
SHP2/GRB2/SOS1/GAB1 -0.041 0.13 -10000 0 -0.42 52 52
INPPL1 0.015 0.012 -10000 0 -10000 0 0
PXN 0.016 0 -10000 0 -10000 0 0
SH3KBP1 0.015 0.033 -10000 0 -0.72 1 1
HGS -0.003 0.097 -10000 0 -0.3 52 52
PLCgamma1/PKC 0 0.004 -10000 0 -10000 0 0
HGF 0.016 0.01 -10000 0 -10000 0 0
RASA1 0.015 0.012 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
PTPRJ 0.014 0.019 -10000 0 -10000 0 0
NCK/PLCgamma1 0.01 0.092 -10000 0 -0.27 52 52
PDPK1 -0.003 0.078 0.48 13 -10000 0 13
HGF/MET/SHIP -0.046 0.14 -10000 0 -0.47 52 52
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.059 0.093 -10000 0 -0.31 5 5
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.55 161 161
NT3 (dimer)/TRKB -0.42 0.39 -10000 0 -0.67 331 331
SHC/Grb2/SOS1/GAB1/PI3K 0.014 0.1 -10000 0 -0.29 53 53
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF 0.006 0.057 -10000 0 -0.72 2 2
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 0.014 0.019 -10000 0 -10000 0 0
NTRK2 -0.34 0.37 -10000 0 -0.72 254 254
NTRK3 -0.006 0.13 -10000 0 -0.72 16 16
NT-4/5 (dimer)/TRKB -0.3 0.32 -10000 0 -0.58 276 276
neuron apoptosis 0.18 0.23 0.54 126 -10000 0 126
SHC 2-3/Grb2 -0.2 0.26 -10000 0 -0.6 126 126
SHC1 0.016 0 -10000 0 -10000 0 0
SHC2 -0.2 0.28 -10000 0 -0.64 121 121
SHC3 -0.18 0.24 -10000 0 -0.55 124 124
STAT3 (dimer) 0.019 0.059 -10000 0 -0.36 12 12
NT3 (dimer)/TRKA -0.21 0.27 -10000 0 -0.52 216 216
RIN/GDP -0.002 0.099 -10000 0 -0.26 6 6
GIPC1 0.015 0.012 -10000 0 -10000 0 0
KRAS 0.013 0.024 -10000 0 -10000 0 0
DNAJA3 -0.091 0.18 -10000 0 -0.44 95 95
RIN/GTP -0.001 0.024 -10000 0 -0.55 1 1
CCND1 -0.001 0.15 -10000 0 -0.94 12 12
MAGED1 0.006 0.04 -10000 0 -10000 0 0
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0.012 0.026 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.002 0.011 -10000 0 -10000 0 0
GRB2 0.013 0.022 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.003 0.015 -10000 0 -10000 0 0
TRKA/NEDD4-2 -0.017 0.09 -10000 0 -0.54 15 15
ELMO1 0.016 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 -0.004 0.041 -10000 0 -0.47 4 4
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
DOCK1 0.011 0.064 -10000 0 -0.72 4 4
GAB2 0.015 0.016 -10000 0 -10000 0 0
RIT2 0.015 0.032 -10000 0 -0.72 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.011 0.039 -10000 0 -0.72 1 1
DNM1 0.016 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0.032 -10000 0 -0.72 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.088 0.18 -10000 0 -0.43 95 95
mol:GDP -0.017 0.14 -10000 0 -0.35 16 16
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.002 0.098 -10000 0 -0.24 11 11
TIAM1 0.015 0.012 -10000 0 -10000 0 0
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
BDNF (dimer)/TRKB -0.22 0.23 -10000 0 -0.46 256 256
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0.006 -10000 0 -10000 0 0
FRS2 family/SHP2 0.001 0.023 -10000 0 -0.46 1 1
SHC/GRB2/SOS1/GAB1 0.001 0.022 -10000 0 -0.41 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.2 0.33 -10000 0 -0.72 150 150
RAP1/GDP -0.036 0.057 -10000 0 -0.23 3 3
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) 0.006 0.057 -10000 0 -0.72 2 2
ubiquitin-dependent protein catabolic process -0.012 0.078 -10000 0 -0.47 15 15
Schwann cell development -0.044 0.037 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.003 0.025 -10000 0 -0.41 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.05 0.018 -10000 0 -10000 0 0
RAP1B 0.016 0.01 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.27 0.26 -10000 0 -0.45 316 316
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.07 0.075 -10000 0 -10000 0 0
STAT3 0.019 0.058 -10000 0 -0.36 12 12
axon guidance -0.26 0.25 -10000 0 -0.43 316 316
MAPK3 0.029 0.016 -10000 0 -10000 0 0
MAPK1 0.029 0.016 -10000 0 -10000 0 0
CDC42/GDP -0.002 0.098 -10000 0 -0.24 10 10
NTF3 -0.2 0.33 -10000 0 -0.72 150 150
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.001 0.009 -10000 0 -10000 0 0
PI3K -0.053 0.16 -10000 0 -0.54 52 52
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0.007 -10000 0 -10000 0 0
GAB1 0.014 0.034 -10000 0 -0.72 1 1
RASGRF1 -0.094 0.19 -10000 0 -0.45 97 97
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L -0.12 0.24 -10000 0 -0.47 161 161
RGS19 0.011 0.028 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.071 -10000 0 -10000 0 0
Rac1/GDP -0.002 0.098 -10000 0 -0.24 10 10
NGF (dimer)/TRKA/GRIT 0.003 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.054 0.19 -10000 0 -0.7 18 18
NGF (dimer)/TRKA/NEDD4-2 -0.012 0.078 -10000 0 -0.47 15 15
MAP2K1 0.048 0.022 -10000 0 -0.38 1 1
NGFR -0.12 0.28 -10000 0 -0.72 95 95
NGF (dimer)/TRKA/GIPC/GAIP 0.039 0.004 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.006 0.1 -10000 0 -0.3 52 52
FRS2 family/SHP2/GRB2/SOS1 0.003 0.024 -10000 0 -0.38 1 1
NRAS 0.014 0.019 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
PRKCI 0.013 0.023 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.042 0.047 -10000 0 -10000 0 0
RASA1 0.015 0.012 -10000 0 -10000 0 0
TRKA/c-Abl -0.001 0.009 -10000 0 -10000 0 0
SQSTM1 0.016 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.2 0.21 -10000 0 -0.41 256 256
NGF (dimer)/TRKA/p62/Atypical PKCs 0.003 0.013 -10000 0 -10000 0 0
MATK 0.011 0.03 -10000 0 -10000 0 0
NEDD4L -0.005 0.12 -10000 0 -0.72 15 15
RAS family/GDP -0.033 0.053 -10000 0 -0.22 1 1
NGF (dimer)/TRKA -0.098 0.2 -10000 0 -0.48 95 95
Rac1/GTP -0.073 0.1 -10000 0 -0.34 42 42
FRS2 family/SHP2/CRK family 0 0.028 -10000 0 -0.41 2 2
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.052 0.25 -10000 0 -0.55 101 101
IHH 0.01 0.047 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 -0.14 0.2 -10000 0 -0.43 172 172
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.14 0.2 0.42 172 -10000 0 172
SMO/beta Arrestin2 -0.001 0.16 -10000 0 -0.65 7 7
SMO -0.009 0.16 -10000 0 -0.7 7 7
AKT1 -0.013 0.16 -10000 0 -0.63 22 22
ARRB2 0.016 0 -10000 0 -10000 0 0
BOC -0.15 0.31 -10000 0 -0.72 118 118
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.009 0.16 -10000 0 -0.68 7 7
STIL 0.012 0.12 -10000 0 -0.43 6 6
DHH N/PTCH2 0 0 -10000 0 -10000 0 0
DHH N/PTCH1 0.002 0.12 -10000 0 -0.39 3 3
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
DHH 0.016 0 -10000 0 -10000 0 0
PTHLH -0.15 0.46 -10000 0 -1.1 101 101
determination of left/right symmetry -0.009 0.16 -10000 0 -0.68 7 7
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
skeletal system development -0.14 0.45 -10000 0 -1.1 101 101
IHH N/Hhip 0.023 0.023 -10000 0 -10000 0 0
DHH N/Hhip -0.001 0.007 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.009 0.16 -10000 0 -0.68 7 7
pancreas development 0.015 0.014 -10000 0 -10000 0 0
HHAT 0.006 0.074 -10000 0 -0.72 5 5
PI3K -0.053 0.16 -10000 0 -0.54 52 52
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.22 0.34 -10000 0 -0.72 169 169
somite specification -0.009 0.16 -10000 0 -0.68 7 7
SHH Np/Cholesterol/PTCH1 0.009 0.12 -10000 0 -0.4 5 5
SHH Np/Cholesterol/PTCH2 -0.005 0.041 -10000 0 -0.42 5 5
SHH Np/Cholesterol/Megalin -0.12 0.2 -10000 0 -0.43 150 150
SHH 0.022 0.057 -10000 0 -0.54 5 5
catabolic process -0.008 0.14 -10000 0 -0.4 6 6
SMO/Vitamin D3 0.006 0.14 -10000 0 -0.52 8 8
SHH Np/Cholesterol/Hhip -0.004 0.042 -10000 0 -0.42 5 5
LRP2 -0.19 0.33 -10000 0 -0.72 148 148
receptor-mediated endocytosis -0.12 0.17 -10000 0 -0.53 45 45
SHH Np/Cholesterol/BOC -0.099 0.18 -10000 0 -0.43 122 122
SHH Np/Cholesterol/CDO -0.007 0.057 -10000 0 -0.48 7 7
mesenchymal cell differentiation 0.004 0.041 0.42 5 -10000 0 5
mol:Vitamin D3 0.013 0.12 -10000 0 -0.38 8 8
IHH N/PTCH2 0.023 0.022 -10000 0 -10000 0 0
CDON 0.012 0.055 -10000 0 -0.72 3 3
IHH N/PTCH1 -0.005 0.14 -10000 0 -0.4 6 6
Megalin/LRPAP1 -0.15 0.24 -10000 0 -0.54 148 148
PTCH2 0.016 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.003 0.043 -10000 0 -0.43 5 5
PTCH1 -0.008 0.14 -10000 0 -0.4 6 6
HHIP 0.015 0.014 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.078 0.11 0.6 2 -10000 0 2
GNAI2 0.016 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.08 0.11 -10000 0 -0.62 2 2
negative regulation of cAMP metabolic process -0.067 0.14 -10000 0 -0.25 194 194
GNAZ 0.006 0.084 -10000 0 -0.72 7 7
GNAI3 0.016 0 -10000 0 -10000 0 0
GNA12 0.016 0 -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 -0.068 0.14 -10000 0 -0.25 194 194
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.25 0.35 -10000 0 -0.72 189 189
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0 0.013 -9999 0 -10000 0 0
VDR 0.013 0.046 -9999 0 -0.72 2 2
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.073 0.046 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.083 0.047 -9999 0 -0.36 2 2
MED1 0.006 0.039 -9999 0 -10000 0 0
mol:9cRA 0.008 0.004 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.034 0.16 -9999 0 -0.32 118 118
RXRs/NUR77 0.035 0.11 -9999 0 -0.4 30 30
RXRs/PPAR -0.19 0.16 -9999 0 -0.28 390 390
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.034 -9999 0 -0.55 2 2
RARs/VDR/DNA/Vit D3 -0.063 0.15 -9999 0 -0.39 86 86
RARA 0.015 0.016 -9999 0 -10000 0 0
NCOA1 0.015 0.032 -9999 0 -0.72 1 1
VDR/VDR/DNA 0.013 0.046 -9999 0 -0.72 2 2
RARs/RARs/DNA/9cRA -0.063 0.15 -9999 0 -0.4 85 85
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.023 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.033 0.16 -9999 0 -0.31 118 118
THRA -0.03 0.18 -9999 0 -0.72 33 33
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.034 -9999 0 -0.55 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.047 0.053 -9999 0 -0.4 6 6
NR1H4 0.016 0.01 -9999 0 -10000 0 0
RXRs/LXRs/DNA 0.078 0.055 -9999 0 -0.35 8 8
NR1H2 0.024 0.003 -9999 0 -10000 0 0
NR1H3 0.022 0.045 -9999 0 -0.71 2 2
RXRs/VDR/DNA/Vit D3 0.045 0.056 -9999 0 -0.37 8 8
NR4A1 -0.017 0.15 -9999 0 -0.72 24 24
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.048 0.031 -9999 0 -0.23 6 6
RXRG 0.015 0.079 -9999 0 -0.72 6 6
RXR alpha/CCPG 0.027 0.01 -9999 0 -10000 0 0
RXRA 0.024 0.003 -9999 0 -10000 0 0
RXRB 0.025 0.004 -9999 0 -10000 0 0
THRB 0.006 0.084 -9999 0 -0.72 7 7
PPARG -0.53 0.32 -9999 0 -0.72 390 390
PPARD 0.016 0.01 -9999 0 -10000 0 0
TNF 0.088 0.044 -9999 0 -10000 0 0
mol:Oxysterols 0.008 0.004 -9999 0 -10000 0 0
cholesterol transport 0.083 0.046 -9999 0 -0.36 2 2
PPARA 0.015 0.032 -9999 0 -0.72 1 1
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.1 0.27 -9999 0 -0.72 85 85
RXRs/NUR77/BCL2 -0.041 0.16 -9999 0 -0.3 131 131
SREBF1 0.087 0.045 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.048 0.053 -9999 0 -0.4 6 6
ABCA1 0.085 0.083 -9999 0 -1.1 2 2
RARs/THRs -0.089 0.17 -9999 0 -0.4 118 118
RXRs/FXR 0.056 0.049 -9999 0 -0.4 6 6
BCL2 -0.13 0.3 -9999 0 -0.72 107 107
Ceramide signaling pathway

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
SPHK2 -0.025 0.17 -10000 0 -0.54 51 51
MAP4K4 0.045 0.065 -10000 0 -10000 0 0
BAG4 0.011 0.03 -10000 0 -10000 0 0
PKC zeta/ceramide -0.03 0.073 0.16 36 -10000 0 36
NFKBIA 0.015 0.032 -10000 0 -0.72 1 1
BIRC3 -0.037 0.18 -10000 0 -0.72 34 34
BAX -0.003 0.039 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.028 0.024 -10000 0 -10000 0 0
BAD -0.018 0.076 0.19 36 -10000 0 36
SMPD1 0.033 0.026 -10000 0 -0.23 1 1
RB1 -0.019 0.077 0.19 35 -0.3 2 37
FADD/Caspase 8 0.052 0.066 -10000 0 -10000 0 0
MAP2K4 -0.019 0.093 0.19 34 -0.42 11 45
NSMAF 0.012 0.056 -10000 0 -0.72 3 3
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.072 -10000 0 -10000 0 0
EGF -0.24 0.35 -10000 0 -0.72 179 179
mol:ceramide -0.03 0.082 0.2 36 -0.12 154 190
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.033 0.19 -10000 0 -0.57 54 54
ASAH1 0.005 0.086 -10000 0 -0.72 7 7
negative regulation of cell cycle -0.02 0.077 0.19 35 -0.3 2 37
cell proliferation -0.17 0.16 -10000 0 -0.34 226 226
BID 0.031 0.052 -10000 0 -10000 0 0
MAP3K1 -0.024 0.085 0.19 35 -0.3 8 43
EIF2A -0.003 0.071 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 0.007 0.068 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.068 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.026 0.076 0.18 37 -0.17 5 42
FADD 0.039 0.069 -10000 0 -0.27 6 6
KSR1 -0.018 0.076 0.19 36 -0.18 1 37
MAPK8 -0.015 0.08 0.18 35 -0.27 11 46
PRKRA -0.018 0.076 0.19 36 -10000 0 36
PDGFA -0.055 0.22 -10000 0 -0.72 51 51
TRAF2 0.015 0.012 -10000 0 -10000 0 0
IGF1 -0.35 0.37 -10000 0 -0.72 264 264
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.03 0.081 0.19 36 -0.12 154 190
CTSD 0.001 0.047 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.17 0.19 -10000 0 -0.37 226 226
PRKCD 0.014 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 -0.033 0.19 -10000 0 -0.57 54 54
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0.037 -10000 0 -0.72 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.037 0.068 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.004 0.019 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.025 0.17 -10000 0 -0.54 51 51
MAP2K1 0.002 0.069 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS 0.026 0.087 0.18 93 -10000 0 93
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.003 0.014 -10000 0 -10000 0 0
EIF2AK2 -0.013 0.074 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0 0.037 -10000 0 -0.46 3 3
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.046 0.041 -10000 0 -10000 0 0
MAP2K2 0.002 0.069 -10000 0 -10000 0 0
SMPD3 0.035 0.03 -10000 0 -0.22 1 1
TNF 0.012 0.025 -10000 0 -10000 0 0
PKC zeta/PAR4 -0.002 0.026 -10000 0 -0.55 1 1
mol:PHOSPHOCHOLINE 0.098 0.14 0.26 215 -10000 0 215
NF kappa B1/RelA/I kappa B alpha 0 0.026 -10000 0 -0.39 2 2
AIFM1 0.026 0.087 0.2 68 -10000 0 68
BCL2 -0.13 0.3 -10000 0 -0.72 107 107
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.018 0.011 -10000 0 -10000 0 0
HSPA8 0.016 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.13 0.23 0.3 1 -0.52 124 125
AKT1 0.017 0.02 -10000 0 -10000 0 0
GSC -0.097 0.43 -10000 0 -1.5 46 46
NKX2-5 -0.004 0.058 -10000 0 -10000 0 0
muscle cell differentiation 0.034 0.11 0.43 27 -10000 0 27
SMAD2-3/SMAD4/SP1 0.026 0.094 -10000 0 -0.45 6 6
SMAD4 -0.013 0.082 -10000 0 -0.4 10 10
CBFB 0.016 0.01 -10000 0 -10000 0 0
SAP18 0.016 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.26 0.23 -10000 0 -0.46 305 305
SMAD3/SMAD4/VDR 0 0.065 -10000 0 -0.43 7 7
MYC -0.026 0.17 -10000 0 -0.73 28 28
CDKN2B 0.023 0.13 -10000 0 -1.5 3 3
AP1 -0.34 0.39 -10000 0 -0.52 376 376
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.065 0.039 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.016 0.11 -10000 0 -0.39 8 8
SP3 0.019 0.005 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 0.01 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.058 0.17 -10000 0 -0.55 49 49
GATA3 -0.068 0.19 -10000 0 -0.7 39 39
SKI/SIN3/HDAC complex/NCoR1 0.056 0.021 -10000 0 -10000 0 0
MEF2C/TIF2 -0.012 0.2 -10000 0 -0.73 32 32
endothelial cell migration -0.032 0.047 -10000 0 -10000 0 0
MAX 0.014 0.002 -10000 0 -10000 0 0
RBBP7 0.012 0.026 -10000 0 -10000 0 0
RBBP4 0.016 0.007 -10000 0 -10000 0 0
RUNX2 0.013 0.021 -10000 0 -10000 0 0
RUNX3 -0.044 0.2 -10000 0 -0.72 42 42
RUNX1 -0.006 0.12 -10000 0 -0.72 15 15
CTBP1 0.016 0.007 -10000 0 -10000 0 0
NR3C1 -0.05 0.21 -10000 0 -0.73 46 46
VDR 0.013 0.046 -10000 0 -0.72 2 2
CDKN1A 0.034 0.11 -10000 0 -1.4 2 2
KAT2B 0 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.02 0.1 -10000 0 -0.42 14 14
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.016 0.007 -10000 0 -10000 0 0
SERPINE1 0.029 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.013 0.066 -10000 0 -0.46 5 5
SMAD3/SMAD4/ATF3 -0.17 0.25 -10000 0 -0.52 174 174
SAP30 0.016 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.01 0.039 -10000 0 -0.42 1 1
JUN -0.34 0.38 -10000 0 -0.51 376 376
SMAD3/SMAD4/IRF7 -0.011 0.068 -10000 0 -0.49 4 4
TFE3 0.015 0.036 -10000 0 -10000 0 0
COL1A2 0.043 0.12 -10000 0 -1.1 3 3
mesenchymal cell differentiation 0.014 0.068 0.46 5 -10000 0 5
DLX1 0.006 0.04 -10000 0 -10000 0 0
TCF3 0.014 0.019 -10000 0 -10000 0 0
FOS -0.51 0.35 -10000 0 -0.74 375 375
SMAD3/SMAD4/Max -0.015 0.067 -10000 0 -0.46 5 5
Cbp/p300/SNIP1 0.004 0.026 -10000 0 -0.44 1 1
ZBTB17 0.014 0.005 -10000 0 -10000 0 0
LAMC1 -0.009 0.21 -10000 0 -0.75 37 37
TGIF2/HDAC complex/SMAD3/SMAD4 -0.014 0.067 -10000 0 -0.46 5 5
IRF7 0.018 0.023 -10000 0 -10000 0 0
ESR1 -0.19 0.3 -10000 0 -0.73 119 119
HNF4A 0.016 0 -10000 0 -10000 0 0
MEF2C -0.003 0.21 -10000 0 -0.76 34 34
SMAD2-3/SMAD4 -0.02 0.081 -10000 0 -0.44 8 8
Cbp/p300/Src-1 0.006 0.036 -10000 0 -0.44 2 2
IGHV3OR16-13 -0.011 0.032 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0.01 -10000 0 -10000 0 0
CREBBP 0.016 0.032 -10000 0 -0.7 1 1
SKIL -0.001 0.05 -10000 0 -10000 0 0
HDAC1 0.016 0.001 -10000 0 -10000 0 0
HDAC2 0.014 0.017 -10000 0 -10000 0 0
SNIP1 0.015 0.004 -10000 0 -10000 0 0
GCN5L2 0.018 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.02 0.1 -10000 0 -0.4 29 29
MSG1/HSC70 -0.31 0.27 -10000 0 -0.54 305 305
SMAD2 0.014 0.035 -10000 0 -10000 0 0
SMAD3 -0.003 0.058 -10000 0 -0.78 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.055 -10000 0 -0.35 3 3
SMAD2/SMAD2/SMAD4 0.012 0.041 -10000 0 -0.42 2 2
NCOR1 0.015 0.032 -10000 0 -0.72 1 1
NCOA2 0.015 0.014 -10000 0 -10000 0 0
NCOA1 0.015 0.032 -10000 0 -0.72 1 1
MYOD/E2A -0.003 0.027 -10000 0 -0.54 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.043 0.089 -10000 0 -0.41 6 6
IFNB1 0.027 0.072 -10000 0 -0.51 2 2
SMAD3/SMAD4/MEF2C -0.026 0.21 -10000 0 -0.76 34 34
CITED1 -0.41 0.36 -10000 0 -0.72 305 305
SMAD2-3/SMAD4/ARC105 -0.012 0.07 -10000 0 -0.45 5 5
RBL1 0.007 0.038 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.023 0.12 -10000 0 -0.44 8 8
RUNX1-3/PEBPB2 -0.048 0.15 -10000 0 -0.47 55 55
SMAD7 -0.18 0.24 -10000 0 -0.54 116 116
MYC/MIZ-1 -0.027 0.12 -10000 0 -0.55 28 28
SMAD3/SMAD4 0.03 0.075 0.28 19 -10000 0 19
IL10 -0.014 0.14 -10000 0 -0.46 40 40
PIASy/HDAC complex 0.014 0.016 -10000 0 -10000 0 0
PIAS3 0.017 0.003 -10000 0 -10000 0 0
CDK2 0.015 0.025 -10000 0 -10000 0 0
IL5 -0.014 0.14 -10000 0 -0.46 40 40
CDK4 0.016 0.018 -10000 0 -10000 0 0
PIAS4 0.014 0.016 -10000 0 -10000 0 0
ATF3 -0.22 0.34 -10000 0 -0.72 169 169
SMAD3/SMAD4/SP1 -0.006 0.073 -10000 0 -0.47 6 6
FOXG1 0.003 0.042 -10000 0 -10000 0 0
FOXO3 0.033 0.015 -10000 0 -10000 0 0
FOXO1 -0.044 0.2 -10000 0 -0.54 71 71
FOXO4 0.033 0.015 -10000 0 -10000 0 0
heart looping -0.003 0.21 -10000 0 -0.74 34 34
CEBPB 0.016 0.033 -10000 0 -0.72 1 1
SMAD3/SMAD4/DLX1 -0.015 0.072 -10000 0 -0.48 5 5
MYOD1 0.012 0.038 -10000 0 -0.72 1 1
SMAD3/SMAD4/HNF4 -0.013 0.066 -10000 0 -0.46 5 5
SMAD3/SMAD4/GATA3 -0.029 0.16 -10000 0 -0.52 41 41
SnoN/SIN3/HDAC complex/NCoR1 -0.001 0.05 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.045 0.15 -10000 0 -0.45 58 58
SMAD3/SMAD4/SP1-3 0.002 0.071 -10000 0 -0.46 6 6
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.026 0.014 -10000 0 -10000 0 0
SIN3B 0.014 0.016 -10000 0 -10000 0 0
SIN3A 0.016 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.014 0.13 -10000 0 -0.47 22 22
ITGB5 0.045 0.092 -10000 0 -0.68 5 5
TGIF/SIN3/HDAC complex/CtBP 0.059 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.079 0.19 -10000 0 -0.53 72 72
AR -0.082 0.25 -10000 0 -0.72 70 70
negative regulation of cell growth -0.04 0.12 -10000 0 -0.4 11 11
SMAD3/SMAD4/MYOD -0.015 0.069 -10000 0 -0.46 6 6
E2F5 -0.001 0.051 -10000 0 -10000 0 0
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.006 0.075 -10000 0 -0.38 7 7
SMAD2-3/SMAD4/FOXO1-3a-4 0.018 0.12 -10000 0 -0.37 14 14
TFDP1 0.012 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.34 0.4 -10000 0 -0.52 376 376
SMAD3/SMAD4/RUNX2 -0.014 0.068 -10000 0 -0.46 5 5
TGIF2 0.016 0.01 -10000 0 -10000 0 0
TGIF1 0.015 0.032 -10000 0 -0.72 1 1
ATF2 0.016 0 -10000 0 -10000 0 0
Syndecan-3-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
CTTN 0.009 0.034 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.25 0.18 -9999 0 -0.52 28 28
Syndecan-3/Neurocan -0.005 0.078 -9999 0 -0.66 7 7
POMC 0.012 0.038 -9999 0 -0.72 1 1
EGFR -0.37 0.37 -9999 0 -0.72 274 274
Syndecan-3/EGFR -0.21 0.21 -9999 0 -0.4 276 276
AGRP 0.016 0.01 -9999 0 -10000 0 0
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.014 0.019 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.015 0.033 -9999 0 -0.72 1 1
APH1A 0.009 0.033 -9999 0 -10000 0 0
NCAN 0.01 0.03 -9999 0 -10000 0 0
long-term memory -0.004 0.077 -9999 0 -0.56 9 9
Syndecan-3/IL8 0.002 0.085 -9999 0 -0.64 8 8
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin -0.004 0.017 -9999 0 -10000 0 0
FYN 0.013 0.045 -9999 0 -0.72 2 2
limb bud formation -0.009 0.079 -9999 0 -0.69 7 7
MC4R 0.015 0.012 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
PTN -0.51 0.34 -9999 0 -0.72 374 374
FGFR/FGF/Syndecan-3 -0.009 0.08 -9999 0 -0.7 7 7
neuron projection morphogenesis -0.24 0.17 -9999 0 -0.46 41 41
Syndecan-3/AgRP -0.008 0.076 -9999 0 -0.66 7 7
Syndecan-3/AgRP/MC4R -0.006 0.074 -9999 0 -0.64 7 7
Fyn/Cortactin -0.006 0.037 -9999 0 -0.54 2 2
SDC3 -0.009 0.081 -9999 0 -0.71 7 7
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.002 0.083 -9999 0 -0.63 8 8
IL8 -0.007 0.064 -9999 0 -0.72 1 1
Syndecan-3/Fyn/Cortactin -0.005 0.079 -9999 0 -0.57 9 9
Syndecan-3/CASK -0.009 0.077 -9999 0 -0.67 7 7
alpha-MSH/MC4R -0.003 0.026 -9999 0 -0.54 1 1
Gamma Secretase 0.004 0.027 -9999 0 -0.38 1 1
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.029 0.01 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.039 0.17 0.67 21 -0.51 1 22
IL27/IL27R/JAK1 -0.081 0.27 -10000 0 -1 28 28
TBX21 -0.058 0.24 -10000 0 -0.63 60 60
IL12B 0.013 0.025 -10000 0 -10000 0 0
IL12A 0.003 0.078 -10000 0 -0.55 10 10
IL6ST -0.018 0.14 -10000 0 -0.73 20 20
IL27RA/JAK1 -0.028 0.25 -10000 0 -1.2 20 20
IL27 -0.067 0.23 -10000 0 -0.73 58 58
TYK2 0.014 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.22 0.15 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.039 0.17 0.67 21 -0.51 1 22
T cell proliferation during immune response 0.039 0.17 0.67 21 -0.51 1 22
MAPKKK cascade -0.039 0.17 0.51 1 -0.67 21 22
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 -0.011 0.061 -10000 0 -10000 0 0
IL12RB1 0.017 0.001 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.046 0.21 -10000 0 -0.61 39 39
IL27/IL27R/JAK2/TYK2 -0.039 0.17 0.51 1 -0.68 21 22
positive regulation of T cell mediated cytotoxicity -0.039 0.17 0.51 1 -0.67 21 22
STAT1 (dimer) -0.074 0.31 0.49 25 -0.93 36 61
JAK2 0.011 0.034 -10000 0 -0.73 1 1
JAK1 0.013 0.045 -10000 0 -0.72 2 2
STAT2 (dimer) -0.03 0.16 0.44 1 -0.65 20 21
T cell proliferation -0.32 0.25 0.47 1 -0.44 390 391
IL12/IL12R/TYK2/JAK2 0.036 0.046 -10000 0 -10000 0 0
IL17A -0.22 0.15 -10000 0 -10000 0 0
mast cell activation 0.039 0.17 0.67 21 -0.51 1 22
IFNG 0.002 0.027 0.12 1 -0.081 20 21
T cell differentiation -0.004 0.007 0.034 1 -0.025 20 21
STAT3 (dimer) -0.03 0.16 0.44 1 -0.65 20 21
STAT5A (dimer) -0.031 0.17 0.44 1 -0.64 22 23
STAT4 (dimer) -0.035 0.17 0.44 1 -0.6 27 28
STAT4 0.005 0.086 -10000 0 -0.72 7 7
T cell activation -0.006 0.026 0.13 18 -10000 0 18
IL27R/JAK2/TYK2 -0.047 0.24 0.4 1 -1.1 23 24
GATA3 -0.096 0.37 -10000 0 -1.4 39 39
IL18 0.005 0.038 -10000 0 -0.55 1 1
positive regulation of mast cell cytokine production -0.029 0.16 0.44 1 -0.63 20 21
IL27/EBI3 -0.058 0.17 -10000 0 -0.55 58 58
IL27RA -0.052 0.26 0.44 1 -1.4 18 19
IL6 -0.52 0.32 -10000 0 -0.71 391 391
STAT5A 0.013 0.045 -10000 0 -0.72 2 2
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.019 0.11 0.5 18 -1.4 1 19
IL1B 0.006 0.062 -10000 0 -0.55 6 6
EBI3 0.012 0.013 -10000 0 -10000 0 0
TNF 0.012 0.017 -10000 0 -10000 0 0
TCGA08_rtk_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
PDGFRA -0.075 0.24 -10000 0 -0.72 65 65
HRAS 0.015 0.012 -10000 0 -10000 0 0
EGFR -0.37 0.37 -10000 0 -0.72 274 274
AKT 0.024 0.044 -10000 0 -0.23 3 3
FOXO3 0.016 0.007 -10000 0 -10000 0 0
AKT1 0.014 0.02 -10000 0 -10000 0 0
FOXO1 -0.083 0.25 -10000 0 -0.72 71 71
AKT3 0.014 0.017 -10000 0 -10000 0 0
FOXO4 0.016 0 -10000 0 -10000 0 0
MET -0.057 0.22 -10000 0 -0.72 52 52
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
PIK3CB 0.016 0.01 -10000 0 -10000 0 0
NRAS 0.014 0.019 -10000 0 -10000 0 0
PIK3CG 0.013 0.023 -10000 0 -10000 0 0
PIK3R3 0.006 0.039 -10000 0 -10000 0 0
PIK3R2 0.014 0.017 -10000 0 -10000 0 0
NF1 0.016 0 -10000 0 -10000 0 0
RAS -0.11 0.15 -10000 0 -0.38 87 87
ERBB2 -0.004 0.06 -10000 0 -0.72 1 1
proliferation/survival/translation -0.009 0.072 0.23 21 -0.23 1 22
PI3K -0.1 0.16 0.22 9 -0.32 134 143
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
KRAS 0.013 0.024 -10000 0 -10000 0 0
FOXO 0.028 0.04 -10000 0 -0.23 1 1
AKT2 0.016 0 -10000 0 -10000 0 0
PTEN -0.002 0.11 -10000 0 -0.72 13 13
S1P3 pathway

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
PDGFRB 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.15 0.22 -9999 0 -0.35 259 259
GNAO1 0.018 0.007 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.025 0.005 -9999 0 -10000 0 0
AKT1 -0.026 0.037 -9999 0 -10000 0 0
AKT3 0.005 0.079 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
GNAI2 0.018 0.007 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.002 0.001 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.19 0.33 -9999 0 -0.72 146 146
mol:Ca2+ -0.054 0.14 -9999 0 -0.23 194 194
MAPK3 -0.041 0.13 -9999 0 -0.62 2 2
MAPK1 -0.041 0.13 -9999 0 -0.62 2 2
JAK2 -0.038 0.13 -9999 0 -0.3 13 13
CXCR4 -0.046 0.13 -9999 0 -0.33 12 12
FLT1 0.019 0.012 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC -0.041 0.13 -9999 0 -0.49 3 3
S1P/S1P3/Gi -0.054 0.14 -9999 0 -0.24 194 194
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.075 0.1 -9999 0 -0.6 2 2
VEGFA -0.001 0.055 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.059 0.14 -9999 0 -0.24 194 194
VEGFR1 homodimer/VEGFA homodimer 0.041 0.022 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.02 0.039 -9999 0 -0.32 7 7
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.008 0.084 -9999 0 -0.72 7 7
G12/G13 -0.001 0.007 -9999 0 -10000 0 0
GNA14 -0.009 0.095 -9999 0 -0.72 7 7
GNA15 0.013 0.021 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
GNA11 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.075 0.1 -9999 0 -0.6 2 2
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.046 0.11 -9999 0 -0.47 20 20
EPHB2 0.006 0.04 -9999 0 -10000 0 0
Syndecan-2/TACI 0.012 0.093 -9999 0 -0.46 20 20
LAMA1 0.016 0.01 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.15 0.21 -9999 0 -0.42 195 195
HRAS 0.015 0.012 -9999 0 -10000 0 0
Syndecan-2/CASK -0.018 0.089 -9999 0 -0.47 20 20
ITGA5 0.016 0.007 -9999 0 -10000 0 0
BAX 0.033 0.087 -9999 0 -10000 0 0
EPB41 0.016 0.007 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.017 0.081 -9999 0 -0.42 21 21
LAMA3 -0.23 0.35 -9999 0 -0.72 176 176
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.46 0.36 -9999 0 -0.72 338 338
Syndecan-2/MMP2 0.008 0.12 -9999 0 -0.54 21 21
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.017 0.095 -9999 0 -0.54 17 17
dendrite morphogenesis 0.015 0.094 -9999 0 -0.45 20 20
Syndecan-2/GM-CSF 0.014 0.095 -9999 0 -0.46 20 20
determination of left/right symmetry 0.003 0.11 -9999 0 -0.54 20 20
Syndecan-2/PKC delta 0.012 0.094 -9999 0 -0.46 20 20
GNB2L1 0.016 0 -9999 0 -10000 0 0
MAPK3 0.021 0.088 -9999 0 -0.41 20 20
MAPK1 0.021 0.088 -9999 0 -0.41 20 20
Syndecan-2/RACK1 -0.015 0.075 -9999 0 -0.39 20 20
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.003 0.11 -9999 0 -0.54 20 20
ITGA2 -0.008 0.13 -9999 0 -0.72 17 17
MAPK8 0.024 0.096 -9999 0 -0.45 21 21
Syndecan-2/alpha2/beta1 Integrin -0.026 0.11 -9999 0 -0.43 33 33
Syndecan-2/Kininogen 0.012 0.093 -9999 0 -0.46 20 20
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.031 0.078 -9999 0 -0.36 20 20
Syndecan-2/CASK/Protein 4.1 -0.016 0.08 -9999 0 -0.42 20 20
extracellular matrix organization 0.012 0.093 -9999 0 -0.45 20 20
actin cytoskeleton reorganization 0.046 0.11 -9999 0 -0.46 20 20
Syndecan-2/Caveolin-2/Ras -0.28 0.22 -9999 0 -0.44 338 338
Syndecan-2/Laminin alpha3 -0.15 0.25 -9999 0 -0.48 189 189
Syndecan-2/RasGAP -0.013 0.071 -9999 0 -0.36 20 20
alpha5/beta1 Integrin 0 0.003 -9999 0 -10000 0 0
PRKCD 0.014 0.017 -9999 0 -10000 0 0
Syndecan-2 dimer 0.015 0.095 -9999 0 -0.46 20 20
GO:0007205 0.004 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.077 -9999 0 -0.35 20 20
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.015 0.032 -9999 0 -0.72 1 1
TNFRSF13B 0.016 0.01 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.017 0.095 -9999 0 -0.54 17 17
Syndecan-2/Synbindin 0.012 0.093 -9999 0 -0.46 20 20
TGFB1 0.016 0.01 -9999 0 -10000 0 0
CASP3 0.023 0.086 -9999 0 -0.41 20 20
FN1 -0.098 0.075 -9999 0 -10000 0 0
Syndecan-2/IL8 0.017 0.099 -9999 0 -0.46 21 21
SDC2 0.003 0.11 -9999 0 -0.54 20 20
KNG1 0.016 0.007 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.012 0.093 -9999 0 -0.46 20 20
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 0.01 0.031 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.012 0.093 -9999 0 -0.46 20 20
Syndecan-2/Syntenin/PI-4-5-P2 -0.017 0.082 -9999 0 -0.42 21 21
Syndecan-2/Ezrin -0.016 0.08 -9999 0 -0.42 20 20
PRKACA 0.024 0.086 -9999 0 -0.41 20 20
angiogenesis 0.017 0.099 -9999 0 -0.46 21 21
MMP2 0.009 0.072 -9999 0 -0.72 5 5
IL8 -0.007 0.064 -9999 0 -0.72 1 1
calcineurin-NFAT signaling pathway 0.012 0.093 -9999 0 -0.45 20 20
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.003 0.037 -9999 0 -0.37 4 4
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.026 -9999 0 -0.31 1 1
AP1 -0.33 0.25 -9999 0 -0.47 378 378
mol:PIP3 -0.21 0.2 -9999 0 -0.38 292 292
AKT1 0.028 0.1 -9999 0 -0.39 5 5
PTK2B 0.024 0.023 -9999 0 -0.2 5 5
RHOA 0.027 0.025 -9999 0 -0.21 2 2
PIK3CB 0.015 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0.032 0.028 -9999 0 -0.37 1 1
MAGI3 0.003 0.066 -9999 0 -0.72 3 3
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis 0.018 0.027 -9999 0 -0.25 5 5
HRAS/GDP -0.001 0.007 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.037 0.04 -9999 0 -0.35 4 4
NF kappa B1 p50/RelA -0.003 0.024 -9999 0 -0.3 1 1
endothelial cell migration 0.017 0.081 -9999 0 -0.81 5 5
ADCY4 -0.038 0.12 -9999 0 -0.4 11 11
ADCY5 -0.037 0.12 -9999 0 -0.42 8 8
ADCY6 -0.036 0.12 -9999 0 -0.45 7 7
ADCY7 -0.036 0.12 -9999 0 -0.42 8 8
ADCY1 -0.036 0.12 -9999 0 -0.45 7 7
ADCY2 -0.039 0.12 -9999 0 -0.41 12 12
ADCY3 -0.036 0.12 -9999 0 -0.42 8 8
ADCY8 -0.036 0.12 -9999 0 -0.42 8 8
ADCY9 -0.036 0.12 -9999 0 -0.42 8 8
GSK3B 0.032 0.022 -9999 0 -0.21 1 1
arachidonic acid secretion -0.024 0.11 -9999 0 -0.42 7 7
GNG2 0.015 0.032 -9999 0 -0.72 1 1
TRIP6 0.024 0.023 -9999 0 -0.48 1 1
GNAO1 0.022 0.032 -9999 0 -0.3 5 5
HRAS 0.015 0.012 -9999 0 -10000 0 0
NFKBIA 0.044 0.033 -9999 0 -0.37 1 1
GAB1 0.014 0.034 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.003 0.009 -9999 0 -10000 0 0
JUN -0.12 0.29 -9999 0 -0.72 97 97
LPA/LPA2/NHERF2 -0.002 0.023 -9999 0 -0.47 1 1
TIAM1 0.003 0.008 -9999 0 -10000 0 0
PIK3R1 -0.057 0.22 -9999 0 -0.72 52 52
mol:IP3 0.032 0.028 -9999 0 -0.38 1 1
PLCB3 0.025 0.023 -9999 0 -0.42 1 1
FOS -0.51 0.34 -9999 0 -0.72 375 375
positive regulation of mitosis -0.024 0.11 -9999 0 -0.42 7 7
LPA/LPA1-2-3 -0.003 0.027 -9999 0 -0.28 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
stress fiber formation 0.031 0.024 -9999 0 -0.2 5 5
GNAZ 0.015 0.064 -9999 0 -0.4 12 12
EGFR/PI3K-beta/Gab1 -0.22 0.22 -9999 0 -0.39 292 292
positive regulation of dendritic cell cytokine production -0.003 0.027 -9999 0 -0.28 5 5
LPA/LPA2/MAGI-3 -0.007 0.04 -9999 0 -0.47 3 3
ARHGEF1 0.038 0.027 -9999 0 -0.23 5 5
GNAI2 0.022 0.032 -9999 0 -0.3 5 5
GNAI3 0.022 0.031 -9999 0 -0.3 5 5
GNAI1 -0.15 0.24 -9999 0 -0.47 190 190
LPA/LPA3 -0.001 0.013 -9999 0 -0.13 5 5
LPA/LPA2 -0.001 0.013 -9999 0 -0.13 5 5
LPA/LPA1 -0.004 0.035 -9999 0 -0.36 5 5
HB-EGF/EGFR -0.26 0.25 -9999 0 -0.49 274 274
HBEGF -0.025 0.07 -9999 0 -0.54 4 4
mol:DAG 0.032 0.028 -9999 0 -0.38 1 1
cAMP biosynthetic process -0.03 0.12 -9999 0 -0.44 7 7
NFKB1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
GNB1 0.015 0.01 -9999 0 -10000 0 0
LYN 0.045 0.028 -9999 0 -0.27 1 1
GNAQ 0.004 0.011 -9999 0 -0.1 5 5
LPAR2 0 0 -9999 0 -10000 0 0
LPAR3 0 0 -9999 0 -10000 0 0
LPAR1 0.004 0.021 -9999 0 -0.2 5 5
IL8 -0.27 0.18 -9999 0 -0.42 282 282
PTK2 0.02 0.027 -9999 0 -0.25 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 0.018 0.027 -9999 0 -0.26 5 5
EGFR -0.37 0.37 -9999 0 -0.72 274 274
PLCG1 0.017 0.022 -9999 0 -0.15 7 7
PLD2 0.018 0.032 -9999 0 -0.28 6 6
G12/G13 -0.002 0.026 -9999 0 -0.26 5 5
PI3K-beta -0.033 0.098 -9999 0 -0.32 52 52
cell migration 0.004 0.016 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.034 -9999 0 -0.72 1 1
PXN 0.031 0.024 -9999 0 -0.21 5 5
HRAS/GTP -0.059 0.085 -9999 0 -0.46 6 6
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.059 0.081 -9999 0 -10000 0 0
PRKCE 0.016 0 -9999 0 -10000 0 0
PRKCD 0.04 0.028 -9999 0 -0.35 1 1
Gi(beta/gamma) -0.031 0.12 -9999 0 -0.48 7 7
mol:LPA 0.004 0.021 -9999 0 -0.2 5 5
TRIP6/p130 Cas/FAK1/Paxillin -0.001 0.023 -9999 0 -10000 0 0
MAPKKK cascade -0.024 0.11 -9999 0 -0.42 7 7
contractile ring contraction involved in cytokinesis 0.027 0.025 -9999 0 -0.21 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 0.003 0.05 -9999 0 -0.37 8 8
GNA15 0.013 0.012 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
MAPT 0.038 0.041 -9999 0 -0.36 4 4
GNA11 0.014 0.011 -9999 0 -10000 0 0
Rac1/GTP 0.004 0.011 -9999 0 -10000 0 0
MMP2 0.017 0.082 -9999 0 -0.82 5 5
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.016 0 -9999 0 -10000 0 0
SPHK1 0.004 0.071 -9999 0 -0.72 4 4
GNAI2 0.016 0.007 -9999 0 -10000 0 0
mol:S1P 0.025 0.032 -9999 0 -0.34 4 4
GNAO1 0.016 0.007 -9999 0 -10000 0 0
mol:Sphinganine-1-P 0.021 0.053 -9999 0 -0.54 4 4
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0 0.023 -9999 0 -0.24 1 1
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.007 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.19 0.33 -9999 0 -0.72 146 146
S1P1/S1P -0.1 0.22 -9999 0 -0.46 146 146
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
S1P/S1P5/G12 -0.001 0.023 -9999 0 -0.26 4 4
S1P/S1P3/Gq 0.03 0.043 -9999 0 -0.31 7 7
S1P/S1P4/Gi -0.057 0.14 -9999 0 -0.24 194 194
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.006 0.084 -9999 0 -0.72 7 7
GNA14 -0.009 0.095 -9999 0 -0.72 7 7
GNA15 0.013 0.021 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
GNA11 0.016 0 -9999 0 -10000 0 0
ABCC1 0.012 0.026 -9999 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.027 0.056 -9999 0 -0.51 5 5
alphaM/beta2 Integrin/GPIbA -0.023 0.036 -9999 0 -10000 0 0
alphaM/beta2 Integrin/proMMP-9 -0.04 0.073 -9999 0 -10000 0 0
PLAUR -0.023 0.07 -9999 0 -10000 0 0
HMGB1 -0.016 0.022 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.023 0.029 -9999 0 -10000 0 0
AGER -0.018 0.04 -9999 0 -0.78 1 1
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG 0.014 0.034 -9999 0 -0.72 1 1
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.13 0.089 -9999 0 -0.63 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.059 0.081 -9999 0 -10000 0 0
CYR61 -0.21 0.34 -9999 0 -0.72 163 163
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.002 0.027 -9999 0 -0.36 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.33 -9999 0 -0.72 149 149
MYH2 0.047 0.057 -9999 0 -0.37 5 5
MST1R 0.005 0.041 -9999 0 -10000 0 0
leukocyte activation during inflammatory response -0.011 0.022 -9999 0 -10000 0 0
APOB 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.009 0.072 -9999 0 -0.72 5 5
JAM3 -0.038 0.19 -9999 0 -0.72 39 39
GP1BA 0.011 0.03 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.042 0.1 -9999 0 -0.52 22 22
alphaM/beta2 Integrin 0.027 0.039 -9999 0 -0.43 1 1
JAM3 homodimer -0.038 0.19 -9999 0 -0.72 39 39
ICAM2 0.004 0.095 -9999 0 -0.72 9 9
ICAM1 0.008 0.045 -9999 0 -0.72 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor 0.027 0.039 -9999 0 -0.43 1 1
cell adhesion -0.022 0.036 -9999 0 -10000 0 0
NFKB1 -0.22 0.18 -9999 0 -0.41 25 25
THY1 0.013 0.024 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.11 0.19 -9999 0 -0.45 120 120
IL6 -0.62 0.42 -9999 0 -0.86 391 391
ITGB2 -0.026 0.042 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration -0.022 0.069 -9999 0 -10000 0 0
alphaM/beta2 Integrin/JAM2/JAM3 -0.17 0.27 -9999 0 -0.56 152 152
JAM2 -0.19 0.33 -9999 0 -0.72 150 150
alphaM/beta2 Integrin/ICAM1 -0.005 0.04 -9999 0 -0.43 1 1
alphaM/beta2 Integrin/uPA/Plg -0.019 0.047 -9999 0 -0.46 1 1
RhoA/GTP 0.043 0.05 -9999 0 -0.34 7 7
positive regulation of phagocytosis 0.001 0.029 -9999 0 -10000 0 0
Ron/MSP -0.005 0.02 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA -0.022 0.071 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR -0.028 0.058 -9999 0 -10000 0 0
PLAU -0.009 0.059 -9999 0 -10000 0 0
PLAT -0.15 0.31 -9999 0 -0.72 120 120
actin filament polymerization 0.046 0.055 -9999 0 -0.36 5 5
MST1 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.01 0.023 -9999 0 -10000 0 0
TNF -0.2 0.17 -9999 0 -0.43 9 9
RAP1B 0.016 0.01 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.031 0.049 -9999 0 -10000 0 0
fibrinolysis -0.019 0.046 -9999 0 -0.46 1 1
HCK 0.013 0.024 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation 0.027 0.039 -9999 0 -0.43 1 1
VTN 0.015 0.012 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.17 0.23 -9999 0 -0.51 163 163
LPA 0.016 0 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
cell migration -0.049 0.059 -9999 0 -0.46 5 5
FN1 -0.098 0.075 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.024 0.033 -9999 0 -10000 0 0
MPO 0.015 0.016 -9999 0 -10000 0 0
KNG1 0.016 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.004 -9999 0 -10000 0 0
ROCK1 0.049 0.048 -9999 0 -0.49 1 1
ELA2 0.016 0 -9999 0 -10000 0 0
PLG 0.015 0.032 -9999 0 -0.72 1 1
CTGF -0.015 0.15 -9999 0 -0.72 22 22
alphaM/beta2 Integrin/Hck -0.024 0.034 -9999 0 -10000 0 0
ITGAM -0.017 0.025 -9999 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.14 0.21 -9999 0 -0.46 149 149
HP 0.016 0 -9999 0 -10000 0 0
leukocyte adhesion -0.21 0.23 -9999 0 -0.56 138 138
SELP -0.19 0.33 -9999 0 -0.72 149 149
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.003 0.026 -9999 0 -0.54 1 1
AKT1 -0.005 0.2 -9999 0 -0.48 51 51
PTK2B 0.001 0.14 -9999 0 -0.51 25 25
VEGFR2 homodimer/Frs2 -0.006 0.14 -9999 0 -0.52 32 32
CAV1 -0.52 0.33 -9999 0 -0.72 385 385
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.056 0.15 -9999 0 -0.54 32 32
endothelial cell proliferation 0.016 0.19 -9999 0 -0.49 30 30
mol:Ca2+ -0.042 0.22 -9999 0 -0.68 30 30
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.049 0.13 -9999 0 -0.54 25 25
RP11-342D11.1 -0.053 0.22 -9999 0 -0.53 55 55
CDH5 0.016 0 -9999 0 -10000 0 0
VEGFA homodimer 0.003 0.053 -9999 0 -0.44 4 4
SHC1 0.016 0 -9999 0 -10000 0 0
SHC2 -0.023 0.16 -9999 0 -0.72 28 28
HRAS/GDP -0.077 0.16 -9999 0 -0.58 29 29
SH2D2A -0.006 0.056 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.062 0.15 -9999 0 -0.52 29 29
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.049 0.16 -9999 0 -0.55 31 31
VEGFR1 homodimer 0.015 0.012 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.083 0.18 -9999 0 -0.65 29 29
GRB10 -0.045 0.23 -9999 0 -0.72 31 31
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
PAK1 -0.01 0.06 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.047 0.13 -9999 0 -0.51 28 28
HRAS 0.015 0.012 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.026 0.085 -9999 0 -0.27 23 23
HIF1A 0.008 0.067 -9999 0 -0.72 4 4
FRS2 0.011 0.039 -9999 0 -0.72 1 1
oxygen and reactive oxygen species metabolic process -0.049 0.13 -9999 0 -0.54 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak -0.013 0.029 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.058 0.15 -9999 0 -0.54 33 33
mol:GDP -0.082 0.17 -9999 0 -0.63 29 29
mol:NADP 0.008 0.16 -9999 0 -0.45 29 29
eNOS/Hsp90 0.016 0.16 -9999 0 -0.42 29 29
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
mol:IP3 -0.043 0.22 -9999 0 -0.69 30 30
HIF1A/ARNT -0.005 0.048 -9999 0 -0.54 4 4
SHB 0.013 0.037 -9999 0 -0.72 1 1
VEGFA -0.018 0.069 -9999 0 -0.23 25 25
VEGFC -0.002 0.11 -9999 0 -0.72 13 13
FAK1/Vinculin 0.028 0.14 -9999 0 -0.48 25 25
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.048 0.14 -9999 0 -0.5 32 32
PTPN6 0.015 0.014 -9999 0 -10000 0 0
EPAS1 -0.029 0.18 -9999 0 -0.76 31 31
mol:L-citrulline 0.008 0.16 -9999 0 -0.45 29 29
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.048 0.14 -9999 0 -0.54 26 26
VEGFR2 homodimer/VEGFA homodimer -0.1 0.21 -9999 0 -0.75 30 30
VEGFR2/3 heterodimer -0.005 0.14 -9999 0 -0.52 31 31
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.038 0.22 -9999 0 -0.69 30 30
VEGFR2 homodimer -0.015 0.16 -9999 0 -0.61 31 31
FLT1 0.015 0.012 -9999 0 -10000 0 0
NEDD4 -0.003 0.079 -9999 0 -0.74 5 5
MAPK3 -0.031 0.2 -9999 0 -0.62 30 30
MAPK1 -0.031 0.2 -9999 0 -0.62 30 30
VEGFA145/NRP2 -0.005 0.041 -9999 0 -10000 0 0
VEGFR1/2 heterodimer -0.005 0.14 -9999 0 -0.52 31 31
KDR -0.015 0.16 -9999 0 -0.61 31 31
VEGFA165/NRP1/VEGFR2 homodimer -0.09 0.19 -9999 0 -0.68 30 30
SRC 0.016 0.007 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.03 0.21 -9999 0 -0.63 30 30
PI3K -0.098 0.19 -9999 0 -0.58 51 51
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.056 0.14 -9999 0 -0.54 31 31
FES -0.045 0.23 -9999 0 -0.7 32 32
GAB1 -0.065 0.15 -9999 0 -0.6 26 26
VEGFR2 homodimer/VEGFA homodimer/Src -0.056 0.14 -9999 0 -0.54 31 31
CTNNB1 0.01 0.064 -9999 0 -0.72 4 4
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.23 0.24 -9999 0 -0.52 148 148
VEGFR2 homodimer/VEGFA homodimer/Yes -0.057 0.14 -9999 0 -0.54 32 32
PI3K/GAB1 -0.015 0.22 -9999 0 -0.54 49 49
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.036 0.14 -9999 0 -0.52 27 27
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.046 0.13 -9999 0 -0.49 42 42
HSP90AA1 0.015 0.012 -9999 0 -10000 0 0
CDC42 -0.044 0.22 -9999 0 -0.7 30 30
actin cytoskeleton reorganization -0.049 0.15 -9999 0 -0.55 31 31
PTK2 0.02 0.15 -9999 0 -0.52 25 25
EDG1 -0.17 0.4 -9999 0 -0.79 148 148
mol:DAG -0.043 0.22 -9999 0 -0.69 30 30
CaM/Ca2+ -0.089 0.17 -9999 0 -0.64 29 29
MAP2K3 -0.032 0.21 -9999 0 -0.66 30 30
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.098 0.21 -9999 0 -0.76 30 30
PLCG1 -0.044 0.22 -9999 0 -0.7 30 30
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.049 0.14 -9999 0 -0.53 27 27
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.015 0.032 -9999 0 -0.72 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.056 0.14 -9999 0 -0.57 26 26
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.056 0.14 -9999 0 -0.54 31 31
cell migration 0.059 0.13 -9999 0 -0.4 23 23
mol:PI-3-4-5-P3 -0.025 0.22 -9999 0 -0.54 51 51
FYN 0.013 0.045 -9999 0 -0.72 2 2
VEGFB/NRP1 -0.094 0.18 -9999 0 -0.64 30 30
mol:NO 0.008 0.16 -9999 0 -0.45 29 29
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.083 0.15 -9999 0 -0.58 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.041 0.24 -9999 0 -0.74 31 31
VHL 0.012 0.027 -9999 0 -10000 0 0
ITGB3 0.014 0.02 -9999 0 -10000 0 0
NOS3 0.004 0.18 -9999 0 -0.51 29 29
VEGFR2 homodimer/VEGFA homodimer/Sck -0.079 0.18 -9999 0 -0.55 55 55
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.03 0.21 -9999 0 -0.65 29 29
PRKCB -0.04 0.21 -9999 0 -0.64 30 30
VCL 0.016 0.007 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.047 0.22 -9999 0 -0.53 55 55
VEGFR1/2 heterodimer/VEGFA homodimer -0.056 0.14 -9999 0 -0.54 31 31
VEGFA165/NRP2 -0.005 0.041 -9999 0 -10000 0 0
MAPKKK cascade -0.071 0.17 -9999 0 -0.61 30 30
NRP2 0.015 0.016 -9999 0 -10000 0 0
VEGFC homodimer -0.002 0.11 -9999 0 -0.72 13 13
NCK1 0.016 0 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.028 0.14 -9999 0 -0.48 25 25
MAP3K13 -0.044 0.22 -9999 0 -0.7 30 30
PDPK1 -0.01 0.2 -9999 0 -0.47 51 51
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.051 0.24 -10000 0 -0.94 24 24
NCK1/PAK1/Dok-R -0.028 0.093 -10000 0 -0.43 24 24
NCK1/Dok-R -0.047 0.23 -10000 0 -1.1 24 24
PIK3CA 0.015 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol -0.008 0.041 0.24 14 -10000 0 14
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.018 0.002 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.008 0.041 0.26 13 -10000 0 13
TNIP2 0.015 0.012 -10000 0 -10000 0 0
NF kappa B/RelA -0.045 0.21 -10000 0 -1 24 24
FN1 -0.098 0.075 -10000 0 -10000 0 0
PLD2 0.039 0.26 -10000 0 -1.1 24 24
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.091 0.23 -10000 0 -0.72 57 57
ELK1 0.054 0.23 -10000 0 -1 24 24
GRB7 0 0.048 -10000 0 -10000 0 0
PAK1 -0.01 0.06 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.051 0.26 -10000 0 -1.1 24 24
CDKN1A 0.05 0.19 -10000 0 -0.68 19 19
ITGA5 0.016 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.046 0.23 -10000 0 -1.1 24 24
CRK 0.015 0.032 -10000 0 -0.72 1 1
mol:NO 0.066 0.19 -10000 0 -0.67 24 24
PLG 0.039 0.26 -10000 0 -1.1 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.003 0.21 -10000 0 -0.9 24 24
GRB2 0.013 0.022 -10000 0 -10000 0 0
PIK3R1 -0.055 0.22 -10000 0 -0.72 52 52
ANGPT2 -0.028 0.2 -10000 0 -0.63 17 17
BMX -0.21 0.34 -10000 0 -1.4 24 24
ANGPT1 0.015 0.23 -10000 0 -1.4 14 14
tube development 0.042 0.21 -10000 0 -0.68 25 25
ANGPT4 0.016 0.001 -10000 0 -10000 0 0
response to hypoxia 0.004 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0 0.31 -10000 0 -1.3 24 24
alpha5/beta1 Integrin 0 0.003 -10000 0 -10000 0 0
FGF2 -0.55 0.31 -10000 0 -0.72 405 405
STAT5A (dimer) 0.044 0.23 -10000 0 -0.84 21 21
mol:L-citrulline 0.066 0.19 -10000 0 -0.67 24 24
AGTR1 -0.32 0.35 -10000 0 -0.72 227 227
MAPK14 0.035 0.27 -10000 0 -1.2 24 24
Tie2/SHP2 -0.031 0.18 -10000 0 -1.2 12 12
TEK 0.027 0.21 -10000 0 -1.3 12 12
RPS6KB1 0.048 0.23 -10000 0 -0.9 24 24
Angiotensin II/AT1 -0.24 0.27 -10000 0 -0.55 227 227
Tie2/Ang1/GRB2 0.036 0.27 -10000 0 -1.2 24 24
MAPK3 0.05 0.24 -10000 0 -1 24 24
MAPK1 0.05 0.24 -10000 0 -1 24 24
Tie2/Ang1/GRB7 0.04 0.27 -10000 0 -1.2 24 24
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.039 0.26 -10000 0 -1.1 24 24
PI3K 0.034 0.27 -10000 0 -1.1 24 24
FES 0.034 0.27 -10000 0 -1.2 24 24
Crk/Dok-R -0.048 0.23 -10000 0 -1.1 24 24
Tie2/Ang1/ABIN2 0.036 0.27 -10000 0 -1.2 24 24
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.055 0.22 -10000 0 -0.83 24 24
STAT5A 0.014 0.045 -10000 0 -0.72 2 2
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.049 0.23 -10000 0 -0.9 24 24
Tie2/Ang2 0.024 0.26 -10000 0 -1 20 20
Tie2/Ang1 0.028 0.28 -10000 0 -1.2 24 24
FOXO1 0.041 0.25 -10000 0 -0.87 25 25
ELF1 0.026 0.018 -10000 0 -10000 0 0
ELF2 0.036 0.26 -10000 0 -1.1 24 24
mol:Choline 0.042 0.25 -10000 0 -1.1 24 24
cell migration -0.013 0.053 -10000 0 -0.24 24 24
FYN 0.037 0.23 -10000 0 -0.8 24 24
DOK2 0.013 0.046 -10000 0 -0.72 2 2
negative regulation of cell cycle 0.052 0.18 -10000 0 -0.61 19 19
ETS1 0.022 0.056 -10000 0 -0.89 1 1
PXN 0.061 0.2 -10000 0 -0.73 24 24
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 0.063 0.21 -10000 0 -0.78 24 24
RAC1 0.016 0 -10000 0 -10000 0 0
TNF 0.02 0.046 -10000 0 -10000 0 0
MAPKKK cascade 0.042 0.25 -10000 0 -1.1 24 24
RASA1 0.015 0.012 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.033 0.27 -10000 0 -1.2 24 24
NCK1 0.016 0 -10000 0 -10000 0 0
vasculogenesis 0.068 0.17 -10000 0 -0.6 24 24
mol:Phosphatidic acid 0.042 0.25 -10000 0 -1.1 24 24
mol:Angiotensin II 0.002 0.001 -10000 0 -10000 0 0
mol:NADP 0.066 0.19 -10000 0 -0.67 24 24
Rac1/GTP -0.053 0.18 -10000 0 -0.83 24 24
MMP2 0.036 0.27 -10000 0 -1.2 24 24
Wnt 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
Noncanonical Wnts/FZD -0.016 0.18 -9999 0 -0.41 72 72
FZD6 -0.024 0.16 -9999 0 -0.72 26 26
WNT6 0.012 0.048 -9999 0 -0.72 2 2
WNT4 0.005 0.05 -9999 0 -0.72 1 1
FZD3 -0.019 0.16 -9999 0 -0.72 25 25
WNT5A -0.029 0.17 -9999 0 -0.72 28 28
WNT11 -0.001 0.1 -9999 0 -0.72 10 10
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.016 0.007 -9999 0 -10000 0 0
CDC42/GTP -0.08 0.11 -9999 0 -0.49 3 3
PLCG1 -0.054 0.13 -9999 0 -0.53 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0.007 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.007 -9999 0 -10000 0 0
cell migration -0.078 0.11 -9999 0 -0.48 3 3
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 -0.054 0.13 -9999 0 -0.64 2 2
MAPK1 -0.054 0.13 -9999 0 -0.64 2 2
S1P/S1P5/Gi -0.068 0.14 -9999 0 -0.25 194 194
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0 0 -9999 0 -10000 0 0
RHOA 0.03 0.006 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.068 0.14 -9999 0 -0.25 194 194
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.006 0.084 -9999 0 -0.72 7 7
S1P/S1P4/G12/G13 0.001 0.006 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.031 0.16 -9999 0 -0.54 2 2
PCK1 -0.85 0.6 -9999 0 -1.2 403 403
HNF4A 0.04 0.17 -9999 0 -10000 0 0
KCNJ11 0.031 0.18 -9999 0 -0.6 2 2
AKT1 0.012 0.11 -9999 0 -0.34 3 3
response to starvation 0.008 0.002 -9999 0 -10000 0 0
DLK1 0.031 0.19 -9999 0 -0.6 2 2
NKX2-1 0.075 0.11 -9999 0 -10000 0 0
ACADM 0.022 0.2 -9999 0 -1.1 6 6
TAT -0.024 0.2 -9999 0 -1 5 5
CEBPB 0.021 0.033 -9999 0 -0.72 1 1
CEBPA 0.02 0.056 -9999 0 -0.72 3 3
TTR -0.038 0.24 -9999 0 -0.59 64 64
PKLR 0.031 0.16 -9999 0 -0.54 2 2
APOA1 0.038 0.19 -9999 0 -10000 0 0
CPT1C 0.03 0.16 -9999 0 -10000 0 0
ALAS1 0.033 0.12 -9999 0 -10000 0 0
TFRC -0.006 0.19 -9999 0 -10000 0 0
FOXF1 -0.002 0.02 -9999 0 -10000 0 0
NF1 0.026 0 -9999 0 -10000 0 0
HNF1A (dimer) 0.04 0.017 -9999 0 -10000 0 0
CPT1A 0.031 0.16 -9999 0 -10000 0 0
HMGCS1 0.03 0.16 -9999 0 -10000 0 0
NR3C1 -0.031 0.21 -9999 0 -0.71 46 46
CPT1B 0.031 0.16 -9999 0 -10000 0 0
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.025 0.008 -9999 0 -10000 0 0
GCK 0.031 0.16 -9999 0 -0.54 2 2
CREB1 -0.16 0.11 -9999 0 -0.24 126 126
IGFBP1 0.007 0.15 -9999 0 -0.94 2 2
PDX1 0.041 0.14 -9999 0 -1.5 1 1
UCP2 0.03 0.16 -9999 0 -0.54 2 2
ALDOB 0.031 0.19 -9999 0 -10000 0 0
AFP -0.096 0.15 -9999 0 -0.43 72 72
BDH1 0.03 0.16 -9999 0 -10000 0 0
HADH 0.027 0.2 -9999 0 -0.99 4 4
F2 0.038 0.19 -9999 0 -10000 0 0
HNF1A 0.04 0.017 -9999 0 -10000 0 0
G6PC -0.083 0.11 -9999 0 -0.53 3 3
SLC2A2 0.039 0.15 -9999 0 -1.3 1 1
INS 0 0.009 -9999 0 -10000 0 0
FOXA1 -0.12 0.26 -9999 0 -0.71 82 82
FOXA3 -0.13 0.13 -9999 0 -0.39 36 36
FOXA2 0.035 0.23 -9999 0 -0.7 2 2
ABCC8 -0.11 0.44 -9999 0 -1 94 94
ALB -0.099 0.16 -9999 0 -0.45 75 75
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.016 0.007 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.072 0.16 0.32 6 -0.36 107 113
FRAP1 0.008 0.05 -10000 0 -10000 0 0
AKT1 -0.032 0.15 0.25 6 -0.38 53 59
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.05 0.1 -10000 0 -0.31 53 53
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.014 0.033 -10000 0 -10000 0 0
TSC2 0.016 0 -10000 0 -10000 0 0
RHEB/GDP -0.043 0.092 0.18 1 -0.4 8 9
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.033 0.14 -10000 0 -0.39 69 69
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.017 0.039 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0.007 -10000 0 -10000 0 0
RPS6KB1 0.002 0.092 -10000 0 -0.3 8 8
MAP3K5 -0.015 0.11 -10000 0 -0.42 35 35
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
apoptosis -0.015 0.11 -10000 0 -0.42 35 35
mol:LY294002 0 0.001 -10000 0 -0.002 62 62
EIF4B 0.012 0.083 -10000 0 -0.27 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.026 0.059 -10000 0 -0.4 1 1
eIF4E/eIF4G1/eIF4A1 -0.005 0.016 -10000 0 -10000 0 0
KIAA1303 0.016 0.01 -10000 0 -10000 0 0
PI3K -0.058 0.18 -10000 0 -0.38 114 114
mTOR/RHEB/GTP/Raptor/GBL 0.031 0.071 -10000 0 -10000 0 0
FKBP1A 0.016 0.01 -10000 0 -10000 0 0
RHEB/GTP -0.042 0.091 0.23 1 -0.39 8 9
mol:Amino Acids 0 0.001 -10000 0 -0.002 62 62
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.066 0.14 0.26 6 -0.33 107 113
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C -0.02 0.16 -10000 0 -0.62 35 35
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.042 0.006 -10000 0 -10000 0 0
TSC1/TSC2 -0.052 0.11 -10000 0 -0.33 53 53
tumor necrosis factor receptor activity 0 0.001 0.002 62 -10000 0 62
RPS6 0.015 0.032 -10000 0 -0.72 1 1
PPP5C 0.014 0.02 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 -0.046 0.15 -10000 0 -0.42 69 69
INS 0.016 0 -10000 0 -10000 0 0
PTEN -0.002 0.11 -10000 0 -0.72 13 13
PDK2 -0.066 0.14 0.26 6 -0.34 107 113
EIF4EBP1 0.022 0.02 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
PPP2R5D 0.017 0.047 -10000 0 -10000 0 0
peptide biosynthetic process 0.032 0 -10000 0 -10000 0 0
RHEB 0.016 0.007 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 13 -0.003 52 65
EEF2 0.032 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.029 0.014 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.003 0.015 -9999 0 -10000 0 0
VLDLR -0.1 0.27 -9999 0 -0.72 83 83
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.013 0.045 -9999 0 -0.72 2 2
ITGA3 0.012 0.047 -9999 0 -0.72 2 2
RELN/VLDLR/Fyn -0.09 0.19 -9999 0 -0.48 100 100
MAPK8IP1/MKK7/MAP3K11/JNK1 0.002 0.022 -9999 0 -0.38 1 1
AKT1 -0.05 0.19 -9999 0 -0.68 23 23
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 0.016 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1 0.004 0.095 -9999 0 -0.44 20 20
LRPAP1/LRP8 -0.022 0.035 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.005 0.093 -9999 0 -0.41 22 22
DAB1/alpha3/beta1 Integrin -0.055 0.16 -9999 0 -0.46 30 30
long-term memory 0.002 0.11 -9999 0 -0.41 31 31
DAB1/LIS1 -0.052 0.17 -9999 0 -0.48 28 28
DAB1/CRLK/C3G -0.054 0.16 -9999 0 -0.46 28 28
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
DAB1/NCK2 -0.052 0.17 -9999 0 -0.48 28 28
ARHGEF2 0.012 0.026 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.016 0.007 -9999 0 -10000 0 0
CDK5R1 0.014 0.019 -9999 0 -10000 0 0
RELN -0.013 0.14 -9999 0 -0.72 20 20
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
RELN/LRP8/Fyn 0.001 0.11 -9999 0 -0.48 22 22
GRIN2A/RELN/LRP8/DAB1/Fyn 0.008 0.094 -9999 0 -0.4 22 22
MAPK8 0.015 0.032 -9999 0 -0.72 1 1
RELN/VLDLR/DAB1 -0.081 0.18 -9999 0 -0.44 98 98
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.087 0.22 -9999 0 -0.44 133 133
RELN/LRP8 0.003 0.1 -9999 0 -0.48 20 20
GRIN2B/RELN/LRP8/DAB1/Fyn 0 0.12 -9999 0 -0.43 31 31
PI3K -0.053 0.16 -9999 0 -0.54 52 52
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.034 -9999 0 -0.54 2 2
RAP1A -0.019 0.16 -9999 0 -0.42 28 28
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.016 0.007 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.002 0.11 -9999 0 -0.72 12 12
NCK2 0.016 0.01 -9999 0 -10000 0 0
neuron differentiation 0.044 0.049 -9999 0 -10000 0 0
neuron adhesion -0.002 0.16 -9999 0 -0.63 6 6
LRP8 -0.03 0.073 -9999 0 -10000 0 0
GSK3B -0.038 0.18 -9999 0 -0.64 23 23
RELN/VLDLR/DAB1/Fyn -0.077 0.16 -9999 0 -0.41 100 100
MAP3K11 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.063 0.2 -9999 0 -0.37 134 134
CDK5 0.012 0.025 -9999 0 -10000 0 0
MAPT 0.013 0.066 -9999 0 -0.66 4 4
neuron migration -0.018 0.18 -9999 0 -0.52 24 24
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.044 0.049 -9999 0 -10000 0 0
RELN/VLDLR -0.062 0.19 -9999 0 -0.45 98 98
IL1-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
UBC13/UEV1A 0 0.006 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.015 0.032 -9999 0 -0.72 1 1
ERC1 0.013 0.023 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.036 0.086 -9999 0 -0.35 21 21
IRAK/TOLLIP 0.03 0.012 -9999 0 -10000 0 0
IKBKB 0.014 0.02 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.009 0.046 -9999 0 -0.54 3 3
IL1A 0.013 0.022 -9999 0 -10000 0 0
IL1B -0.043 0.2 -9999 0 -0.57 62 62
IRAK/TRAF6/p62/Atypical PKCs 0.003 0.013 -9999 0 -10000 0 0
IL1R2 0.003 0.066 -9999 0 -0.72 3 3
IL1R1 -0.066 0.23 -9999 0 -0.72 59 59
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.14 -9999 0 -0.34 63 63
TOLLIP 0.016 0.007 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 -0.001 0.02 -9999 0 -0.46 1 1
IKK complex/ELKS 0.082 0.02 -9999 0 -0.34 1 1
JUN -0.009 0.16 -9999 0 -0.59 5 5
MAP3K7 0.016 0.007 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.12 0.24 -9999 0 -0.75 46 46
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.044 0.13 -9999 0 -0.41 59 59
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.04 0.12 -9999 0 -0.38 59 59
IL1 beta fragment/IL1R1/IL1RAP -0.098 0.21 -9999 0 -0.49 104 104
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.054 0.062 -9999 0 -0.33 1 1
IRAK1 0.022 0.012 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.071 0.17 -9999 0 -0.55 59 59
IRAK4 0.016 0.01 -9999 0 -10000 0 0
PRKCI 0.013 0.023 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PI3K -0.053 0.16 -9999 0 -0.54 52 52
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.017 0.15 -9999 0 -0.48 23 23
CHUK 0.015 0.032 -9999 0 -0.72 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.098 0.21 -9999 0 -0.49 104 104
IL1 beta/IL1R2 -0.057 0.17 -9999 0 -0.49 64 64
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0.017 -9999 0 -0.34 1 1
NF kappa B1 p50/RelA -0.11 0.21 -9999 0 -0.67 46 46
IRAK3 0.012 0.039 -9999 0 -0.72 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.087 0.19 -9999 0 -0.44 104 104
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.1 -9999 0 -0.29 59 59
IL1 alpha/IL1R1/IL1RAP -0.05 0.14 -9999 0 -0.46 59 59
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
SQSTM1 0.016 0.007 -9999 0 -10000 0 0
MYD88 0.016 0.01 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.041 0.004 -9999 0 -10000 0 0
IL1RAP 0.016 0.007 -9999 0 -10000 0 0
UBE2N 0.016 0.01 -9999 0 -10000 0 0
IRAK/TRAF6 -0.07 0.16 -9999 0 -0.57 25 25
CASP1 -0.068 0.23 -9999 0 -0.72 60 60
IL1RN/IL1R2 -0.018 0.053 -9999 0 -0.54 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.09 0.2 -9999 0 -0.46 104 104
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.009 0.12 -9999 0 -0.34 59 59
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
IL1RN -0.006 0.056 -9999 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0 0.017 -9999 0 -0.36 1 1
MAP2K6 0.047 0.063 -9999 0 -0.35 13 13
Regulation of Telomerase

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
Telomerase catalytic core complex -0.066 0.13 -10000 0 -0.6 13 13
RAD9A 0.016 0 -10000 0 -10000 0 0
AP1 -0.46 0.35 -10000 0 -0.65 376 376
IFNAR2 0.018 0.003 -10000 0 -10000 0 0
AKT1 -0.035 0.12 -10000 0 -0.25 108 108
ER alpha/Oestrogen -0.14 0.22 -10000 0 -0.55 119 119
NFX1/SIN3/HDAC complex 0.06 0.01 -10000 0 -10000 0 0
EGF -0.23 0.35 -10000 0 -0.72 179 179
SMG5 0.014 0.02 -10000 0 -10000 0 0
SMG6 0.016 0 -10000 0 -10000 0 0
SP3/HDAC2 0.023 0.015 -10000 0 -10000 0 0
TERT/c-Abl -0.062 0.11 -10000 0 -0.56 13 13
SAP18 0.017 0.001 -10000 0 -10000 0 0
MRN complex 0 0.004 -10000 0 -10000 0 0
WT1 -0.04 0.078 -10000 0 -10000 0 0
WRN 0.016 0.01 -10000 0 -10000 0 0
SP1 0.019 0.003 -10000 0 -10000 0 0
SP3 0.017 0.003 -10000 0 -10000 0 0
TERF2IP 0.016 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.051 0.091 -10000 0 -0.54 9 9
Mad/Max 0.022 0.011 -10000 0 -10000 0 0
TERT -0.068 0.13 -10000 0 -0.62 13 13
CCND1 -0.071 0.2 -10000 0 -1.2 13 13
MAX 0.017 0.003 -10000 0 -10000 0 0
RBBP7 0.012 0.026 -10000 0 -10000 0 0
RBBP4 0.016 0.007 -10000 0 -10000 0 0
TERF2 -0.001 0.029 -10000 0 -0.66 1 1
PTGES3 0.015 0.032 -10000 0 -0.72 1 1
SIN3A 0.017 0.001 -10000 0 -10000 0 0
Telomerase/911 0.037 0.025 -10000 0 -10000 0 0
CDKN1B 0.011 0.12 -10000 0 -0.76 10 10
RAD1 0.015 0.012 -10000 0 -10000 0 0
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
SAP30 0.016 0.007 -10000 0 -10000 0 0
TRF2/PARP2 -0.001 0.023 -10000 0 -0.53 1 1
UBE3A 0.017 0.003 -10000 0 -10000 0 0
JUN -0.12 0.29 -10000 0 -0.72 97 97
E6 0.001 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.006 -10000 0 -10000 0 0
FOS -0.51 0.34 -10000 0 -0.72 375 375
IFN-gamma/IRF1 0 0.073 -10000 0 -0.35 10 10
PARP2 0.016 0 -10000 0 -10000 0 0
BLM -0.034 0.075 -10000 0 -10000 0 0
Telomerase 0.008 0.026 -10000 0 -10000 0 0
IRF1 0.01 0.046 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.72 119 119
KU/TER 0 0 -10000 0 -10000 0 0
ATM/TRF2 -0.001 0.019 -10000 0 -0.43 1 1
ubiquitin-dependent protein catabolic process 0.067 0.01 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.067 0.01 -10000 0 -10000 0 0
HDAC1 0.017 0.001 -10000 0 -10000 0 0
HDAC2 0.017 0.018 -10000 0 -10000 0 0
ATM 0 0.011 0.25 1 -10000 0 1
SMAD3 0.026 0.026 -10000 0 -0.54 1 1
ABL1 0.016 0 -10000 0 -10000 0 0
MXD1 0.017 0.008 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
HUS1 0.015 0.012 -10000 0 -10000 0 0
RPS6KB1 0.013 0.023 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.055 0.12 -10000 0 -0.59 12 12
NR2F2 -0.01 0.13 -10000 0 -0.72 16 16
MAPK3 0.03 0.026 -10000 0 -0.54 1 1
MAPK1 0.03 0.026 -10000 0 -0.54 1 1
TGFB1/TGF beta receptor Type II 0.015 0.01 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
HNRNPC 0.016 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0.011 0.25 1 -10000 0 1
NBN 0.016 0.007 -10000 0 -10000 0 0
EGFR -0.37 0.37 -10000 0 -0.72 274 274
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.45 0.33 -10000 0 -0.64 370 370
MYC -0.022 0.16 -10000 0 -0.72 28 28
IL2 0.018 0.033 -10000 0 -0.72 1 1
KU 0 0 -10000 0 -10000 0 0
RAD50 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.015 0.012 -10000 0 -10000 0 0
TGFB1 0.015 0.01 -10000 0 -10000 0 0
TRF2/BLM 0.022 0.042 -10000 0 -0.53 1 1
FRAP1 0.016 0 -10000 0 -10000 0 0
KU/TERT -0.055 0.11 -10000 0 -0.55 13 13
SP1/HDAC2 0.026 0.016 -10000 0 -10000 0 0
PINX1 0.016 0 -10000 0 -10000 0 0
Telomerase/EST1A -0.051 0.091 -10000 0 -0.55 8 8
Smad3/Myc 0.005 0.11 -10000 0 -0.46 29 29
911 complex 0 0.009 -10000 0 -10000 0 0
IFNG -0.016 0.075 -10000 0 -0.71 1 1
Telomerase/PinX1 -0.051 0.091 -10000 0 -0.55 8 8
Telomerase/AKT1/mTOR/p70S6K 0.015 0.062 -10000 0 -0.48 2 2
SIN3B 0.015 0.016 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
Telomerase/EST1B -0.052 0.092 -10000 0 -0.53 10 10
response to DNA damage stimulus 0.004 0.003 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.001 0.018 -10000 0 -0.4 1 1
TRF2/WRN -0.001 0.024 -10000 0 -0.53 1 1
Telomerase/hnRNP C1/C2 -0.051 0.091 -10000 0 -0.55 8 8
E2F1 -0.004 0.056 -10000 0 -10000 0 0
ZNFX1 0.014 0.021 -10000 0 -10000 0 0
PIF1 0.01 0.032 -10000 0 -10000 0 0
NCL 0.016 0 -10000 0 -10000 0 0
DKC1 0.015 0.014 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.031 0.12 -9999 0 -0.46 38 38
E-cadherin/beta catenin -0.039 0.14 -9999 0 -0.54 37 37
CTNNB1 0.01 0.064 -9999 0 -0.72 4 4
JUP 0.013 0.036 -9999 0 -0.72 1 1
CDH1 -0.032 0.18 -9999 0 -0.72 33 33
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.039 0.052 -9999 0 -0.36 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.036 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin/Src 0.033 0.066 -9999 0 -0.52 4 4
AP1 -0.29 0.25 -9999 0 -0.67 109 109
ILK 0.028 0.052 -9999 0 -0.38 4 4
bone resorption 0.061 0.049 -9999 0 -0.36 1 1
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.047 0.065 -9999 0 -0.33 4 4
ITGAV 0.02 0.033 -9999 0 -0.71 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.003 0.034 -9999 0 -0.54 2 2
alphaV/beta3 Integrin/Osteopontin 0.041 0.065 -9999 0 -0.43 4 4
MAP3K1 0.024 0.068 -9999 0 -0.41 8 8
JUN -0.12 0.29 -9999 0 -0.72 97 97
MAPK3 0.043 0.052 -9999 0 -0.34 4 4
MAPK1 0.043 0.052 -9999 0 -0.34 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.034 0.065 -9999 0 -0.37 9 9
ITGB3 0.019 0.019 -9999 0 -10000 0 0
NFKBIA 0.055 0.052 -9999 0 -10000 0 0
FOS -0.51 0.34 -9999 0 -0.72 375 375
CD44 0.014 0.035 -9999 0 -0.72 1 1
CHUK 0.015 0.032 -9999 0 -0.72 1 1
PLAU 0.033 0.058 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.018 0.04 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.001 0.026 -9999 0 -0.52 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.027 0.055 -9999 0 -0.38 4 4
VAV3 0.011 0.1 -9999 0 -0.4 26 26
MAP3K14 0.035 0.052 -9999 0 -0.38 4 4
ROCK2 0.015 0.033 -9999 0 -0.72 1 1
SPP1 -0.05 0.093 -9999 0 -0.71 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.012 0.082 -9999 0 -0.36 26 26
MMP2 -0.22 0.22 -9999 0 -0.54 104 104
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.001 0.048 -10000 0 -10000 0 0
GNB1/GNG2 -0.017 0.051 -10000 0 -0.17 52 52
AKT1 0.072 0.088 -10000 0 -0.19 50 50
EGF -0.24 0.35 -10000 0 -0.72 179 179
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.059 0.04 -10000 0 -10000 0 0
mol:Ca2+ 0.075 0.12 -10000 0 -0.28 52 52
LYN 0.059 0.04 -10000 0 -0.27 1 1
RhoA/GTP -0.011 0.035 -10000 0 -0.13 2 2
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.079 0.14 -10000 0 -0.32 52 52
GNG2 0.015 0.032 -10000 0 -0.72 1 1
ARRB2 0.016 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.04 0.037 -10000 0 -0.45 2 2
G beta5/gamma2 -0.022 0.066 -10000 0 -0.22 51 51
PRKCH 0.073 0.14 -10000 0 -0.34 52 52
DNM1 0.016 0.007 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 -0.001 0.005 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.004 0.086 -10000 0 -0.72 7 7
G12 family/GTP -0.027 0.086 -10000 0 -0.28 52 52
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.012 0.055 -10000 0 -0.72 3 3
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.063 0.079 0.35 5 -10000 0 5
mol:NADP 0.016 0 -10000 0 -10000 0 0
RAB11A 0.016 0.01 -10000 0 -10000 0 0
PRKG1 0.016 0 -10000 0 -10000 0 0
mol:IP3 0.077 0.14 -10000 0 -0.35 52 52
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.076 0.18 -10000 0 -0.47 52 52
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.062 0.041 -10000 0 -10000 0 0
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.06 0.04 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.016 0 -10000 0 -10000 0 0
PRKCB1 0.073 0.14 -10000 0 -0.35 52 52
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.076 0.19 -10000 0 -0.5 52 52
LCK 0.063 0.042 -10000 0 -0.27 1 1
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.002 0.031 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.04 0.015 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.002 0.031 -10000 0 -10000 0 0
MAPK14 0.076 0.098 -10000 0 -0.21 52 52
TGM2/GTP 0.082 0.16 -10000 0 -0.38 52 52
MAPK11 0.076 0.098 -10000 0 -0.21 52 52
ARHGEF1 0.06 0.076 -10000 0 -0.16 52 52
GNAI2 0.016 0.007 -10000 0 -10000 0 0
JNK cascade 0.078 0.15 -10000 0 -0.37 52 52
RAB11/GDP 0.014 0.01 -10000 0 -10000 0 0
ICAM1 0.071 0.12 -10000 0 -0.28 52 52
cAMP biosynthetic process 0.074 0.13 -10000 0 -0.32 52 52
Gq family/GTP/EBP50 0.021 0.03 -10000 0 -0.24 1 1
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.059 0.04 -10000 0 -0.27 1 1
GNB5 0.015 0.032 -10000 0 -0.72 1 1
GNB1 0.016 0.01 -10000 0 -10000 0 0
EGF/EGFR -0.037 0.098 -10000 0 -0.28 12 12
VCAM1 0.067 0.13 -10000 0 -0.31 52 52
TP beta/Gq family/GDP/G beta5/gamma2 0.04 0.037 -10000 0 -0.45 2 2
platelet activation 0.097 0.13 -10000 0 -0.28 52 52
PGI2/IP 0 0.001 -10000 0 -10000 0 0
PRKACA 0.023 0.042 -10000 0 -0.33 7 7
Gq family/GDP/G beta5/gamma2 0.038 0.038 -10000 0 -0.43 2 2
TXA2/TP beta/beta Arrestin2 0 0.004 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.033 0.04 -10000 0 -0.31 7 7
mol:DAG 0.075 0.16 -10000 0 -0.4 52 52
EGFR -0.37 0.37 -10000 0 -0.72 274 274
TXA2/TP alpha 0.084 0.17 -10000 0 -0.43 52 52
Gq family/GTP -0.003 0.032 -10000 0 -0.28 7 7
YES1 0.059 0.046 -10000 0 -0.4 2 2
GNAI2/GTP -0.005 0.035 -10000 0 -0.3 4 4
PGD2/DP -0.009 0.064 -10000 0 -0.55 7 7
SLC9A3R1 -0.022 0.069 -10000 0 -10000 0 0
FYN 0.058 0.046 -10000 0 -0.29 4 4
mol:NO 0.016 0 -10000 0 -10000 0 0
GNA15 0.013 0.021 -10000 0 -10000 0 0
PGK/cGMP 0 0 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.006 0.044 -10000 0 -10000 0 0
NOS3 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.075 0.14 -10000 0 -0.33 52 52
PRKCB 0.068 0.14 -10000 0 -0.34 52 52
PRKCE 0.076 0.14 -10000 0 -0.34 52 52
PRKCD 0.073 0.15 -10000 0 -0.37 52 52
PRKCG 0.073 0.15 -10000 0 -0.36 52 52
muscle contraction 0.081 0.18 -10000 0 -0.45 52 52
PRKCZ 0.073 0.14 -10000 0 -0.33 52 52
ARR3 0.016 0 -10000 0 -10000 0 0
TXA2/TP beta -0.005 0.039 -10000 0 -0.34 3 3
PRKCQ 0.072 0.14 -10000 0 -0.34 52 52
MAPKKK cascade 0.075 0.16 -10000 0 -0.41 52 52
SELE 0.057 0.16 -10000 0 -0.4 52 52
TP beta/GNAI2/GDP/G beta/gamma -0.003 0.033 -10000 0 -0.33 1 1
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 -0.009 0.095 -10000 0 -0.72 7 7
chemotaxis 0.071 0.22 -10000 0 -0.6 52 52
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.015 0.014 -10000 0 -10000 0 0
GNA11 0.016 0 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.006 -10000 0 -10000 0 0
Canonical Wnt 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
HDAC1 0.011 0.027 -10000 0 -10000 0 0
AES 0.01 0.023 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.001 0.024 -10000 0 -0.54 1 1
SMAD4 0.013 0.045 -10000 0 -0.72 2 2
DKK2 0.007 0.074 -10000 0 -0.72 5 5
TLE1 -0.016 0.14 -10000 0 -0.72 18 18
MACF1 0.017 0 -10000 0 -10000 0 0
CTNNB1 0.16 0.076 0.29 3 -10000 0 3
WIF1 -0.53 0.32 -10000 0 -0.72 394 394
beta catenin/RanBP3 0.04 0.13 0.45 47 -10000 0 47
KREMEN2 -0.078 0.08 -10000 0 -10000 0 0
DKK1 -0.075 0.21 -10000 0 -0.72 46 46
beta catenin/beta TrCP1 0.16 0.072 0.29 2 -10000 0 2
FZD1 0.015 0.032 -10000 0 -0.72 1 1
AXIN2 -0.02 0.22 -10000 0 -1.4 11 11
AXIN1 0.017 0.01 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.019 0.042 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.13 0.1 -10000 0 -0.52 3 3
Axin1/APC/GSK3 0.002 0.014 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.11 0.033 -10000 0 -10000 0 0
HNF1A 0.01 0.028 0.27 1 -10000 0 1
CTBP1 0.01 0.025 -10000 0 -10000 0 0
MYC -0.065 0.35 -10000 0 -1.5 28 28
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.04 0.068 -10000 0 -0.5 5 5
NKD1 0.013 0.019 -10000 0 -10000 0 0
TCF4 0 0.086 -10000 0 -0.71 7 7
TCF3 0.009 0.03 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.02 -10000 0 -0.4 1 1
Ran/GTP 0.002 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.031 0.14 0.46 45 -0.41 1 46
LEF1 -0.014 0.068 -10000 0 -10000 0 0
DVL1 0.11 0.062 0.23 2 -10000 0 2
CSNK2A1 0.017 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.12 0.11 -10000 0 -0.46 3 3
DKK1/LRP6/Kremen 2 -0.025 0.16 -10000 0 -0.5 46 46
LRP6 0.016 0.012 -10000 0 -10000 0 0
CSNK1A1 0.011 0.027 -10000 0 -10000 0 0
NLK 0.005 0.042 -10000 0 -10000 0 0
CCND1 -0.033 0.24 -10000 0 -1.5 12 12
WNT1 0.017 0.001 -10000 0 -10000 0 0
GSK3A 0.017 0.001 -10000 0 -10000 0 0
GSK3B 0.015 0.01 -10000 0 -10000 0 0
FRAT1 0.015 0.01 -10000 0 -10000 0 0
PPP2R5D 0.065 0.028 -10000 0 -10000 0 0
APC 0.054 0.02 -10000 0 -0.37 1 1
WNT1/LRP6/FZD1 0.2 0.12 0.27 393 -10000 0 393
CREBBP 0.008 0.04 -10000 0 -0.73 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.001 0.11 -9999 0 -0.72 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.006 0.084 -9999 0 -0.72 7 7
RAC1-CDC42/GTP/PAK family -0.14 0.14 -9999 0 -0.25 324 324
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.015 0.032 -9999 0 -0.72 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.013 0.045 -9999 0 -0.72 2 2
MAP3K12 0.016 0 -9999 0 -10000 0 0
FGR 0.016 0 -9999 0 -10000 0 0
p38 alpha/TAB1 0 0.033 -9999 0 -0.35 1 1
PRKG1 0.016 0 -9999 0 -10000 0 0
DUSP8 0.016 0.007 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.005 0.028 -9999 0 -0.34 1 1
apoptosis -0.005 0.028 -9999 0 -0.34 1 1
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.016 0.01 -9999 0 -10000 0 0
DUSP1 -0.3 0.36 -9999 0 -0.72 225 225
PAK1 -0.01 0.06 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.004 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.035 0.06 -9999 0 -0.28 12 12
BLK 0.003 0.045 -9999 0 -10000 0 0
HCK 0.013 0.024 -9999 0 -10000 0 0
MAP2K3 0.016 0.007 -9999 0 -10000 0 0
DUSP16 0.014 0.034 -9999 0 -0.72 1 1
DUSP10 0.013 0.037 -9999 0 -0.72 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.045 0.046 -9999 0 -0.38 1 1
positive regulation of innate immune response 0.044 0.066 -9999 0 -0.3 12 12
LCK 0 0.049 -9999 0 -10000 0 0
p38alpha-beta/MKP7 0.05 0.066 -9999 0 -0.28 13 13
p38alpha-beta/MKP5 0.051 0.066 -9999 0 -0.28 13 13
PGK/cGMP 0 0 -9999 0 -10000 0 0
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.1 0.19 -9999 0 -0.31 230 230
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.44 0.36 -9999 0 -0.72 324 324
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.03 0 -9999 0 -10000 0 0
SMARCC1 0.011 0.026 -9999 0 -0.46 1 1
REL 0.01 0.028 -9999 0 -10000 0 0
HDAC7 -0.004 0.14 -9999 0 -0.54 10 10
JUN -0.12 0.29 -9999 0 -0.72 97 97
EP300 0.016 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0.088 -9999 0 -0.55 12 12
FOXO1 -0.083 0.25 -9999 0 -0.72 71 71
T-DHT/AR 0.001 0.15 -9999 0 -0.56 10 10
MAP2K6 -0.003 0.11 -9999 0 -0.73 12 12
BRM/BAF57 0 0.005 -9999 0 -10000 0 0
MAP2K4 0.005 0.085 -9999 0 -0.72 7 7
SMARCA2 0.017 0 -9999 0 -10000 0 0
PDE9A -0.095 0.29 -9999 0 -1.2 31 31
NCOA2 0.016 0.014 -9999 0 -10000 0 0
CEBPA 0.012 0.055 -9999 0 -0.72 3 3
EHMT2 0.017 0 -9999 0 -10000 0 0
cell proliferation 0.06 0.14 -9999 0 -0.45 6 6
NR0B1 -0.16 0.31 -9999 0 -0.72 124 124
EGR1 -0.59 0.28 -9999 0 -0.72 437 437
RXRs/9cRA -0.004 0.045 -9999 0 -0.42 6 6
AR/RACK1/Src 0.031 0.1 -9999 0 -0.39 19 19
AR/GR -0.043 0.17 -9999 0 -0.42 64 64
GNB2L1 0.017 0 -9999 0 -10000 0 0
PKN1 0.015 0.012 -9999 0 -10000 0 0
RCHY1 0.011 0.064 -9999 0 -0.72 4 4
epidermal growth factor receptor activity 0.001 0 -9999 0 -10000 0 0
MAPK8 0.018 0.072 -9999 0 -0.54 8 8
T-DHT/AR/TIF2/CARM1 0.029 0.1 -9999 0 -0.4 19 19
SRC 0.032 0.093 -9999 0 -0.41 19 19
NR3C1 -0.048 0.21 -9999 0 -0.72 46 46
KLK3 -0.068 0.091 -9999 0 -0.42 1 1
APPBP2 0.012 0.016 -9999 0 -10000 0 0
TRIM24 0.016 0.014 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.034 0.087 -9999 0 -0.44 19 19
TMPRSS2 -0.28 0.5 -9999 0 -1.2 128 128
RXRG 0.007 0.079 -9999 0 -0.72 6 6
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.016 0 -9999 0 -10000 0 0
RXRB 0.016 0 -9999 0 -10000 0 0
CARM1 0.015 0.017 -9999 0 -10000 0 0
NR2C2 0.014 0.019 -9999 0 -10000 0 0
KLK2 0.05 0.088 -9999 0 -0.53 1 1
AR -0.012 0.13 -9999 0 -0.29 79 79
SENP1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.015 0.012 -9999 0 -10000 0 0
MDM2 0.01 0.026 -9999 0 -10000 0 0
SRY 0.006 0.073 -9999 0 -0.72 5 5
GATA2 0.007 0.038 -9999 0 -10000 0 0
MYST2 0.012 0.037 -9999 0 -0.72 1 1
HOXB13 -0.04 0.078 -9999 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.026 0.1 -9999 0 -0.4 19 19
positive regulation of transcription 0.007 0.038 -9999 0 -10000 0 0
DNAJA1 0.013 0.012 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.034 -9999 0 -0.36 4 4
NCOA1 0.022 0.034 -9999 0 -0.75 1 1
SPDEF -0.063 0.23 -9999 0 -0.72 56 56
T-DHT/AR/TIF2 0.038 0.066 -9999 0 -0.38 1 1
T-DHT/AR/Hsp90 0.013 0.11 -9999 0 -0.43 19 19
GSK3B 0.015 0.011 -9999 0 -10000 0 0
NR2C1 0.014 0.032 -9999 0 -0.72 1 1
mol:T-DHT 0.02 0.1 -9999 0 -0.45 19 19
SIRT1 0.016 0.007 -9999 0 -10000 0 0
ZMIZ2 0.015 0 -9999 0 -10000 0 0
POU2F1 0.024 0.024 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.086 0.21 -9999 0 -0.41 137 137
CREBBP 0.015 0.032 -9999 0 -0.72 1 1
SMARCE1 0.017 0.01 -9999 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.023 0.025 -9999 0 -10000 0 0
STMN1 -0.009 0.068 -9999 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.015 0.078 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.18 0.13 -9999 0 -0.26 385 385
BIRC5 -0.088 0.079 -9999 0 -10000 0 0
DES 0.006 0.1 -9999 0 -0.61 13 13
Aurora C/Aurora B/INCENP 0.028 0.036 -9999 0 -10000 0 0
Aurora B/TACC1 -0.011 0.12 -9999 0 -0.48 31 31
Aurora B/PP2A 0.017 0.034 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.017 0.011 -9999 0 -0.19 1 1
mitotic metaphase/anaphase transition -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.054 0.079 -9999 0 -10000 0 0
Cul3 protein complex -0.34 0.22 -9999 0 -0.47 385 385
KIF2C 0.016 0.013 -9999 0 -10000 0 0
PEBP1 0.013 0.033 -9999 0 -0.74 1 1
KIF20A -0.092 0.078 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.017 0.033 -9999 0 -10000 0 0
SEPT1 0.013 0.023 -9999 0 -10000 0 0
SMC2 0.009 0.034 -9999 0 -10000 0 0
SMC4 -0.002 0.051 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.036 0.012 -9999 0 -10000 0 0
PSMA3 0.016 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.001 -9999 0 -10000 0 0
H3F3B 0.014 0.024 -9999 0 -0.41 1 1
AURKB -0.015 0.065 -9999 0 -10000 0 0
AURKC 0.013 0.022 -9999 0 -10000 0 0
CDCA8 -0.065 0.082 -9999 0 -10000 0 0
cytokinesis -0.01 0.03 -9999 0 -10000 0 0
Aurora B/Septin1 0.008 0.035 -9999 0 -10000 0 0
AURKA -0.05 0.081 -9999 0 -10000 0 0
INCENP 0 0.047 -9999 0 -10000 0 0
KLHL13 -0.52 0.33 -9999 0 -0.72 382 382
BUB1 -0.12 0.059 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.012 0.099 -9999 0 -10000 0 0
EVI5 0.015 0.032 -9999 0 -0.73 1 1
RhoA/GTP 0.017 0.07 -9999 0 -10000 0 0
SGOL1 -0.03 0.074 -9999 0 -10000 0 0
CENPA 0.012 0.019 -9999 0 -10000 0 0
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.018 0.033 -9999 0 -10000 0 0
NCAPD2 0.008 0.035 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.018 0.032 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.037 0.077 -9999 0 -10000 0 0
NPM1 0.017 0.009 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
KLHL9 0.002 0.1 -9999 0 -0.72 10 10
mitotic prometaphase -0.002 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.033 -9999 0 -10000 0 0
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.01 0.079 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.017 0.009 -9999 0 -10000 0 0
MYLK -0.11 0.19 -9999 0 -0.41 152 152
KIF23 -0.083 0.08 -9999 0 -10000 0 0
VIM -0.044 0.17 -9999 0 -0.56 49 49
RACGAP1 -0.03 0.074 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.017 0.009 -9999 0 -10000 0 0
Chromosomal passenger complex 0.003 0.032 -9999 0 -0.23 1 1
Chromosomal passenger complex/EVI5 0.074 0.094 -9999 0 -0.59 1 1
TACC1 -0.028 0.17 -9999 0 -0.72 31 31
PPP2R5D 0.015 0.012 -9999 0 -10000 0 0
CUL3 0.012 0.055 -9999 0 -0.72 3 3
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.012 0.073 -10000 0 -0.3 5 5
TBX21 -0.094 0.39 -10000 0 -1.2 46 46
B2M 0.016 0.033 -10000 0 -0.72 1 1
TYK2 0.009 0.017 -10000 0 -10000 0 0
IL12RB1 0.009 0.017 -10000 0 -10000 0 0
GADD45B -0.037 0.25 -10000 0 -0.8 34 34
IL12RB2 -0.018 0.077 -10000 0 -0.72 2 2
GADD45G -0.029 0.22 -10000 0 -0.71 31 31
natural killer cell activation -0.004 0.019 -10000 0 -10000 0 0
RELB 0.013 0.023 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.006 0.055 -10000 0 -0.73 1 1
IL2RA 0.006 0.039 -10000 0 -10000 0 0
IFNG -0.021 0.074 -10000 0 -0.72 1 1
STAT3 (dimer) -0.019 0.21 -10000 0 -0.56 33 33
HLA-DRB5 0.005 0.008 -10000 0 -10000 0 0
FASLG -0.045 0.24 -10000 0 -0.8 19 19
NF kappa B2 p52/RelB -0.09 0.19 -10000 0 -0.52 73 73
CD4 0.005 0.008 -10000 0 -10000 0 0
SOCS1 0.015 0.012 -10000 0 -10000 0 0
EntrezGene:6955 -0.017 0.014 -10000 0 -10000 0 0
CD3D -0.002 0.038 -10000 0 -10000 0 0
CD3E 0.005 0.011 -10000 0 -10000 0 0
CD3G -0.024 0.11 -10000 0 -0.73 11 11
IL12Rbeta2/JAK2 -0.002 0.066 -10000 0 -0.55 3 3
CCL3 -0.042 0.24 -10000 0 -0.78 19 19
CCL4 -0.042 0.24 -10000 0 -0.67 30 30
HLA-A 0.014 0.026 -10000 0 -10000 0 0
IL18/IL18R 0.027 0.16 -10000 0 -0.49 45 45
NOS2 -0.045 0.24 -10000 0 -0.53 76 76
IL12/IL12R/TYK2/JAK2/SPHK2 0.012 0.073 -10000 0 -0.3 5 5
IL1R1 -0.14 0.46 -10000 0 -1.3 64 64
IL4 0.022 0.017 -10000 0 -10000 0 0
JAK2 0.008 0.037 -10000 0 -0.74 1 1
EntrezGene:6957 -0.015 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.006 0.076 -10000 0 -0.43 7 7
RAB7A 0.009 0.21 -10000 0 -0.68 19 19
lysosomal transport 0.011 0.2 -10000 0 -0.59 28 28
FOS -0.88 0.64 -10000 0 -1.3 376 376
STAT4 (dimer) -0.006 0.24 -10000 0 -0.66 40 40
STAT5A (dimer) -0.09 0.21 -10000 0 -0.54 75 75
GZMA -0.051 0.23 -10000 0 -0.54 74 74
GZMB -0.046 0.24 -10000 0 -0.85 18 18
HLX 0.013 0.045 -10000 0 -0.72 2 2
LCK -0.052 0.24 -10000 0 -0.56 73 73
TCR/CD3/MHC II/CD4 -0.12 0.13 -10000 0 -0.35 43 43
IL2/IL2R 0.007 0.039 -10000 0 -0.41 1 1
MAPK14 -0.008 0.24 -10000 0 -0.72 35 35
CCR5 -0.033 0.22 -10000 0 -0.7 32 32
IL1B -0.002 0.083 -10000 0 -0.73 6 6
STAT6 -0.028 0.16 -10000 0 -0.51 32 32
STAT4 0.005 0.086 -10000 0 -0.72 7 7
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 -0.011 0.06 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
NFKB2 0.015 0.012 -10000 0 -10000 0 0
IL12B 0.007 0.029 -10000 0 -10000 0 0
CD8A 0.002 0.002 -10000 0 -10000 0 0
CD8B 0.014 0.027 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.012 0.072 0.29 5 -10000 0 5
IL2RB 0.013 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.23 -10000 0 -0.61 40 40
IL2RG 0.006 0.039 -10000 0 -10000 0 0
IL12 0.001 0.084 -10000 0 -0.55 10 10
STAT5A 0.013 0.045 -10000 0 -0.72 2 2
CD247 -0.041 0.16 -10000 0 -0.73 25 25
IL2 0.015 0.033 -10000 0 -0.72 1 1
SPHK2 0.016 0 -10000 0 -10000 0 0
FRAP1 0.016 0 -10000 0 -10000 0 0
IL12A -0.006 0.1 -10000 0 -0.73 10 10
IL12/IL12R/TYK2/JAK2 -0.052 0.26 -10000 0 -0.6 74 74
MAP2K3 -0.013 0.24 -10000 0 -0.72 35 35
RIPK2 0.014 0.02 -10000 0 -10000 0 0
MAP2K6 -0.017 0.24 -10000 0 -0.71 37 37
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.033 -10000 0 -0.74 1 1
IL18RAP -0.043 0.21 -10000 0 -0.73 45 45
IL12Rbeta1/TYK2 0.012 0.025 -10000 0 -10000 0 0
EOMES 0.015 0.031 -10000 0 -10000 0 0
STAT1 (dimer) -0.011 0.21 -10000 0 -0.57 33 33
T cell proliferation -0.004 0.2 -10000 0 -0.55 39 39
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.036 -10000 0 -0.73 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.07 0.18 -10000 0 -0.64 38 38
ATF2 0.003 0.23 -10000 0 -0.66 35 35
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.11 0.099 0.18 1 -0.27 4 5
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.014 0.02 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.014 0.02 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.1 0.14 -10000 0 -0.22 290 290
YWHAZ 0.014 0.017 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.005 0.11 -10000 0 -0.54 21 21
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.015 0.012 -10000 0 -10000 0 0
YWHAB 0.015 0.012 -10000 0 -10000 0 0
SNARE/Synip 0.001 0.01 -10000 0 -10000 0 0
YWHAG 0.016 0.01 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0.023 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.015 0.032 -10000 0 -0.72 1 1
GYS1 0.04 0.003 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.015 0.032 -10000 0 -0.72 1 1
TC10/GTP/CIP4/Exocyst -0.002 0.029 -10000 0 -0.47 2 2
AS160/14-3-3 0.049 0.047 -10000 0 -10000 0 0
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 -0.11 0.15 -10000 0 -0.24 290 290
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.033 0.002 -10000 0 -10000 0 0
SFN 0.011 0.05 -10000 0 -0.72 2 2
LNPEP 0.015 0.016 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
Coregulation of Androgen receptor activity

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
NRIP1 0.003 0.1 -9999 0 -0.72 10 10
SVIL 0.001 0.11 -9999 0 -0.72 12 12
ZNF318 0.003 0.005 -9999 0 -10000 0 0
JMJD2C 0.026 0.001 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.062 0.17 -9999 0 -0.48 70 70
CARM1 0.015 0.017 -9999 0 -10000 0 0
PRDX1 0.015 0.014 -9999 0 -10000 0 0
PELP1 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.012 0.064 -9999 0 -0.72 4 4
AKT1 0.013 0.02 -9999 0 -10000 0 0
PTK2B 0.017 0 -9999 0 -10000 0 0
MED1 0.005 0.039 -9999 0 -10000 0 0
MAK -0.005 0.033 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.018 0.007 -9999 0 -10000 0 0
GSN -0.18 0.33 -9999 0 -0.72 144 144
NCOA2 0.015 0.014 -9999 0 -10000 0 0
NCOA6 0.018 0.007 -9999 0 -10000 0 0
DNA-PK 0.003 0.014 -9999 0 -10000 0 0
NCOA4 0.014 0.045 -9999 0 -0.72 2 2
PIAS3 0.018 0 -9999 0 -10000 0 0
cell proliferation -0.02 0.033 -9999 0 -10000 0 0
XRCC5 0.015 0 -9999 0 -10000 0 0
UBE3A 0.019 0.001 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.073 0.17 -9999 0 -0.49 71 71
FHL2 -0.15 0.35 -9999 0 -1.1 58 58
RANBP9 0.018 0.007 -9999 0 -10000 0 0
JMJD1A -0.008 0.062 -9999 0 -10000 0 0
CDK6 0.005 0.086 -9999 0 -0.72 7 7
TGFB1I1 0.014 0.055 -9999 0 -0.72 3 3
T-DHT/AR/CyclinD1 -0.071 0.2 -9999 0 -0.5 82 82
XRCC6 0.015 0 -9999 0 -10000 0 0
T-DHT/AR -0.077 0.2 -9999 0 -0.47 89 89
CTDSP1 0.017 0 -9999 0 -10000 0 0
CTDSP2 0.013 0.001 -9999 0 -10000 0 0
BRCA1 0.015 0.024 -9999 0 -10000 0 0
TCF4 0.004 0.084 -9999 0 -0.72 7 7
CDKN2A -0.013 0.062 -9999 0 -10000 0 0
SRF 0.01 0.043 -9999 0 -10000 0 0
NKX3-1 -0.081 0.11 -9999 0 -0.32 33 33
KLK3 0.013 0.038 -9999 0 -10000 0 0
TMF1 0.017 0 -9999 0 -10000 0 0
HNRNPA1 0.015 0 -9999 0 -10000 0 0
AOF2 0.018 0.007 -9999 0 -10000 0 0
APPL1 0.025 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.085 0.16 -9999 0 -0.48 70 70
AR -0.097 0.25 -9999 0 -0.73 70 70
UBA3 0.001 0 -9999 0 -10000 0 0
PATZ1 0.014 0.007 -9999 0 -10000 0 0
PAWR 0.013 0.037 -9999 0 -0.72 1 1
PRKDC 0.009 0.031 -9999 0 -10000 0 0
PA2G4 0.014 0.007 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.057 0.16 -9999 0 -0.45 70 70
RPS6KA3 0.015 0.046 -9999 0 -0.72 2 2
T-DHT/AR/ARA70 -0.063 0.18 -9999 0 -0.48 72 72
LATS2 0.001 0.1 -9999 0 -0.72 10 10
T-DHT/AR/PRX1 -0.077 0.15 -9999 0 -0.45 70 70
Cyclin D3/CDK11 p58 0 0.004 -9999 0 -10000 0 0
VAV3 -0.032 0.15 -9999 0 -0.72 22 22
KLK2 0.001 0.077 -9999 0 -10000 0 0
CASP8 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.044 0.16 -9999 0 -0.44 70 70
TMPRSS2 -0.25 0.49 -9999 0 -1.1 128 128
CCND1 -0.027 0.12 -9999 0 -0.72 12 12
PIAS1 0.019 0.007 -9999 0 -10000 0 0
mol:T-DHT -0.018 0.041 -9999 0 -0.081 147 147
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.019 0.016 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.091 0.17 -9999 0 -0.49 77 77
CMTM2 0.016 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.001 0.037 -9999 0 -10000 0 0
CCND3 0.016 0.007 -9999 0 -10000 0 0
TGIF1 0.013 0.032 -9999 0 -0.72 1 1
FKBP4 0.012 0.031 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.019 0.067 -9999 0 -10000 0 0
mol:Halofuginone 0.004 0.002 -9999 0 -10000 0 0
ITGA1 0.013 0.045 -9999 0 -0.72 2 2
CDKN1A -0.12 0.079 -9999 0 -0.59 2 2
PRL-3/alpha Tubulin -0.003 0.016 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.04 -9999 0 -10000 0 0
AGT -0.013 0.063 -9999 0 -10000 0 0
CCNA2 -0.32 0.17 -9999 0 -0.43 170 170
TUBA1B 0.015 0.012 -9999 0 -10000 0 0
EGR1 -0.43 0.21 -9999 0 -0.53 437 437
CDK2/Cyclin E1 -0.098 0.083 -9999 0 -0.55 2 2
MAPK3 0.025 0.021 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta -0.001 0.011 -9999 0 -10000 0 0
MAPK1 0.025 0.021 -9999 0 -10000 0 0
PTP4A1 -0.32 0.17 -9999 0 -0.49 3 3
PTP4A3 0.01 0.031 -9999 0 -10000 0 0
PTP4A2 0.013 0.022 -9999 0 -10000 0 0
ITGB1 0.025 0.021 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
RAC1 -0.12 0.073 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.29 0.16 -9999 0 -0.44 6 6
RABGGTA 0.016 0 -9999 0 -10000 0 0
BCAR1 -0.001 0.008 -9999 0 -10000 0 0
RHOC -0.12 0.073 -9999 0 -10000 0 0
RHOA -0.12 0.073 -9999 0 -10000 0 0
cell motility -0.12 0.078 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.29 0.16 -9999 0 -0.44 6 6
PRL-3/alpha1 Integrin -0.005 0.036 -9999 0 -0.54 2 2
ROCK1 -0.12 0.079 -9999 0 -10000 0 0
RABGGTB 0.016 0 -9999 0 -10000 0 0
CDK2 0.012 0.025 -9999 0 -10000 0 0
mitosis -0.32 0.17 -9999 0 -0.49 3 3
ATF5 0.015 0.014 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.027 0.01 -9999 0 -10000 0 0
Syndecan-4/Syndesmos 0.042 0.02 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.073 0.17 -9999 0 -0.4 1 1
Syndecan-4/ADAM12 0.049 0.03 -9999 0 -10000 0 0
CCL5 0.004 0.086 -9999 0 -0.72 7 7
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0.007 -9999 0 -10000 0 0
ITGA5 0.016 0.007 -9999 0 -10000 0 0
SDCBP 0.015 0.032 -9999 0 -0.72 1 1
PLG 0.003 0.031 -9999 0 -0.7 1 1
ADAM12 -0.013 0.069 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.015 0.012 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.038 0.025 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.042 0.02 -9999 0 -10000 0 0
Syndecan-4/CXCL12/CXCR4 -0.07 0.18 -9999 0 -0.42 1 1
Syndecan-4/Laminin alpha3 -0.09 0.19 -9999 0 -10000 0 0
MDK 0.004 0.043 -9999 0 -10000 0 0
Syndecan-4/FZD7 -0.077 0.18 -9999 0 -10000 0 0
Syndecan-4/Midkine 0.046 0.025 -9999 0 -10000 0 0
FZD7 -0.2 0.34 -9999 0 -0.72 158 158
Syndecan-4/FGFR1/FGF -0.25 0.16 -9999 0 -0.64 13 13
THBS1 0.012 0.027 -9999 0 -10000 0 0
integrin-mediated signaling pathway 0.042 0.026 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.073 0.17 -9999 0 -0.4 1 1
Syndecan-4/TACI 0.042 0.021 -9999 0 -10000 0 0
CXCR4 0.004 0.043 -9999 0 -10000 0 0
cell adhesion 0.031 0.008 -9999 0 -10000 0 0
Syndecan-4/Dynamin 0.042 0.02 -9999 0 -10000 0 0
Syndecan-4/TSP1 0.043 0.022 -9999 0 -10000 0 0
Syndecan-4/GIPC 0.042 0.02 -9999 0 -10000 0 0
Syndecan-4/RANTES 0.037 0.049 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 0.016 0.01 -9999 0 -10000 0 0
LAMA3 -0.23 0.35 -9999 0 -0.72 176 176
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.017 0.014 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin 0.042 0.02 -9999 0 -10000 0 0
TFPI -0.27 0.36 -9999 0 -0.72 207 207
F2 0.018 0.001 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0 0.003 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.078 0.18 -9999 0 -10000 0 0
ACTN1 0.016 0 -9999 0 -10000 0 0
TNC 0.01 0.042 -9999 0 -0.72 1 1
Syndecan-4/CXCL12 -0.082 0.18 -9999 0 -10000 0 0
FGF6 0.013 0.045 -9999 0 -0.72 2 2
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.21 0.34 -9999 0 -0.72 165 165
TNFRSF13B 0.016 0.01 -9999 0 -10000 0 0
FGF2 -0.55 0.31 -9999 0 -0.72 405 405
FGFR1 -0.007 0.12 -9999 0 -0.72 15 15
Syndecan-4/PI-4-5-P2 0.031 0.02 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.1 0.078 -9999 0 -10000 0 0
cell migration -0.02 0.013 -9999 0 -10000 0 0
PRKCD 0.003 0.018 -9999 0 -10000 0 0
vasculogenesis 0.042 0.022 -9999 0 -10000 0 0
SDC4 0.034 0.022 -9999 0 -10000 0 0
Syndecan-4/Tenascin C 0.043 0.027 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.02 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.041 0.026 -9999 0 -10000 0 0
MMP9 -0.057 0.082 -9999 0 -10000 0 0
Rac1/GTP 0.025 0.014 -9999 0 -10000 0 0
cytoskeleton organization 0.042 0.02 -9999 0 -10000 0 0
GIPC1 0.015 0.012 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.11 0.19 -9999 0 -10000 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.016 0.01 -9999 0 -10000 0 0
CCL5 0.004 0.086 -9999 0 -0.72 7 7
SDCBP 0.015 0.032 -9999 0 -0.72 1 1
FGFR/FGF2/Syndecan-1 -0.026 0.098 -9999 0 -0.26 46 46
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.015 0.094 -9999 0 -0.27 1 1
Syndecan-1/Syntenin -0.016 0.095 -9999 0 -0.39 1 1
MAPK3 0.004 0.087 -9999 0 -10000 0 0
HGF/MET -0.053 0.16 -9999 0 -0.54 52 52
TGFB1/TGF beta receptor Type II 0.016 0.01 -9999 0 -10000 0 0
BSG 0.015 0.014 -9999 0 -10000 0 0
keratinocyte migration -0.015 0.093 -9999 0 -0.27 1 1
Syndecan-1/RANTES -0.02 0.11 -9999 0 -0.53 7 7
Syndecan-1/CD147 -0.004 0.091 -9999 0 -10000 0 0
Syndecan-1/Syntenin/PIP2 -0.023 0.087 -9999 0 -0.38 1 1
LAMA5 0.015 0.014 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.023 0.085 -9999 0 -0.37 1 1
MMP7 -0.1 0.27 -9999 0 -0.72 85 85
HGF 0.016 0.01 -9999 0 -10000 0 0
Syndecan-1/CASK -0.026 0.093 -9999 0 -0.25 46 46
Syndecan-1/HGF/MET -0.044 0.16 -9999 0 -0.46 52 52
regulation of cell adhesion 0.014 0.085 -9999 0 -10000 0 0
HPSE 0.003 0.045 -9999 0 -10000 0 0
positive regulation of cell migration -0.026 0.098 -9999 0 -0.26 46 46
SDC1 -0.027 0.099 -9999 0 -0.26 46 46
Syndecan-1/Collagen -0.026 0.098 -9999 0 -0.26 46 46
PPIB 0.016 0.01 -9999 0 -10000 0 0
MET -0.057 0.22 -9999 0 -0.72 52 52
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.059 0.081 -9999 0 -10000 0 0
MAPK1 0.004 0.087 -9999 0 -10000 0 0
homophilic cell adhesion -0.026 0.098 -9999 0 -0.26 46 46
MMP1 -0.09 0.078 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 -0.019 0.15 -9999 0 -0.72 23 23
PLK4 -0.01 0.06 -9999 0 -10000 0 0
regulation of centriole replication -0.014 0.12 -9999 0 -0.56 23 23
Noncanonical Wnt signaling pathway

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.015 0.032 -9999 0 -0.72 1 1
GNB1/GNG2 -0.041 0.15 -9999 0 -0.68 19 19
mol:DAG 0.013 0.15 -9999 0 -0.6 19 19
PLCG1 0.012 0.16 -9999 0 -0.63 19 19
YES1 -0.006 0.17 -9999 0 -0.73 18 18
FZD3 -0.019 0.16 -9999 0 -0.72 25 25
FZD6 -0.024 0.16 -9999 0 -0.72 26 26
G protein 0.012 0.16 -9999 0 -0.64 19 19
MAP3K7 0.033 0.13 -9999 0 -0.48 19 19
mol:Ca2+ 0.014 0.14 -9999 0 -0.58 19 19
mol:IP3 0.013 0.15 -9999 0 -0.6 19 19
NLK 0.031 0.016 -9999 0 -10000 0 0
GNB1 0.016 0.01 -9999 0 -10000 0 0
CAMK2A 0.023 0.14 -9999 0 -0.53 19 19
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.016 0.18 -9999 0 -0.41 72 72
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.007 0.17 -9999 0 -0.71 18 18
GO:0007205 0.013 0.15 -9999 0 -0.59 19 19
WNT6 0.012 0.048 -9999 0 -0.72 2 2
WNT4 0.005 0.05 -9999 0 -0.72 1 1
NFAT1/CK1 alpha -0.035 0.14 -9999 0 -0.64 18 18
GNG2 0.015 0.032 -9999 0 -0.72 1 1
WNT5A -0.029 0.17 -9999 0 -0.72 28 28
WNT11 -0.001 0.1 -9999 0 -0.72 10 10
CDC42 0.004 0.16 -9999 0 -0.68 18 18
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.007 0.15 -9999 0 -0.53 37 37
KLHL20 -0.014 0.049 -9999 0 -0.22 8 8
CYFIP2 -0.002 0.052 -9999 0 -10000 0 0
Rac1/GDP 0.046 0.1 -9999 0 -0.31 37 37
ENAH 0.01 0.15 -9999 0 -0.53 37 37
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0.01 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.064 -9999 0 -0.72 4 4
CDC42/GTP -0.018 0.064 -9999 0 -0.45 1 1
ABI1/Sra1/Nap1 -0.011 0.032 -9999 0 -0.18 3 3
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.028 0.11 -9999 0 -0.41 37 37
RAPGEF1 0.03 0.13 -9999 0 -0.44 37 37
CTNND1 0.016 0.007 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.039 0.14 -9999 0 -0.55 37 37
CRK 0.02 0.14 -9999 0 -0.48 38 38
E-cadherin/gamma catenin/alpha catenin -0.028 0.11 -9999 0 -0.46 34 34
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.007 0.058 -9999 0 -0.42 10 10
DLG1 0.01 0.15 -9999 0 -0.53 37 37
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.03 0.065 -9999 0 -0.31 3 3
MLLT4 0.002 0.1 -9999 0 -0.72 10 10
ARF6/GTP/NME1/Tiam1 0.003 0.015 -9999 0 -10000 0 0
PI3K -0.038 0.083 -9999 0 -0.42 3 3
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.036 0.13 -9999 0 -0.54 34 34
TIAM1 0.015 0.012 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.026 0.1 -9999 0 -0.39 37 37
AKT1 -0.02 0.048 -9999 0 -0.22 3 3
PIK3R1 -0.056 0.22 -9999 0 -0.72 52 52
CDH1 -0.032 0.18 -9999 0 -0.72 33 33
RhoA/GDP 0.046 0.1 -9999 0 -0.31 37 37
actin cytoskeleton organization -0.007 0.039 -9999 0 -0.18 4 4
CDC42/GDP 0.046 0.1 -9999 0 -0.31 37 37
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.01 0.082 -9999 0 -0.3 34 34
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.028 0.11 -9999 0 -0.41 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin -0.027 0.1 -9999 0 -0.4 37 37
mol:GDP 0.039 0.12 -9999 0 -0.36 38 38
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0.036 -9999 0 -0.72 1 1
p120 catenin/RhoA/GDP -0.023 0.081 -9999 0 -0.34 8 8
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0.003 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.018 0.059 -9999 0 -0.22 17 17
NME1 0.011 0.029 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.009 0.15 -9999 0 -0.53 38 38
regulation of cell-cell adhesion -0.017 0.056 -9999 0 -0.38 1 1
WASF2 -0.004 0.017 -9999 0 -10000 0 0
Rap1/GTP -0.021 0.074 -9999 0 -0.42 2 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.022 0.094 -9999 0 -0.38 34 34
CCND1 0.019 0.072 -9999 0 -0.27 17 17
VAV2 0.024 0.14 -9999 0 -0.47 37 37
RAP1/GDP -0.015 0.081 -9999 0 -0.37 3 3
adherens junction assembly 0.011 0.15 -9999 0 -0.51 38 38
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0.007 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.024 0.093 -9999 0 -0.36 38 38
E-cadherin/beta catenin -0.029 0.11 -9999 0 -0.45 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.003 0.15 -9999 0 -0.53 37 37
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
Rac1/GTP -0.025 0.077 -9999 0 -0.35 11 11
E-cadherin/beta catenin/alpha catenin -0.031 0.12 -9999 0 -0.46 37 37
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.04 0.14 -9999 0 -0.56 37 37
IL2 signaling events mediated by PI3K

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
BCL2L1 0.046 0.08 -10000 0 -10000 0 0
UGCG 0.009 0.046 -10000 0 -0.75 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.015 0.17 -10000 0 -0.37 41 41
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.027 0.047 -10000 0 -0.74 1 1
mol:DAG -0.005 0.075 -10000 0 -0.99 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.088 0.15 -10000 0 -0.46 41 41
FRAP1 -0.014 0.23 -10000 0 -0.54 41 41
FOXO3 0.026 0.16 -10000 0 -0.51 12 12
AKT1 0.016 0.17 -10000 0 -0.42 35 35
GAB2 0.012 0.017 -10000 0 -10000 0 0
SMPD1 -0.001 0.018 -10000 0 -10000 0 0
SGMS1 -0.005 0.053 -10000 0 -0.66 3 3
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 -0.025 0.14 -10000 0 -0.46 52 52
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation 0.025 0.09 -10000 0 -0.28 10 10
EIF3A 0.016 0.007 -10000 0 -10000 0 0
PI3K -0.031 0.17 -10000 0 -0.54 52 52
RPS6KB1 0.008 0.073 -10000 0 -10000 0 0
mol:sphingomyelin -0.005 0.075 -10000 0 -0.99 3 3
natural killer cell activation -0.001 0.005 -10000 0 -0.013 27 27
JAK3 0.016 0.008 -10000 0 -10000 0 0
PIK3R1 -0.057 0.22 -10000 0 -0.72 52 52
JAK1 0.013 0.046 -10000 0 -0.72 2 2
NFKB1 0.016 0 -10000 0 -10000 0 0
MYC -0.006 0.27 -10000 0 -1 28 28
MYB -0.066 0.37 -10000 0 -1.3 43 43
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.11 -10000 0 -0.35 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.025 0.071 -10000 0 -0.59 1 1
mol:PI-3-4-5-P3 0.039 0.11 -10000 0 -0.34 2 2
Rac1/GDP -0.015 0.13 -10000 0 -0.41 52 52
T cell proliferation 0.038 0.1 -10000 0 -0.32 2 2
SHC1 0.013 0.007 -10000 0 -10000 0 0
RAC1 0.016 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.02 -10000 0 -0.067 43 43
PRKCZ 0.038 0.1 -10000 0 -0.34 2 2
NF kappa B1 p50/RelA -0.086 0.15 -10000 0 -0.45 41 41
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.031 0.087 -10000 0 -10000 0 0
HSP90AA1 0.015 0.012 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA 0.004 0.04 -10000 0 -10000 0 0
IL2RB 0.013 0.024 -10000 0 -10000 0 0
TERT 0.014 0.035 -10000 0 -0.72 1 1
E2F1 0 0.13 -10000 0 -0.44 43 43
SOS1 0.013 0.008 -10000 0 -10000 0 0
RPS6 0.015 0.032 -10000 0 -0.72 1 1
mol:cAMP -0.001 0.01 0.031 43 -10000 0 43
PTPN11 0.013 0.008 -10000 0 -10000 0 0
IL2RG 0.006 0.039 -10000 0 -10000 0 0
actin cytoskeleton organization 0.038 0.1 -10000 0 -0.32 2 2
GRB2 0.01 0.023 -10000 0 -10000 0 0
IL2 0.014 0.034 -10000 0 -0.72 1 1
PIK3CA 0.016 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.008 0.13 -10000 0 -0.39 52 52
LCK 0 0.049 -10000 0 -10000 0 0
BCL2 -0.11 0.41 -10000 0 -0.91 107 107
Arf6 trafficking events

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
SLC2A4 -0.41 0.36 -10000 0 -0.72 303 303
CLTC 0.038 0.014 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.026 0.04 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.009 -10000 0 -10000 0 0
EXOC4 0.016 0 -10000 0 -10000 0 0
CD59 0.029 0.041 -10000 0 -0.32 3 3
CPE -0.066 0.19 -10000 0 -0.47 96 96
CTNNB1 0.01 0.064 -10000 0 -0.72 4 4
membrane fusion 0.025 0.043 -10000 0 -10000 0 0
CTNND1 0.039 0.013 -10000 0 -10000 0 0
DNM2 0.016 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.023 -10000 0 -10000 0 0
TSHR 0.02 0.043 -10000 0 -0.47 4 4
INS 0.024 0.008 -10000 0 -10000 0 0
BIN1 0.016 0.007 -10000 0 -10000 0 0
mol:Choline 0.025 0.043 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.015 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.009 -10000 0 -10000 0 0
JUP 0.032 0.022 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0 0.003 -10000 0 -10000 0 0
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.015 0.069 -10000 0 -0.34 1 1
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0.046 -10000 0 -0.72 2 2
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.008 0.036 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.054 0.015 -10000 0 -0.29 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.016 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.012 0.049 0.38 2 -10000 0 2
positive regulation of phagocytosis 0.024 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.002 0.029 -10000 0 -0.47 2 2
ACAP1 0.023 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.03 0.02 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.041 0.027 -10000 0 -10000 0 0
JIP4/KLC1 0 0.003 -10000 0 -10000 0 0
EXOC1 0.016 0 -10000 0 -10000 0 0
exocyst 0.054 0.015 -10000 0 -0.3 1 1
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0.003 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.039 0.013 -10000 0 -10000 0 0
NME1 0.021 0.015 -10000 0 -10000 0 0
clathrin coat assembly 0.038 0.014 -10000 0 -10000 0 0
IL2RA 0.031 0.019 -10000 0 -10000 0 0
VAMP3 0.024 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.2 0.17 -10000 0 -0.34 303 303
EXOC6 0.014 0.034 -10000 0 -0.72 1 1
PLD1 -0.012 0.061 -10000 0 -0.32 21 21
PLD2 -0.001 0.014 -10000 0 -0.32 1 1
EXOC5 0.016 0 -10000 0 -10000 0 0
PIP5K1C 0.037 0.023 -10000 0 -10000 0 0
SDC1 0.025 0.021 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.015 -10000 0 -10000 0 0
EXOC7 0.016 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.012 0.05 -10000 0 -0.39 2 2
mol:Phosphatidic acid 0.025 0.043 -10000 0 -10000 0 0
endocytosis 0 0.003 -10000 0 -10000 0 0
SCAMP2 0.016 0 -10000 0 -10000 0 0
ADRB2 -0.17 0.2 -10000 0 -0.36 286 286
EXOC3 0.016 0 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.03 0.014 -10000 0 -10000 0 0
KLC1 0.016 0 -10000 0 -10000 0 0
AVPR2 0.044 0.028 -10000 0 -0.36 2 2
RALA 0.016 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.009 0.044 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN 0.002 0.13 -10000 0 -0.38 17 17
IKBKB 0.047 0.046 0.23 1 -10000 0 1
AKT1 0.031 0.082 0.26 13 -0.26 8 21
IKBKG 0.051 0.046 0.23 1 -10000 0 1
CALM1 0.028 0.074 -10000 0 -0.36 12 12
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
MAP3K1 0.048 0.11 -10000 0 -0.56 14 14
MAP3K7 0.016 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.078 0.24 15 -0.39 12 27
DOK1 0.014 0.019 -10000 0 -10000 0 0
AP-1 -0.11 0.12 -10000 0 -0.26 112 112
LYN 0.015 0.01 -10000 0 -10000 0 0
BLNK 0.011 0.029 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
BCR complex -0.019 0.089 -10000 0 -0.54 14 14
CD22 -0.02 0.11 -10000 0 -0.68 14 14
CAMK2G 0.036 0.07 -10000 0 -0.41 5 5
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.006 0.055 -10000 0 -0.38 2 2
GO:0007205 0.019 0.079 0.24 15 -0.4 12 27
SYK 0.01 0.032 -10000 0 -10000 0 0
ELK1 0.027 0.075 -10000 0 -0.37 12 12
NFATC1 0.036 0.092 -10000 0 -0.45 16 16
B-cell antigen/BCR complex -0.019 0.089 -10000 0 -0.54 14 14
PAG1/CSK -0.002 0.014 -10000 0 -10000 0 0
NFKBIB 0.032 0.019 0.12 1 -10000 0 1
HRAS 0.033 0.069 -10000 0 -0.35 12 12
NFKBIA 0.032 0.019 0.12 1 -10000 0 1
NF-kappa-B/RelA/I kappa B beta 0.036 0.018 0.13 1 -10000 0 1
RasGAP/Csk -0.007 0.089 -10000 0 -0.49 14 14
mol:GDP 0.017 0.074 0.23 15 -0.37 12 27
PTEN -0.002 0.11 -10000 0 -0.72 13 13
CD79B -0.005 0.12 -10000 0 -0.72 14 14
NF-kappa-B/RelA/I kappa B alpha 0.036 0.018 0.13 1 -10000 0 1
GRB2 0.013 0.022 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.012 0.14 -10000 0 -0.56 15 15
PIK3R1 -0.056 0.22 -10000 0 -0.72 52 52
mol:IP3 0.019 0.08 0.24 15 -0.4 12 27
CSK 0.016 0.01 -10000 0 -10000 0 0
FOS -0.24 0.19 -10000 0 -0.36 363 363
CHUK 0.05 0.049 0.23 1 -0.44 1 2
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.008 0.049 -10000 0 -0.4 4 4
PTPN6 -0.018 0.1 -10000 0 -0.63 14 14
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 0.031 0.015 -10000 0 -10000 0 0
VAV2 -0.016 0.11 -10000 0 -0.65 14 14
ubiquitin-dependent protein catabolic process 0.037 0.019 0.13 1 -10000 0 1
BTK 0.005 0.014 -10000 0 -10000 0 0
CD19 -0.024 0.11 -10000 0 -0.68 14 14
MAP4K1 0.013 0.023 -10000 0 -10000 0 0
CD72 -0.017 0.066 -10000 0 -10000 0 0
PAG1 0.012 0.025 -10000 0 -10000 0 0
MAPK14 0.055 0.092 -10000 0 -0.46 14 14
SH3BP5 -0.007 0.13 -10000 0 -0.72 17 17
PIK3AP1 0.025 0.086 0.27 13 -0.44 12 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.037 0.073 -10000 0 -0.62 4 4
RAF1 0.041 0.065 -10000 0 -0.38 5 5
RasGAP/p62DOK/SHIP -0.007 0.085 -10000 0 -0.48 14 14
CD79A 0.007 0.037 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.1 0.12 0.21 1 -0.25 112 113
RASA1 0.015 0.012 -10000 0 -10000 0 0
MAPK3 0.056 0.058 -10000 0 -0.33 4 4
MAPK1 0.056 0.058 -10000 0 -0.33 4 4
CD72/SHP1 0.042 0.11 -10000 0 -0.58 14 14
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.054 0.094 -10000 0 -0.46 14 14
actin cytoskeleton organization 0.037 0.1 -10000 0 -0.54 14 14
NF-kappa-B/RelA 0.076 0.035 0.24 1 -10000 0 1
Calcineurin -0.014 0.062 -10000 0 -0.33 14 14
PI3K -0.038 0.1 -10000 0 -0.48 15 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.003 0.089 0.27 15 -0.47 12 27
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 0.031 0.13 -10000 0 -0.72 14 14
DAPP1 -0.007 0.14 -10000 0 -0.82 14 14
cytokine secretion 0.036 0.086 -10000 0 -0.42 16 16
mol:DAG 0.019 0.08 0.24 15 -0.4 12 27
PLCG2 0 0.11 -10000 0 -0.72 11 11
MAP2K1 0.049 0.062 -10000 0 -0.37 4 4
B-cell antigen/BCR complex/FcgammaRIIB -0.013 0.1 -10000 0 -0.58 14 14
mol:PI-3-4-5-P3 -0.021 0.095 0.34 13 -0.34 14 27
ETS1 0.043 0.068 -10000 0 -0.38 5 5
B-cell antigen/BCR complex/LYN/SYK/BLNK 0 0.072 -10000 0 -0.39 14 14
B-cell antigen/BCR complex/LYN -0.018 0.12 -10000 0 -0.72 14 14
MALT1 0.016 0.007 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 0.036 0.11 -10000 0 -0.58 14 14
B-cell antigen/BCR complex/LYN/SYK -0.013 0.11 -10000 0 -0.61 14 14
CARD11 0.025 0.076 0.24 15 -0.37 12 27
FCGR2B 0.01 0.065 -10000 0