Thyroid Adenocarcinoma: PARADIGM pathway analysis of mRNASeq expression data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 47 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
Ephrin A reverse signaling 199
Signaling events mediated by Stem cell factor receptor (c-Kit) 123
Signaling events regulated by Ret tyrosine kinase 115
Reelin signaling pathway 102
Wnt signaling 85
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 83
IL4-mediated signaling events 79
PDGFR-alpha signaling pathway 75
Noncanonical Wnt signaling pathway 74
FOXA2 and FOXA3 transcription factor networks 71
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
Ephrin A reverse signaling 199 1395 7 -0.55 0 1000 -1000 -0.028 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 123 9596 78 -0.79 0.23 1000 -1000 -0.075 -1000
Signaling events regulated by Ret tyrosine kinase 115 9488 82 -0.48 0.013 1000 -1000 -0.079 -1000
Reelin signaling pathway 102 5729 56 -0.63 0.034 1000 -1000 -0.088 -1000
Wnt signaling 85 598 7 -0.45 0.013 1000 -1000 -0.029 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 83 5675 68 -0.88 0.35 1000 -1000 -0.13 -1000
IL4-mediated signaling events 79 7210 91 -1.3 0.66 1000 -1000 -0.12 -1000
PDGFR-alpha signaling pathway 75 3341 44 -0.53 0.033 1000 -1000 -0.065 -1000
Noncanonical Wnt signaling pathway 74 1946 26 -0.45 0.013 1000 -1000 -0.086 -1000
FOXA2 and FOXA3 transcription factor networks 71 3278 46 -0.98 0.02 1000 -1000 -0.07 -1000
Signaling events mediated by the Hedgehog family 70 3690 52 -0.43 0.23 1000 -1000 -0.077 -1000
Nongenotropic Androgen signaling 61 3216 52 -0.33 0.16 1000 -1000 -0.064 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 57 3100 54 -0.63 0.027 1000 -1000 -0.096 -1000
Calcium signaling in the CD4+ TCR pathway 55 1705 31 -0.52 0.013 1000 -1000 -0.082 -1000
Nephrin/Neph1 signaling in the kidney podocyte 53 1813 34 -0.16 0.013 1000 -1000 -0.07 -1000
Glypican 1 network 49 2362 48 -0.4 0.029 1000 -1000 -0.05 -1000
Endothelins 49 4798 96 -0.43 0.013 1000 -1000 -0.082 -1000
HIF-1-alpha transcription factor network 45 3450 76 -0.6 0.04 1000 -1000 -0.11 -1000
Ephrin B reverse signaling 44 2120 48 -0.28 0.19 1000 -1000 -0.076 -1000
Glypican 2 network 44 177 4 -0.079 -0.014 1000 -1000 -0.031 -1000
TCR signaling in naïve CD8+ T cells 42 3998 93 -0.2 0.091 1000 -1000 -0.085 -1000
BMP receptor signaling 41 3326 81 -0.6 0.023 1000 -1000 -0.1 -1000
Glucocorticoid receptor regulatory network 41 4756 114 -0.57 0.37 1000 -1000 -0.079 -1000
IGF1 pathway 41 2377 57 -0.19 0.051 1000 -1000 -0.093 -1000
IL23-mediated signaling events 41 2461 60 -0.34 0.021 1000 -1000 -0.15 -1000
Arf6 signaling events 36 2273 62 -0.32 0.02 1000 -1000 -0.073 -1000
Syndecan-1-mediated signaling events 35 1195 34 -0.21 0.013 1000 -1000 -0.07 -1000
TCGA08_retinoblastoma 35 286 8 -0.12 0.07 1000 -1000 -0.023 -1000
Coregulation of Androgen receptor activity 34 2607 76 -0.78 0.06 1000 -1000 -0.049 -1000
Signaling mediated by p38-alpha and p38-beta 34 1538 44 -0.24 0.013 1000 -1000 -0.053 -1000
Hedgehog signaling events mediated by Gli proteins 30 1980 65 -0.69 0.063 1000 -1000 -0.061 -1000
EPHB forward signaling 29 2479 85 -0.28 0.14 1000 -1000 -0.095 -1000
IL12-mediated signaling events 28 2474 87 -0.42 0.019 1000 -1000 -0.12 -1000
amb2 Integrin signaling 28 2342 82 -0.27 0.013 1000 -1000 -0.091 -1000
Syndecan-4-mediated signaling events 27 1847 67 -0.24 0.013 1000 -1000 -0.088 -1000
IL6-mediated signaling events 26 1985 75 -0.22 0.061 1000 -1000 -0.08 -1000
Ras signaling in the CD4+ TCR pathway 26 454 17 -0.098 0.012 1000 -1000 -0.043 -1000
Thromboxane A2 receptor signaling 25 2654 105 -0.21 0.029 1000 -1000 -0.071 -1000
Osteopontin-mediated events 24 921 38 -0.27 0.013 1000 -1000 -0.1 -1000
EGFR-dependent Endothelin signaling events 24 524 21 -0.11 0.013 1000 -1000 -0.071 -1000
FAS signaling pathway (CD95) 21 1011 47 -0.29 0.025 1000 -1000 -0.042 -1000
IL27-mediated signaling events 21 1092 51 -0.2 0.049 1000 -1000 -0.08 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 20 1750 85 -0.3 0.013 1000 -1000 -0.078 -1000
Visual signal transduction: Rods 20 1060 52 -0.18 0.013 1000 -1000 -0.084 -1000
ErbB2/ErbB3 signaling events 19 1276 65 -0.14 0.027 1000 -1000 -0.067 -1000
Regulation of p38-alpha and p38-beta 19 1046 54 -0.49 0.013 1000 -1000 -0.062 -1000
Plasma membrane estrogen receptor signaling 19 1712 86 -0.2 0.021 1000 -1000 -0.078 -1000
Syndecan-2-mediated signaling events 18 1278 69 -0.21 0.038 1000 -1000 -0.061 -1000
LPA receptor mediated events 18 1887 102 -0.27 0.03 1000 -1000 -0.099 -1000
JNK signaling in the CD4+ TCR pathway 17 293 17 -0.1 0.016 1000 -1000 -0.078 -1000
Integrins in angiogenesis 17 1492 84 -0.22 0.029 1000 -1000 -0.096 -1000
Angiopoietin receptor Tie2-mediated signaling 17 1520 88 -0.32 0.028 1000 -1000 -0.11 -1000
BCR signaling pathway 16 1635 99 -0.18 0.023 1000 -1000 -0.093 -1000
Regulation of nuclear SMAD2/3 signaling 15 2080 136 -0.33 0.067 1000 -1000 -0.079 -1000
p75(NTR)-mediated signaling 15 1962 125 -0.38 0.068 1000 -1000 -0.1 -1000
Fc-epsilon receptor I signaling in mast cells 15 1458 97 -0.22 0.03 1000 -1000 -0.087 -1000
Visual signal transduction: Cones 14 568 38 -0.1 0.013 1000 -1000 -0.072 -1000
IL1-mediated signaling events 14 898 62 -0.13 0.066 1000 -1000 -0.091 -1000
TCGA08_rtk_signaling 14 370 26 -0.25 0.024 1000 -1000 -0.022 -1000
Regulation of Androgen receptor activity 14 1002 70 -0.48 0.034 1000 -1000 -0.067 -1000
Signaling events mediated by PTP1B 13 994 76 -0.26 0.021 1000 -1000 -0.085 -1000
Aurora C signaling 13 94 7 -0.056 0.005 1000 -1000 -0.042 -1000
RXR and RAR heterodimerization with other nuclear receptor 13 694 52 -0.27 0.051 1000 -1000 -0.062 -1000
Effects of Botulinum toxin 13 338 26 -0.18 0.019 1000 -1000 -0.062 -1000
Neurotrophic factor-mediated Trk receptor signaling 13 1669 120 -0.34 0.042 1000 -1000 -0.083 -1000
Aurora B signaling 13 891 67 -0.39 0.014 1000 -1000 -0.064 -1000
LPA4-mediated signaling events 12 146 12 -0.11 0.016 1000 -1000 -0.023 -1000
ErbB4 signaling events 12 894 69 -0.13 0.059 1000 -1000 -0.091 -1000
Syndecan-3-mediated signaling events 12 429 35 -0.17 0.013 1000 -1000 -0.063 -1000
VEGFR1 specific signals 12 675 56 -0.082 0.042 1000 -1000 -0.083 -1000
Presenilin action in Notch and Wnt signaling 11 694 61 -0.22 0.047 1000 -1000 -0.07 -1000
FOXM1 transcription factor network 11 593 51 -0.21 0.04 1000 -1000 -0.15 -1000
Signaling events mediated by HDAC Class III 10 404 40 -0.36 0.024 1000 -1000 -0.051 -1000
IL2 signaling events mediated by STAT5 10 235 22 -0.059 0.04 1000 -1000 -0.046 -1000
Rapid glucocorticoid signaling 10 215 20 -0.095 0.015 1000 -1000 -0.034 -1000
Signaling events mediated by PRL 10 349 34 -0.13 0.013 1000 -1000 -0.052 -1000
Class IB PI3K non-lipid kinase events 10 30 3 -0.001 -1000 1000 -1000 -0.014 -1000
a4b1 and a4b7 Integrin signaling 9 47 5 -0.03 0.006 1000 -1000 -0.032 -1000
Insulin-mediated glucose transport 9 314 32 -0.21 0.037 1000 -1000 -0.066 -1000
IFN-gamma pathway 9 615 68 -0.1 0.041 1000 -1000 -0.1 -1000
Ceramide signaling pathway 9 726 76 -0.18 0.024 1000 -1000 -0.061 -1000
IL2 signaling events mediated by PI3K 9 523 58 -0.058 0.032 1000 -1000 -0.079 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 9 425 45 -0.09 0.039 1000 -1000 -0.081 -1000
Nectin adhesion pathway 8 526 63 -0.25 0.038 1000 -1000 -0.076 -1000
S1P1 pathway 8 308 36 -0.051 0.029 1000 -1000 -0.056 -1000
Retinoic acid receptors-mediated signaling 8 483 58 -0.11 0.033 1000 -1000 -0.07 -1000
Stabilization and expansion of the E-cadherin adherens junction 8 608 74 -0.18 0.086 1000 -1000 -0.09 -1000
Regulation of Telomerase 8 841 102 -0.31 0.053 1000 -1000 -0.099 -1000
Caspase cascade in apoptosis 7 540 74 -0.09 0.029 1000 -1000 -0.054 -1000
Cellular roles of Anthrax toxin 7 306 39 -0.09 0.019 1000 -1000 -0.033 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 7 653 83 -0.21 0.052 1000 -1000 -0.084 -1000
Class I PI3K signaling events 7 558 73 -0.26 0.025 1000 -1000 -0.073 -1000
Insulin Pathway 7 536 74 -0.076 0.037 1000 -1000 -0.096 -1000
BARD1 signaling events 6 363 57 -0.028 0.055 1000 -1000 -0.07 -1000
Sphingosine 1-phosphate (S1P) pathway 6 185 28 -0.2 0.032 1000 -1000 -0.052 -1000
Class I PI3K signaling events mediated by Akt 6 415 68 -0.21 0.051 1000 -1000 -0.057 -1000
S1P3 pathway 6 291 42 -0.2 0.049 1000 -1000 -0.055 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 207 33 -0.18 0.035 1000 -1000 -0.065 -1000
mTOR signaling pathway 5 316 53 -0.036 0.023 1000 -1000 -0.06 -1000
TRAIL signaling pathway 5 263 48 -0.081 0.052 1000 -1000 -0.062 -1000
ceramide signaling pathway 5 293 49 -0.09 0.031 1000 -1000 -0.042 -1000
Canonical NF-kappaB pathway 4 184 39 -0.09 0.069 1000 -1000 -0.076 -1000
Arf6 downstream pathway 4 212 43 -0.16 0.086 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class I 4 495 104 -0.09 0.06 1000 -1000 -0.072 -1000
FoxO family signaling 4 297 64 -0.21 0.16 1000 -1000 -0.076 -1000
Canonical Wnt signaling pathway 4 251 51 -0.047 0.069 1000 -1000 -0.062 -1000
Paxillin-independent events mediated by a4b1 and a4b7 3 138 37 -0.032 0.033 1000 -1000 -0.068 -1000
S1P5 pathway 3 57 17 -0.013 0.024 1000 -1000 -0.043 -1000
Signaling events mediated by VEGFR1 and VEGFR2 3 420 125 -0.039 0.084 1000 -1000 -0.11 -1000
E-cadherin signaling in the nascent adherens junction 3 299 76 -0.16 0.072 1000 -1000 -0.088 -1000
S1P4 pathway 3 92 25 -0.013 0.032 1000 -1000 -0.047 -1000
Circadian rhythm pathway 2 48 22 -0.05 0.013 1000 -1000 -0.076 -1000
Aurora A signaling 2 134 60 -0.051 0.038 1000 -1000 -0.063 -1000
EPO signaling pathway 2 151 55 -0.05 0.066 1000 -1000 -0.095 -1000
Signaling mediated by p38-gamma and p38-delta 2 32 15 0 0.031 1000 -1000 -0.029 -1000
Paxillin-dependent events mediated by a4b1 2 75 36 -0.03 0.024 1000 -1000 -0.071 -1000
Atypical NF-kappaB pathway 2 86 31 -0.024 0.047 1000 -1000 -0.06 -1000
PDGFR-beta signaling pathway 2 218 97 -0.19 0.066 1000 -1000 -0.091 -1000
p38 MAPK signaling pathway 2 109 44 -0.027 0.028 1000 -1000 -0.063 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 32 23 -0.028 0.049 1000 -1000 -0.078 -1000
Signaling events mediated by HDAC Class II 1 132 75 -0.049 0.034 1000 -1000 -0.076 -1000
PLK2 and PLK4 events 1 5 3 0.009 0.021 1000 -1000 -0.02 -1000
PLK1 signaling events 1 108 85 -0.048 0.024 1000 -1000 -0.049 -1000
HIF-2-alpha transcription factor network 1 64 43 -0.2 0.21 1000 -1000 -0.082 -1000
E-cadherin signaling in keratinocytes 1 66 43 -0.006 0.051 1000 -1000 -0.067 -1000
TCGA08_p53 0 0 7 -0.081 0.052 1000 -1000 -0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 0 0.03 1000 -1000 -0.055 -1000
Arf6 trafficking events 0 63 71 -0.024 0.045 1000 -1000 -0.085 -1000
E-cadherin signaling events 0 0 5 0 0.013 1000 -1000 -0.043 -1000
Arf1 pathway 0 12 54 -0.005 0.035 1000 -1000 -0.053 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.013 1000 -1000 -0.059 -1000
Total 2952 166020 7203 -30 -990 131000 -131000 -9.3 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.47 0.33 -9999 0 -0.65 271 271
EFNA5 -0.14 0.33 -9999 0 -0.84 66 66
FYN -0.42 0.32 -9999 0 -0.6 271 271
neuron projection morphogenesis -0.47 0.33 -9999 0 -0.65 271 271
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.47 0.33 -9999 0 -0.66 271 271
EPHA5 -0.55 0.41 -9999 0 -0.86 245 245
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 -0.21 0.22 -10000 0 -0.4 219 219
CRKL -0.21 0.24 -10000 0 -0.42 212 212
HRAS -0.18 0.22 -10000 0 -0.51 29 29
mol:PIP3 -0.21 0.22 -10000 0 -0.4 212 212
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.013 0 -10000 0 -10000 0 0
GAB1 -0.23 0.25 -10000 0 -0.45 212 212
FOXO3 -0.19 0.22 -10000 0 -0.38 212 212
AKT1 -0.21 0.23 -10000 0 -0.41 212 212
BAD -0.19 0.22 -10000 0 -0.38 212 212
megakaryocyte differentiation -0.24 0.24 -10000 0 -0.45 216 216
GSK3B -0.19 0.22 -10000 0 -0.38 212 212
RAF1 -0.14 0.18 -10000 0 -0.46 17 17
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.23 0.25 -10000 0 -0.45 212 212
STAT1 -0.58 0.58 -10000 0 -1.1 212 212
HRAS/SPRED1 -0.17 0.15 -10000 0 -0.46 17 17
cell proliferation -0.23 0.24 -10000 0 -0.44 213 213
PIK3CA 0.01 0.045 -10000 0 -0.86 1 1
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.23 0.24 -10000 0 -0.44 212 212
HRAS/SPRED2 -0.17 0.15 -10000 0 -0.46 17 17
LYN/TEC/p62DOK -0.23 0.2 -10000 0 -0.41 212 212
MAPK3 -0.091 0.13 -10000 0 -0.32 14 14
STAP1 -0.25 0.25 -10000 0 -0.47 212 212
GRAP2 -0.045 0.21 -10000 0 -0.79 27 27
JAK2 -0.5 0.45 -10000 0 -0.89 212 212
STAT1 (dimer) -0.56 0.57 -10000 0 -1.1 212 212
mol:Gleevec 0.007 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.24 0.21 -10000 0 -0.42 214 214
actin filament polymerization -0.23 0.24 -10000 0 -0.44 212 212
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.34 -10000 0 -0.64 212 212
PIK3R1 0.012 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.21 0.19 -10000 0 -0.37 203 203
PI3K -0.23 0.21 -10000 0 -0.42 212 212
PTEN 0.011 0.045 -10000 0 -0.86 1 1
SCF/KIT/EPO/EPOR -0.73 0.72 -10000 0 -1.4 212 212
MAPK8 -0.23 0.25 -10000 0 -0.45 213 213
STAT3 (dimer) -0.23 0.24 -10000 0 -0.44 212 212
positive regulation of transcription -0.073 0.11 -10000 0 -0.26 13 13
mol:GDP -0.22 0.19 -10000 0 -0.55 32 32
PIK3C2B -0.23 0.25 -10000 0 -0.45 212 212
CBL/CRKL -0.19 0.22 -10000 0 -0.39 212 212
FER -0.23 0.25 -10000 0 -0.45 213 213
SH2B3 -0.23 0.25 -10000 0 -0.45 212 212
PDPK1 -0.19 0.21 -10000 0 -0.37 212 212
SNAI2 -0.23 0.25 -10000 0 -0.45 212 212
positive regulation of cell proliferation -0.4 0.42 -10000 0 -0.77 212 212
KITLG 0.001 0.08 -10000 0 -0.89 3 3
cell motility -0.4 0.42 -10000 0 -0.77 212 212
PTPN6 0.02 0.017 -10000 0 -10000 0 0
EPOR -0.13 0.17 -10000 0 -0.56 3 3
STAT5A (dimer) -0.33 0.34 -10000 0 -0.63 212 212
SOCS1 0.01 0.032 -10000 0 -0.3 4 4
cell migration 0.23 0.25 0.45 213 -10000 0 213
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.002 0.021 -10000 0 -0.32 1 1
VAV1 -0.013 0.1 -10000 0 -0.86 2 2
GRB10 -0.23 0.25 -10000 0 -0.45 212 212
PTPN11 0.016 0.014 -10000 0 -10000 0 0
SCF/KIT -0.26 0.25 -10000 0 -0.48 212 212
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.1 0.15 -10000 0 -0.36 14 14
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.79 0.76 -10000 0 -1.5 212 212
MAP2K2 -0.1 0.15 -10000 0 -0.36 14 14
SHC/Grb2/SOS1 -0.23 0.2 -10000 0 -0.41 212 212
STAT5A -0.34 0.36 -10000 0 -0.65 212 212
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.23 0.24 -10000 0 -0.44 212 212
SHC/GRAP2 -0.043 0.16 -10000 0 -0.66 24 24
PTPRO -0.25 0.25 -10000 0 -0.46 216 216
SH2B2 -0.23 0.25 -10000 0 -0.45 212 212
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.24 0.26 -10000 0 -0.46 213 213
CREBBP 0.018 0.02 -10000 0 -10000 0 0
BCL2 -0.19 0.39 -10000 0 -1.6 22 22
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.091 0.072 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.26 0.2 -9999 0 -0.43 180 180
JUN -0.33 0.32 -9999 0 -0.69 137 137
HRAS 0.012 0.016 -9999 0 -0.3 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.4 0.34 -9999 0 -0.64 233 233
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.4 0.34 -9999 0 -0.64 233 233
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.31 0.27 -9999 0 -0.54 215 215
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.36 0.31 -9999 0 -0.58 233 233
GRB7 -0.033 0.11 -9999 0 -0.3 56 56
RET51/GFRalpha1/GDNF -0.4 0.34 -9999 0 -0.64 233 233
MAPKKK cascade -0.32 0.27 -9999 0 -0.51 233 233
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.36 0.32 -9999 0 -0.6 224 224
lamellipodium assembly -0.24 0.19 -9999 0 -0.39 215 215
RET51/GFRalpha1/GDNF/SHC -0.4 0.34 -9999 0 -0.64 233 233
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
RET9/GFRalpha1/GDNF/SHC -0.31 0.27 -9999 0 -0.54 215 215
RET9/GFRalpha1/GDNF/Shank3 -0.31 0.27 -9999 0 -0.54 215 215
MAPK3 -0.32 0.31 -9999 0 -0.54 233 233
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.12 0.32 -9999 0 -0.86 59 59
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.33 0.29 -9999 0 -0.7 99 99
DOK5 -0.1 0.3 -9999 0 -0.86 51 51
GFRA1 -0.48 0.43 -9999 0 -0.85 216 216
MAPK8 -0.23 0.23 -9999 0 -0.59 66 66
HRAS/GTP -0.37 0.32 -9999 0 -0.59 233 233
tube development -0.29 0.25 -9999 0 -0.5 215 215
MAPK1 -0.32 0.31 -9999 0 -0.54 233 233
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.19 0.19 -9999 0 -0.35 215 215
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -10000 0 0
PDLIM7 0.009 0.035 -9999 0 -0.3 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.45 0.4 -9999 0 -0.7 241 241
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.4 0.34 -9999 0 -0.64 233 233
RET51/GFRalpha1/GDNF/Dok5 -0.47 0.41 -9999 0 -0.72 243 243
PRKCA -0.038 0.2 -9999 0 -0.86 22 22
HRAS/GDP -0.001 0.01 -9999 0 -10000 0 0
CREB1 -0.25 0.24 -9999 0 -0.44 215 215
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.19 0.19 -9999 0 -0.35 215 215
RET51/GFRalpha1/GDNF/Grb7 -0.42 0.35 -9999 0 -0.67 233 233
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.17 0.33 -9999 0 -0.86 66 66
DOK4 0.013 0 -9999 0 -10000 0 0
JNK cascade -0.32 0.31 -9999 0 -0.67 137 137
RET9/GFRalpha1/GDNF/FRS2 -0.31 0.27 -9999 0 -0.54 215 215
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.19 0.19 -9999 0 -0.35 215 215
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.25 0.24 -9999 0 -0.42 233 233
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.25 0.24 -9999 0 -0.42 233 233
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.29 0.32 -9999 0 -0.49 233 233
PI3K -0.37 0.34 -9999 0 -0.63 215 215
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.29 0.25 -9999 0 -0.5 215 215
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.23 0.22 -9999 0 -0.39 215 215
RET51/GFRalpha1/GDNF/FRS2 -0.4 0.34 -9999 0 -0.64 233 233
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.07 0.26 -9999 0 -0.86 36 36
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.29 0.32 -9999 0 -0.49 233 233
RET51/GFRalpha1/GDNF/PKC alpha -0.43 0.39 -9999 0 -0.69 233 233
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF 0 0.035 -9999 0 -0.3 5 5
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.45 0.38 -9999 0 -0.69 242 242
Rac1/GTP -0.29 0.23 -9999 0 -0.47 215 215
RET9/GFRalpha1/GDNF -0.34 0.29 -9999 0 -0.59 215 215
GFRalpha1/GDNF -0.38 0.33 -9999 0 -0.67 215 215
Reelin signaling pathway

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
CDK5R1/CDK5 -0.002 0.017 -9999 0 -10000 0 0
VLDLR -0.012 0.15 -9999 0 -0.86 11 11
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 0.009 0.035 -9999 0 -0.3 5 5
RELN/VLDLR/Fyn -0.44 0.27 -9999 0 -0.59 284 284
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.003 0.035 -9999 0 -0.49 2 2
AKT1 -0.24 0.17 -9999 0 -0.34 284 284
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 0.007 0.006 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.42 0.26 -9999 0 -0.56 284 284
LRPAP1/LRP8 -0.026 0.13 -9999 0 -0.66 15 15
RELN/LRP8/DAB1/Fyn -0.39 0.24 -9999 0 -0.52 284 284
DAB1/alpha3/beta1 Integrin -0.37 0.24 -9999 0 -0.48 286 286
long-term memory -0.39 0.26 -9999 0 -0.52 285 285
DAB1/LIS1 -0.38 0.24 -9999 0 -0.5 286 286
DAB1/CRLK/C3G -0.36 0.24 -9999 0 -0.52 146 146
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
DAB1/NCK2 -0.38 0.24 -9999 0 -0.5 286 286
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.024 0.16 -9999 0 -0.63 22 22
CDK5R1 0.01 0.028 -9999 0 -0.3 3 3
RELN -0.63 0.38 -9999 0 -0.86 282 282
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.45 0.28 -9999 0 -0.6 284 284
GRIN2A/RELN/LRP8/DAB1/Fyn -0.41 0.27 -9999 0 -0.54 285 285
MAPK8 0.008 0.063 -9999 0 -0.86 2 2
RELN/VLDLR/DAB1 -0.41 0.25 -9999 0 -0.55 284 284
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.39 0.26 -9999 0 -0.53 286 286
RELN/LRP8 -0.45 0.28 -9999 0 -0.6 284 284
GRIN2B/RELN/LRP8/DAB1/Fyn -0.39 0.24 -9999 0 -0.52 284 284
PI3K -0.002 0.034 -9999 0 -0.66 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.022 -9999 0 -10000 0 0
RAP1A -0.32 0.24 -9999 0 -0.84 21 21
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.003 0.017 -9999 0 -0.3 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.13 -9999 0 -0.51 14 14
neuron adhesion -0.3 0.23 -9999 0 -0.75 25 25
LRP8 -0.021 0.17 -9999 0 -0.86 15 15
GSK3B -0.22 0.16 -9999 0 -0.62 10 10
RELN/VLDLR/DAB1/Fyn -0.39 0.24 -9999 0 -0.52 284 284
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.27 0.18 -9999 0 -0.36 284 284
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.034 0.086 -9999 0 -0.31 16 16
neuron migration -0.31 0.22 -9999 0 -0.43 283 283
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.13 -9999 0 -0.52 14 14
RELN/VLDLR -0.42 0.27 -9999 0 -0.56 286 286
Wnt signaling

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
Noncanonical Wnts/FZD -0.3 0.29 -9999 0 -0.49 246 246
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.007 0.039 -9999 0 -0.3 6 6
WNT4 -0.29 0.41 -9999 0 -0.84 135 135
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.011 0.14 -9999 0 -0.86 10 10
WNT11 -0.45 0.43 -9999 0 -0.86 201 201
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.045 0.16 -10000 0 -0.53 26 26
NFATC2 -0.2 0.36 -10000 0 -0.82 78 78
NFATC3 -0.088 0.13 -10000 0 -10000 0 0
CD40LG -0.71 0.58 -10000 0 -1.2 198 198
ITCH 0.05 0.017 -10000 0 -10000 0 0
CBLB 0.05 0.017 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.49 0.51 -10000 0 -1.3 88 88
JUNB -0.001 0.11 -10000 0 -0.86 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.018 -10000 0 -0.34 1 1
T cell anergy 0.03 0.063 -10000 0 -0.5 1 1
TLE4 -0.21 0.42 -10000 0 -0.91 88 88
Jun/NFAT1-c-4/p21SNFT -0.65 0.62 -10000 0 -1.2 181 181
AP-1/NFAT1-c-4 -0.88 0.8 -10000 0 -1.5 200 200
IKZF1 -0.15 0.32 -10000 0 -0.77 61 61
T-helper 2 cell differentiation -0.29 0.34 -10000 0 -0.83 83 83
AP-1/NFAT1 -0.42 0.5 -10000 0 -0.95 157 157
CALM1 0.028 0.011 -10000 0 -10000 0 0
EGR2 -0.78 0.86 -10000 0 -1.7 171 171
EGR3 -0.55 0.74 -10000 0 -1.7 92 92
NFAT1/FOXP3 -0.19 0.32 -10000 0 -0.74 75 75
EGR1 -0.18 0.36 -10000 0 -0.86 84 84
JUN -0.2 0.36 -10000 0 -0.86 88 88
EGR4 -0.055 0.22 -10000 0 -0.84 27 27
mol:Ca2+ 0.016 0.012 -10000 0 -10000 0 0
GBP3 -0.14 0.3 -10000 0 -0.74 60 60
FOSL1 -0.033 0.11 -10000 0 -0.3 56 56
NFAT1-c-4/MAF/IRF4 -0.54 0.56 -10000 0 -1.1 169 169
DGKA -0.13 0.28 -10000 0 -0.7 55 55
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.53 0.56 -10000 0 -1.1 180 180
CTLA4 -0.22 0.37 -10000 0 -0.85 75 75
NFAT1-c-4 (dimer)/EGR1 -0.63 0.67 -10000 0 -1.3 181 181
NFAT1-c-4 (dimer)/EGR4 -0.56 0.56 -10000 0 -1.1 185 185
FOS -0.23 0.38 -10000 0 -0.86 103 103
IFNG -0.39 0.53 -10000 0 -1.2 92 92
T cell activation -0.42 0.44 -10000 0 -0.99 121 121
MAF 0.013 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.35 0.42 0.8 136 -10000 0 136
TNF -0.59 0.59 -10000 0 -1.1 184 184
FASLG -0.72 0.79 -10000 0 -1.5 187 187
TBX21 -0.04 0.19 -10000 0 -0.77 22 22
BATF3 -0.01 0.089 -10000 0 -0.32 26 26
PRKCQ -0.001 0.11 -10000 0 -0.86 6 6
PTPN1 -0.13 0.28 -10000 0 -0.73 49 49
NFAT1-c-4/ICER1 -0.52 0.55 -10000 0 -1 180 180
GATA3 -0.037 0.2 -10000 0 -0.86 22 22
T-helper 1 cell differentiation -0.38 0.5 -10000 0 -1.2 92 92
IL2RA -0.44 0.44 -10000 0 -1.1 95 95
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.13 0.28 -10000 0 -0.71 54 54
E2F1 -0.077 0.14 -10000 0 -0.29 119 119
PPARG -0.002 0.1 -10000 0 -0.61 9 9
SLC3A2 -0.13 0.28 -10000 0 -0.69 57 57
IRF4 -0.092 0.21 -10000 0 -0.4 96 96
PTGS2 -0.7 0.58 -10000 0 -1.2 192 192
CSF2 -0.75 0.55 -10000 0 -1.2 202 202
JunB/Fra1/NFAT1-c-4 -0.52 0.54 -10000 0 -1.1 155 155
IL4 -0.3 0.36 -10000 0 -0.9 77 77
IL5 -0.68 0.55 -10000 0 -1.2 192 192
IL2 -0.44 0.45 -10000 0 -1 121 121
IL3 -0.095 0.063 -10000 0 -10000 0 0
RNF128 0.048 0.049 -10000 0 -0.91 1 1
NFATC1 -0.36 0.42 -10000 0 -0.81 133 133
CDK4 0.21 0.25 0.6 40 -10000 0 40
PTPRK -0.13 0.28 -10000 0 -0.7 55 55
IL8 -0.7 0.56 -10000 0 -1.2 191 191
POU2F1 0.012 0.016 -10000 0 -10000 0 0
IL4-mediated signaling 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
BCL2L1 -0.59 0.45 -10000 0 -1.1 148 148
STAT6 (cleaved dimer) -0.65 0.46 -10000 0 -1 204 204
IGHG1 -0.2 0.14 -10000 0 -0.36 28 28
IGHG3 -0.58 0.44 -10000 0 -0.95 184 184
AKT1 -0.31 0.26 -10000 0 -0.67 72 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.25 0.25 -10000 0 -0.68 52 52
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.34 0.28 -10000 0 -0.7 89 89
THY1 -0.59 0.45 -10000 0 -1.1 133 133
MYB -0.009 0.13 -10000 0 -0.86 8 8
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.41 0.32 -10000 0 -0.7 156 156
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.65 74 74
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.01 0.081 -10000 0 -0.3 28 28
SOCS5 0.029 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.62 0.45 -10000 0 -0.98 198 198
SOCS1 -0.4 0.29 -10000 0 -0.72 116 116
SOCS3 -0.38 0.38 -10000 0 -1 65 65
FCER2 -0.56 0.42 -10000 0 -0.96 158 158
PARP14 0.012 0.004 -10000 0 -10000 0 0
CCL17 -0.67 0.49 -10000 0 -1.1 161 161
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.22 -10000 0 -0.64 39 39
T cell proliferation -0.6 0.47 -10000 0 -1.1 159 159
IL4R/JAK1 -0.59 0.45 -10000 0 -1.1 145 145
EGR2 -0.93 0.74 -10000 0 -1.6 187 187
JAK2 -0.015 0.025 -10000 0 -10000 0 0
JAK3 -0.058 0.13 -10000 0 -0.3 87 87
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.002 0.009 -10000 0 -10000 0 0
COL1A2 -0.2 0.17 -10000 0 -0.62 15 15
CCL26 -0.61 0.46 -10000 0 -1.1 148 148
IL4R -0.63 0.48 -10000 0 -1.1 151 151
PTPN6 0.028 0.009 -10000 0 -10000 0 0
IL13RA2 -0.71 0.59 -10000 0 -1.3 156 156
IL13RA1 -0.015 0.025 -10000 0 -10000 0 0
IRF4 -0.3 0.43 -10000 0 -1.2 56 56
ARG1 -0.14 0.12 -10000 0 -10000 0 0
CBL -0.38 0.3 -10000 0 -0.68 134 134
GTF3A 0.016 0.01 -10000 0 -10000 0 0
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
IL13RA1/JAK2 -0.022 0.035 -10000 0 -10000 0 0
IRF4/BCL6 -0.28 0.39 -10000 0 -1.2 49 49
CD40LG -0.096 0.29 -10000 0 -0.81 51 51
MAPK14 -0.39 0.32 -10000 0 -0.73 126 126
mitosis -0.3 0.24 -10000 0 -0.63 72 72
STAT6 -0.67 0.53 -10000 0 -1.1 182 182
SPI1 0.001 0.07 -10000 0 -0.3 7 7
RPS6KB1 -0.28 0.24 -10000 0 -0.64 53 53
STAT6 (dimer) -0.67 0.53 -10000 0 -1.1 182 182
STAT6 (dimer)/PARP14 -0.63 0.49 -10000 0 -1.1 175 175
mast cell activation 0.015 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.31 0.27 -10000 0 -0.66 86 86
FRAP1 -0.31 0.26 -10000 0 -0.67 72 72
LTA -0.61 0.47 -10000 0 -1.1 127 127
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.66 0.51 1.1 182 -10000 0 182
CCL11 -0.58 0.44 -10000 0 -1 147 147
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.31 0.27 -10000 0 -0.65 82 82
IL2RG -0.049 0.2 -10000 0 -0.51 47 47
IL10 -0.61 0.48 -10000 0 -1.1 137 137
IRS1 -0.07 0.26 -10000 0 -0.86 36 36
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.099 -10000 0 -10000 0 0
IL5 -0.6 0.45 -10000 0 -1.1 134 134
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.48 0.34 -10000 0 -0.82 148 148
COL1A1 -0.25 0.24 -10000 0 -0.78 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.59 0.47 -10000 0 -1.1 128 128
IL2R gamma/JAK3 -0.078 0.18 -10000 0 -0.5 46 46
TFF3 -1.3 0.64 -10000 0 -1.6 305 305
ALOX15 -0.6 0.46 -10000 0 -1.1 133 133
MYBL1 0.012 0.016 -10000 0 -0.3 1 1
T-helper 2 cell differentiation -0.51 0.37 -10000 0 -0.84 170 170
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.017 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.3 0.25 -10000 0 -0.64 69 69
mol:PI-3-4-5-P3 -0.31 0.26 -10000 0 -0.67 72 72
PI3K -0.33 0.28 -10000 0 -0.72 72 72
DOK2 0 0.08 -10000 0 -0.39 12 12
ETS1 0.029 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.24 0.21 -10000 0 -0.62 43 43
ITGB3 -0.61 0.48 -10000 0 -1.1 137 137
PIGR -0.63 0.5 -10000 0 -1.2 142 142
IGHE 0.05 0.037 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.2 -10000 0 -0.6 43 43
BCL6 0.011 0.045 -10000 0 -0.85 1 1
OPRM1 -0.6 0.45 -10000 0 -1.1 150 150
RETNLB -0.6 0.45 -10000 0 -1.1 139 139
SELP -0.6 0.47 -10000 0 -1.1 142 142
AICDA -0.58 0.44 -10000 0 -1 141 141
PDGFR-alpha signaling pathway

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
PDGFRA -0.26 0.4 -9999 0 -0.87 116 116
PDGF/PDGFRA/CRKL -0.2 0.3 -9999 0 -0.66 116 116
positive regulation of JUN kinase activity -0.16 0.24 -9999 0 -0.51 116 116
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.21 0.31 -9999 0 -0.67 116 116
AP1 -0.53 0.66 -9999 0 -1.5 106 106
mol:IP3 -0.2 0.32 -9999 0 -0.68 116 116
PLCG1 -0.2 0.32 -9999 0 -0.68 116 116
PDGF/PDGFRA/alphaV Integrin -0.2 0.31 -9999 0 -0.66 116 116
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.2 0.32 -9999 0 -0.68 116 116
CAV3 -0.002 0.034 -9999 0 -0.3 5 5
CAV1 -0.012 0.15 -9999 0 -0.86 11 11
SHC/Grb2/SOS1 -0.16 0.24 -9999 0 -0.52 116 116
PDGF/PDGFRA/Shf -0.2 0.3 -9999 0 -0.66 116 116
FOS -0.48 0.63 -9999 0 -1.4 106 106
JUN -0.18 0.3 -9999 0 -0.73 88 88
oligodendrocyte development -0.2 0.31 -9999 0 -0.66 116 116
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.2 0.32 -9999 0 -0.68 116 116
PDGF/PDGFRA -0.26 0.4 -9999 0 -0.87 116 116
actin cytoskeleton reorganization -0.2 0.3 -9999 0 -0.66 116 116
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.18 0.26 -9999 0 -0.57 117 117
PDGF/PDGFRA/Crk/C3G -0.17 0.26 -9999 0 -0.57 116 116
JAK1 -0.19 0.31 -9999 0 -0.66 116 116
ELK1/SRF -0.15 0.24 -9999 0 -0.52 116 116
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.012 0.016 -9999 0 -0.3 1 1
CSNK2A1 0.027 0.028 -9999 0 -10000 0 0
GO:0007205 -0.21 0.33 -9999 0 -0.7 116 116
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.16 0.24 -9999 0 -0.51 116 116
PDGF/PDGFRA/SHB -0.2 0.3 -9999 0 -0.66 116 116
PDGF/PDGFRA/Caveolin-1 -0.22 0.33 -9999 0 -0.69 121 121
ITGAV 0.011 0.045 -9999 0 -0.86 1 1
ELK1 -0.19 0.3 -9999 0 -0.63 116 116
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
PDGF/PDGFRA/Crk -0.2 0.3 -9999 0 -0.66 116 116
JAK-STAT cascade -0.19 0.31 -9999 0 -0.66 116 116
cell proliferation -0.2 0.3 -9999 0 -0.66 116 116
Noncanonical Wnt signaling 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
NFATC2 -0.097 0.29 -9999 0 -0.86 48 48
GNB1/GNG2 -0.28 0.25 -9999 0 -0.62 102 102
mol:DAG -0.23 0.24 -9999 0 -0.57 97 97
PLCG1 -0.24 0.25 -9999 0 -0.6 97 97
YES1 -0.28 0.28 -9999 0 -0.65 102 102
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.26 0.23 -9999 0 -0.6 97 97
MAP3K7 -0.19 0.21 -9999 0 -0.47 97 97
mol:Ca2+ -0.23 0.24 -9999 0 -0.55 97 97
mol:IP3 -0.23 0.24 -9999 0 -0.57 97 97
NLK -0.012 0.01 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.21 0.22 -9999 0 -0.51 97 97
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.3 0.29 -9999 0 -0.49 246 246
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.28 0.28 -9999 0 -0.65 102 102
GO:0007205 -0.23 0.24 -9999 0 -0.56 97 97
WNT6 0.007 0.039 -9999 0 -0.3 6 6
WNT4 -0.29 0.41 -9999 0 -0.84 135 135
NFAT1/CK1 alpha -0.31 0.26 -9999 0 -0.63 116 116
GNG2 0.013 0 -9999 0 -10000 0 0
WNT5A -0.011 0.14 -9999 0 -0.86 10 10
WNT11 -0.45 0.43 -9999 0 -0.86 201 201
CDC42 -0.26 0.26 -9999 0 -0.61 102 102
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.55 0.56 -9999 0 -1.1 153 153
PCK1 -0.35 0.5 -9999 0 -1.3 59 59
HNF4A -0.71 0.68 -9999 0 -1.3 185 185
KCNJ11 -0.52 0.56 -9999 0 -1.1 142 142
AKT1 -0.039 0.13 -9999 0 -10000 0 0
response to starvation -0.017 0.035 -9999 0 -10000 0 0
DLK1 -0.52 0.56 -9999 0 -1.1 143 143
NKX2-1 -0.17 0.21 -9999 0 -10000 0 0
ACADM -0.55 0.56 -9999 0 -1.1 152 152
TAT -0.2 0.22 -9999 0 -0.73 3 3
CEBPB 0.013 0.004 -9999 0 -10000 0 0
CEBPA 0.004 0.089 -9999 0 -0.86 4 4
TTR -0.19 0.22 -9999 0 -0.77 22 22
PKLR -0.56 0.56 -9999 0 -1.1 157 157
APOA1 -0.98 0.91 -9999 0 -1.8 198 198
CPT1C -0.56 0.56 -9999 0 -1.1 167 167
ALAS1 -0.17 0.21 -9999 0 -10000 0 0
TFRC -0.26 0.29 -9999 0 -0.74 22 22
FOXF1 -0.01 0.089 -9999 0 -0.86 4 4
NF1 0.02 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.015 0.006 -9999 0 -10000 0 0
CPT1A -0.55 0.56 -9999 0 -1.1 151 151
HMGCS1 -0.55 0.56 -9999 0 -1.1 152 152
NR3C1 0.019 0.015 -9999 0 -10000 0 0
CPT1B -0.55 0.56 -9999 0 -1.1 156 156
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.71 0.72 -9999 0 -1.4 173 173
CREB1 0.001 0.052 -9999 0 -10000 0 0
IGFBP1 -0.19 0.2 -9999 0 -0.57 1 1
PDX1 -0.18 0.22 -9999 0 -0.6 1 1
UCP2 -0.55 0.56 -9999 0 -1.1 153 153
ALDOB -0.52 0.56 -9999 0 -1.1 142 142
AFP -0.044 0.11 -9999 0 -0.43 14 14
BDH1 -0.55 0.56 -9999 0 -1.1 151 151
HADH -0.51 0.56 -9999 0 -1.1 138 138
F2 -0.66 0.65 -9999 0 -1.3 163 163
HNF1A 0.015 0.006 -9999 0 -10000 0 0
G6PC -0.002 0.087 -9999 0 -10000 0 0
SLC2A2 -0.24 0.27 -9999 0 -10000 0 0
INS -0.008 0.017 -9999 0 -10000 0 0
FOXA1 -0.06 0.14 -9999 0 -0.34 61 61
FOXA3 -0.065 0.17 -9999 0 -0.47 27 27
FOXA2 -0.59 0.63 -9999 0 -1.2 164 164
ABCC8 -0.82 0.78 -9999 0 -1.5 197 197
ALB -0.094 0.32 -9999 0 -1.3 23 23
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.13 0.27 -10000 0 -0.72 27 27
IHH -0.23 0.39 -10000 0 -0.88 102 102
SHH Np/Cholesterol/GAS1 -0.12 0.22 -10000 0 -0.54 79 79
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.12 0.22 0.54 79 -10000 0 79
SMO/beta Arrestin2 -0.11 0.26 -10000 0 -0.5 104 104
SMO -0.12 0.27 -10000 0 -0.54 105 105
AKT1 -0.032 0.12 -10000 0 -0.33 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.005 0.12 -10000 0 -0.86 8 8
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.12 0.26 -10000 0 -0.53 105 105
STIL -0.092 0.21 -10000 0 -0.6 16 16
DHH N/PTCH2 -0.1 0.24 -10000 0 -0.67 59 59
DHH N/PTCH1 -0.12 0.24 -10000 0 -0.48 107 107
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
DHH 0.006 0.077 -10000 0 -0.86 3 3
PTHLH -0.18 0.38 -10000 0 -1.2 27 27
determination of left/right symmetry -0.12 0.26 -10000 0 -0.53 105 105
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.17 0.38 -10000 0 -1.2 27 27
IHH N/Hhip -0.43 0.42 -10000 0 -0.78 213 213
DHH N/Hhip -0.28 0.33 -10000 0 -0.67 157 157
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.12 0.26 -10000 0 -0.53 105 105
pancreas development -0.35 0.42 -10000 0 -0.85 158 158
HHAT 0.011 0.045 -10000 0 -0.86 1 1
PI3K -0.002 0.034 -10000 0 -0.66 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.17 0.35 -10000 0 -0.86 78 78
somite specification -0.12 0.26 -10000 0 -0.53 105 105
SHH Np/Cholesterol/PTCH1 -0.1 0.22 -10000 0 -0.43 105 105
SHH Np/Cholesterol/PTCH2 -0.086 0.2 -10000 0 -0.54 58 58
SHH Np/Cholesterol/Megalin -0.14 0.24 -10000 0 -0.55 98 98
SHH 0.007 0.05 -10000 0 -0.66 1 1
catabolic process -0.13 0.27 -10000 0 -0.54 104 104
SMO/Vitamin D3 -0.11 0.24 -10000 0 -0.47 105 105
SHH Np/Cholesterol/Hhip -0.23 0.26 -10000 0 -0.54 157 157
LRP2 -0.21 0.38 -10000 0 -0.86 97 97
receptor-mediated endocytosis -0.21 0.24 -10000 0 -0.74 37 37
SHH Np/Cholesterol/BOC -0.017 0.086 -10000 0 -0.55 9 9
SHH Np/Cholesterol/CDO -0.16 0.24 -10000 0 -0.54 110 110
mesenchymal cell differentiation 0.23 0.26 0.53 157 -10000 0 157
mol:Vitamin D3 -0.1 0.22 -10000 0 -0.44 105 105
IHH N/PTCH2 -0.25 0.36 -10000 0 -0.68 144 144
CDON -0.24 0.39 -10000 0 -0.86 109 109
IHH N/PTCH1 -0.14 0.27 -10000 0 -0.55 104 104
Megalin/LRPAP1 -0.17 0.29 -10000 0 -0.66 97 97
PTCH2 -0.12 0.31 -10000 0 -0.86 57 57
SHH Np/Cholesterol -0.006 0.037 -10000 0 -0.54 1 1
PTCH1 -0.13 0.27 -10000 0 -0.54 104 104
HHIP -0.35 0.42 -10000 0 -0.85 158 158
Nongenotropic Androgen signaling

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
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.21 0.26 -10000 0 -0.53 149 149
regulation of S phase of mitotic cell cycle -0.12 0.18 -10000 0 -0.35 150 150
GNAO1 -0.013 0.14 -10000 0 -0.86 10 10
HRAS 0.012 0.016 -10000 0 -0.3 1 1
SHBG/T-DHT -0.012 0.085 -10000 0 -0.59 8 8
PELP1 0.012 0.001 -10000 0 -10000 0 0
AKT1 0.012 0.001 -10000 0 -10000 0 0
MAP2K1 -0.16 0.24 -10000 0 -0.46 149 149
T-DHT/AR -0.26 0.33 -10000 0 -0.67 149 149
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 103 103
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.01 0.045 -10000 0 -0.86 1 1
mol:GDP -0.25 0.31 -10000 0 -0.64 149 149
cell proliferation -0.2 0.29 -10000 0 -0.7 57 57
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
FOS -0.25 0.4 -10000 0 -0.89 103 103
mol:Ca2+ -0.026 0.031 -10000 0 -0.073 66 66
MAPK3 -0.18 0.27 -10000 0 -0.62 62 62
MAPK1 -0.083 0.13 -10000 0 -0.31 56 56
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 103 103
cAMP biosynthetic process 0.011 0.088 -10000 0 -0.55 8 8
GNG2 0.013 0 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 103 103
HRAS/GTP -0.2 0.24 -10000 0 -0.5 149 149
actin cytoskeleton reorganization -0.001 0.024 -10000 0 -0.47 1 1
SRC 0.012 0.016 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 103 103
PI3K -0.002 0.03 -10000 0 -0.58 1 1
apoptosis 0.16 0.25 0.52 103 -10000 0 103
T-DHT/AR/PELP1 -0.23 0.29 -10000 0 -0.59 149 149
HRAS/GDP -0.24 0.3 -10000 0 -0.61 150 150
CREB1 -0.18 0.28 -10000 0 -0.57 103 103
RAC1-CDC42/GTP -0.001 0.024 -10000 0 -0.48 1 1
AR -0.33 0.42 -10000 0 -0.86 149 149
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.17 0.25 -10000 0 -0.48 149 149
RAC1-CDC42/GDP -0.23 0.28 -10000 0 -0.58 149 149
T-DHT/AR/PELP1/Src -0.21 0.26 -10000 0 -0.54 149 149
MAP2K2 -0.16 0.24 -10000 0 -0.46 149 149
T-DHT/AR/PELP1/Src/PI3K -0.12 0.19 -10000 0 -0.35 150 150
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG -0.005 0.12 -10000 0 -0.86 8 8
Gi family/GNB1/GNG2/GDP -0.016 0.11 -10000 0 -0.56 11 11
mol:T-DHT 0 0.001 0.002 56 -0.003 46 102
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.01 0.035 -10000 0 -0.67 1 1
Gi family/GTP -0.091 0.13 -10000 0 -0.52 11 11
CDC42 0.013 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.012 0.15 -9999 0 -0.86 11 11
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.45 0.28 -9999 0 -0.6 284 284
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.4 0.26 -9999 0 -0.54 284 284
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.007 0.006 -9999 0 -10000 0 0
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.12 0.32 -9999 0 -0.86 59 59
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.026 0.13 -9999 0 -0.66 15 15
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.01 0.028 -9999 0 -0.3 3 3
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.003 0.028 -9999 0 -0.3 3 3
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.44 0.27 -9999 0 -0.59 284 284
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.3 0.21 -9999 0 -0.76 13 13
MAP1B 0 0.005 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.34 0.24 -9999 0 -0.47 284 284
RELN -0.63 0.38 -9999 0 -0.86 282 282
PAFAH/LIS1 -0.066 0.22 -9999 0 -0.57 59 59
LIS1/CLIP170 0.027 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.24 0.15 -9999 0 -0.57 13 13
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.25 0.18 -9999 0 -0.36 139 139
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.32 0.23 -9999 0 -0.46 186 186
LIS1/IQGAP1 0.027 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.023 -9999 0 -10000 0 0
PAFAH1B2 0.008 0.063 -9999 0 -0.86 2 2
MAP1B/LIS1/Dynein heavy chain 0.026 0.004 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.3 0.18 -9999 0 -0.72 13 13
LRP8 -0.021 0.17 -9999 0 -0.86 15 15
NDEL1/Katanin 60 -0.3 0.21 -9999 0 -0.76 13 13
P39/CDK5 -0.35 0.24 -9999 0 -0.48 284 284
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.027 0 -9999 0 -10000 0 0
CDK5 -0.37 0.25 -9999 0 -0.5 284 284
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.38 0.23 -9999 0 -0.51 284 284
RELN/VLDLR -0.42 0.27 -9999 0 -0.56 286 286
CDC42 0 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.009 0.079 -9999 0 -0.6 6 6
NFATC2 -0.078 0.2 -9999 0 -0.61 48 48
NFATC3 0.001 0.027 -9999 0 -10000 0 0
CD40LG -0.42 0.41 -9999 0 -0.88 143 143
PTGS2 -0.41 0.41 -9999 0 -0.89 134 134
JUNB -0.001 0.11 -9999 0 -0.86 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.013 -9999 0 -10000 0 0
CaM/Ca2+ -0.006 0.013 -9999 0 -10000 0 0
CALM1 0.008 0.008 -9999 0 -10000 0 0
JUN -0.2 0.37 -9999 0 -0.86 88 88
mol:Ca2+ -0.01 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 -0.033 0.11 -9999 0 -0.3 56 56
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.25 0.28 -9999 0 -0.6 124 124
FOS -0.23 0.39 -9999 0 -0.86 103 103
IFNG -0.42 0.41 -9999 0 -0.86 152 152
AP-1/NFAT1-c-4 -0.52 0.52 -9999 0 -1.1 135 135
FASLG -0.4 0.39 -9999 0 -0.85 140 140
NFAT1-c-4/ICER1 -0.096 0.19 -9999 0 -0.54 53 53
IL2RA -0.39 0.39 -9999 0 -0.85 131 131
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.46 0.37 -9999 0 -0.81 171 171
JunB/Fra1/NFAT1-c-4 -0.12 0.19 -9999 0 -0.53 58 58
IL4 -0.38 0.37 -9999 0 -0.82 131 131
IL2 -0.013 0.026 -9999 0 -10000 0 0
IL3 -0.031 0.03 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.01 0.089 -9999 0 -0.32 26 26
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.012 0.016 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.16 0.3 0.7 86 -10000 0 86
KIRREL -0.052 0.21 -10000 0 -0.88 23 23
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.16 0.3 -10000 0 -0.7 86 86
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.12 0.23 -10000 0 -0.54 86 86
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.069 0.19 -10000 0 -0.4 86 86
FYN -0.1 0.23 -10000 0 -0.51 86 86
mol:Ca2+ -0.12 0.23 -10000 0 -0.54 86 86
mol:DAG -0.12 0.23 -10000 0 -0.54 86 86
NPHS2 -0.014 0.034 -10000 0 -10000 0 0
mol:IP3 -0.12 0.23 -10000 0 -0.54 86 86
regulation of endocytosis -0.11 0.21 -10000 0 -0.48 86 86
Nephrin/NEPH1/podocin/Cholesterol -0.12 0.24 -10000 0 -0.55 86 86
establishment of cell polarity -0.16 0.3 -10000 0 -0.7 86 86
Nephrin/NEPH1/podocin/NCK1-2 -0.11 0.22 -10000 0 -0.5 86 86
Nephrin/NEPH1/beta Arrestin2 -0.11 0.21 -10000 0 -0.49 86 86
NPHS1 -0.16 0.33 -10000 0 -0.86 68 68
Nephrin/NEPH1/podocin -0.12 0.22 -10000 0 -0.52 86 86
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.12 0.23 -10000 0 -0.54 86 86
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.12 0.23 -10000 0 -0.54 86 86
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.1 0.24 -10000 0 -0.52 88 88
cytoskeleton organization -0.094 0.25 -10000 0 -0.54 86 86
Nephrin/NEPH1 -0.12 0.23 -10000 0 -0.53 86 86
Nephrin/NEPH1/ZO-1 -0.13 0.25 -10000 0 -0.58 86 86
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.002 0.03 -10000 0 -0.57 1 1
fibroblast growth factor receptor signaling pathway -0.002 0.03 -10000 0 -0.57 1 1
LAMA1 -0.052 0.23 -10000 0 -0.84 29 29
PRNP 0.013 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.091 0.23 -10000 0 -0.66 52 52
SMAD2 0.029 0.039 -10000 0 -0.52 1 1
GPC1/PrPc/Cu2+ 0 0.008 -10000 0 -10000 0 0
GPC1/Laminin alpha1 -0.05 0.17 -10000 0 -0.66 28 28
TDGF1 -0.35 0.43 -10000 0 -0.86 159 159
CRIPTO/GPC1 -0.28 0.33 -10000 0 -0.66 159 159
APP/GPC1 -0.001 0.01 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.22 0.3 -10000 0 -0.57 159 159
FLT1 0.013 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.006 0.039 -10000 0 -0.57 1 1
SERPINC1 0.012 0.003 -10000 0 -10000 0 0
FYN -0.22 0.3 -10000 0 -0.57 159 159
FGR -0.23 0.3 -10000 0 -0.57 159 159
positive regulation of MAPKKK cascade -0.29 0.33 -10000 0 -0.65 160 160
SLIT2 -0.11 0.3 -10000 0 -0.86 52 52
GPC1/NRG -0.066 0.2 -10000 0 -0.66 37 37
NRG1 -0.073 0.26 -10000 0 -0.84 38 38
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.042 -10000 0 -0.57 2 2
LYN -0.22 0.3 -10000 0 -0.57 159 159
mol:Spermine 0.011 0.011 -10000 0 -10000 0 0
cell growth -0.002 0.03 -10000 0 -0.57 1 1
BMP signaling pathway -0.012 0.016 0.3 1 -10000 0 1
SRC -0.22 0.3 -10000 0 -0.57 159 159
TGFBR1 0.004 0.052 -10000 0 -0.3 11 11
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.25 0.38 -10000 0 -0.7 141 141
GPC1 0.012 0.016 -10000 0 -0.3 1 1
TGFBR1 (dimer) 0.004 0.052 -10000 0 -0.3 11 11
VEGFA 0.008 0.063 -10000 0 -0.86 2 2
BLK -0.4 0.4 -10000 0 -0.71 216 216
HCK -0.23 0.3 -10000 0 -0.58 159 159
FGF2 0.013 0 -10000 0 -10000 0 0
FGFR1 0.011 0.045 -10000 0 -0.86 1 1
VEGFR1 homodimer 0.013 0 -10000 0 -10000 0 0
TGFBR2 0.011 0.045 -10000 0 -0.86 1 1
cell death 0 0.01 -10000 0 -10000 0 0
ATIII/GPC1 -0.001 0.01 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.2 0.29 -10000 0 -0.66 101 101
LCK -0.24 0.3 -10000 0 -0.58 163 163
neuron differentiation -0.065 0.2 -10000 0 -0.66 37 37
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.011 0.044 -10000 0 -0.85 1 1
Endothelins

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
AKT1 -0.058 0.15 -9999 0 -0.59 9 9
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.14 0.28 -9999 0 -0.7 45 45
EDN1 -0.049 0.13 -9999 0 -0.84 6 6
EDN3 -0.43 0.43 -9999 0 -0.86 191 191
EDN2 -0.01 0.11 -9999 0 -0.4 21 21
HRAS/GDP -0.12 0.24 -9999 0 -0.54 67 67
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.092 0.18 -9999 0 -0.4 73 73
ADCY4 -0.1 0.2 -9999 0 -0.54 54 54
ADCY5 -0.18 0.27 -9999 0 -0.6 94 94
ADCY6 -0.1 0.2 -9999 0 -0.54 54 54
ADCY7 -0.1 0.2 -9999 0 -0.54 54 54
ADCY1 -0.11 0.22 -9999 0 -0.57 56 56
ADCY2 -0.15 0.25 -9999 0 -0.59 81 81
ADCY3 -0.1 0.2 -9999 0 -0.54 54 54
ADCY8 -0.2 0.21 -9999 0 -0.56 74 74
ADCY9 -0.1 0.2 -9999 0 -0.54 54 54
arachidonic acid secretion -0.19 0.32 -9999 0 -0.65 106 106
ETB receptor/Endothelin-1/Gq/GTP -0.1 0.21 -9999 0 -0.44 93 93
GNAO1 -0.013 0.14 -9999 0 -0.86 10 10
HRAS 0.01 0.017 -9999 0 -0.3 1 1
ETA receptor/Endothelin-1/G12/GTP -0.026 0.16 -9999 0 -0.55 9 9
ETA receptor/Endothelin-1/Gs/GTP -0.093 0.23 -9999 0 -0.57 55 55
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.076 0.17 -9999 0 -0.5 31 31
EDNRB 0.002 0.091 -9999 0 -0.74 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.16 0.24 -9999 0 -0.64 44 44
CYSLTR1 -0.064 0.17 -9999 0 -0.72 12 12
SLC9A1 -0.025 0.075 -9999 0 -0.32 6 6
mol:GDP -0.13 0.26 -9999 0 -0.56 75 75
SLC9A3 -0.054 0.19 -9999 0 -0.81 17 17
RAF1 -0.17 0.3 -9999 0 -0.6 96 96
JUN -0.29 0.52 -9999 0 -1.2 92 92
JAK2 -0.058 0.15 -9999 0 -0.59 9 9
mol:IP3 -0.12 0.23 -9999 0 -0.49 87 87
ETA receptor/Endothelin-1 -0.046 0.2 -9999 0 -0.54 18 18
PLCB1 0.008 0.045 -9999 0 -0.86 1 1
PLCB2 0.003 0.045 -9999 0 -0.3 8 8
ETA receptor/Endothelin-3 -0.36 0.35 -9999 0 -0.7 192 192
FOS -0.28 0.48 -9999 0 -1 104 104
Gai/GDP -0.002 0.11 -9999 0 -0.65 10 10
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.13 0.24 -9999 0 -0.58 51 51
BCAR1 0.013 0.002 -9999 0 -10000 0 0
PRKCB1 -0.12 0.22 -9999 0 -0.48 87 87
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.095 0.29 -9999 0 -0.86 47 47
Gs family/GDP -0.2 0.26 -9999 0 -0.57 103 103
ETA receptor/Endothelin-1/Gq/GTP -0.12 0.21 -9999 0 -0.46 85 85
MAPK14 -0.069 0.17 -9999 0 -0.39 53 53
TRPC6 -0.15 0.29 -9999 0 -0.75 44 44
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.011 0.045 -9999 0 -0.86 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.081 0.18 -9999 0 -0.4 71 71
ETB receptor/Endothelin-2 -0.023 0.1 -9999 0 -0.66 8 8
ETB receptor/Endothelin-3 -0.34 0.34 -9999 0 -0.67 193 193
ETB receptor/Endothelin-1 -0.025 0.12 -9999 0 -0.66 10 10
MAPK3 -0.25 0.44 -9999 0 -0.9 108 108
MAPK1 -0.25 0.44 -9999 0 -0.89 109 109
Rac1/GDP -0.11 0.24 -9999 0 -0.53 66 66
cAMP biosynthetic process -0.15 0.22 -9999 0 -0.57 62 62
MAPK8 -0.17 0.32 -9999 0 -0.62 98 98
SRC 0.012 0.016 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.008 0.074 -9999 0 -0.28 18 18
p130Cas/CRK/Src/PYK2 -0.15 0.29 -9999 0 -0.61 76 76
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.11 0.24 -9999 0 -0.53 66 66
COL1A2 -0.045 0.17 -9999 0 -0.7 8 8
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.6 7 7
mol:DAG -0.12 0.23 -9999 0 -0.5 87 87
MAP2K2 -0.2 0.35 -9999 0 -0.69 111 111
MAP2K1 -0.2 0.35 -9999 0 -0.69 111 111
EDNRA -0.043 0.099 -9999 0 -0.53 5 5
positive regulation of muscle contraction -0.043 0.13 -9999 0 -0.54 8 8
Gq family/GDP -0.2 0.3 -9999 0 -0.69 91 91
HRAS/GTP -0.14 0.26 -9999 0 -0.57 78 78
PRKCH -0.11 0.22 -9999 0 -0.5 73 73
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.14 0.26 -9999 0 -0.56 89 89
PRKCB -0.13 0.22 -9999 0 -0.52 71 71
PRKCE -0.11 0.23 -9999 0 -0.52 72 72
PRKCD -0.11 0.22 -9999 0 -0.51 70 70
PRKCG -0.12 0.23 -9999 0 -0.52 70 70
regulation of vascular smooth muscle contraction -0.32 0.56 -9999 0 -1.2 104 104
PRKCQ -0.12 0.24 -9999 0 -0.52 75 75
PLA2G4A -0.21 0.36 -9999 0 -0.72 106 106
GNA14 -0.2 0.37 -9999 0 -0.86 91 91
GNA15 -0.02 0.098 -9999 0 -0.31 35 35
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 0.003 0.077 -9999 0 -0.86 3 3
Rac1/GTP -0.026 0.16 -9999 0 -0.55 9 9
MMP1 -0.088 0.15 -9999 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.21 0.42 -9999 0 -0.98 41 41
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.3 0.34 -9999 0 -0.83 90 90
SMAD4 0.014 0.002 -9999 0 -10000 0 0
ID2 -0.21 0.42 -9999 0 -0.97 42 42
AP1 -0.31 0.48 -9999 0 -0.98 120 120
ABCG2 -0.21 0.43 -9999 0 -0.94 54 54
HIF1A -0.014 0.066 -9999 0 -10000 0 0
TFF3 -0.6 0.53 -9999 0 -1.1 163 163
GATA2 0.014 0.016 -9999 0 -0.3 1 1
AKT1 -0.043 0.1 -9999 0 -10000 0 0
response to hypoxia -0.064 0.11 -9999 0 -0.24 20 20
MCL1 -0.21 0.42 -9999 0 -0.95 47 47
NDRG1 -0.21 0.42 -9999 0 -0.95 47 47
SERPINE1 -0.22 0.43 -9999 0 -0.97 47 47
FECH -0.21 0.42 -9999 0 -0.95 47 47
FURIN -0.21 0.42 -9999 0 -0.95 46 46
NCOA2 -0.039 0.21 -9999 0 -0.86 23 23
EP300 -0.07 0.18 -9999 0 -0.34 86 86
HMOX1 -0.21 0.43 -9999 0 -0.94 53 53
BHLHE40 -0.22 0.43 -9999 0 -0.96 51 51
BHLHE41 -0.21 0.43 -9999 0 -0.97 45 45
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.035 -9999 0 -10000 0 0
ENG 0.04 0.089 -9999 0 -10000 0 0
JUN -0.19 0.37 -9999 0 -0.86 88 88
RORA -0.21 0.43 -9999 0 -0.96 47 47
ABCB1 -0.076 0.18 -9999 0 -1.5 5 5
TFRC -0.21 0.42 -9999 0 -0.95 47 47
CXCR4 -0.21 0.42 -9999 0 -0.95 47 47
TF -0.27 0.5 -9999 0 -1.1 71 71
CITED2 -0.24 0.47 -9999 0 -1 58 58
HIF1A/ARNT -0.31 0.38 -9999 0 -1 57 57
LDHA -0.041 0.05 -9999 0 -10000 0 0
ETS1 -0.21 0.42 -9999 0 -0.93 53 53
PGK1 -0.21 0.42 -9999 0 -0.96 44 44
NOS2 -0.23 0.43 -9999 0 -0.96 52 52
ITGB2 -0.22 0.43 -9999 0 -0.96 51 51
ALDOA -0.21 0.42 -9999 0 -0.94 50 50
Cbp/p300/CITED2 -0.34 0.51 -9999 0 -1.1 85 85
FOS -0.22 0.39 -9999 0 -0.86 103 103
HK2 -0.21 0.43 -9999 0 -0.94 52 52
SP1 0.022 0.006 -9999 0 -10000 0 0
GCK -0.42 0.73 -9999 0 -1.5 110 110
HK1 -0.21 0.42 -9999 0 -0.96 44 44
NPM1 -0.21 0.42 -9999 0 -0.97 43 43
EGLN1 -0.21 0.42 -9999 0 -0.98 40 40
CREB1 0.021 0 -9999 0 -10000 0 0
PGM1 -0.21 0.42 -9999 0 -0.93 51 51
SMAD3 0.014 0.002 -9999 0 -10000 0 0
EDN1 -0.18 0.32 -9999 0 -0.76 52 52
IGFBP1 -0.22 0.43 -9999 0 -0.98 44 44
VEGFA -0.17 0.39 -9999 0 -0.76 62 62
HIF1A/JAB1 -0.013 0.02 -9999 0 -10000 0 0
CP -0.39 0.57 -9999 0 -1.1 117 117
CXCL12 -0.26 0.49 -9999 0 -1.1 64 64
COPS5 0.014 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.002 -9999 0 -10000 0 0
BNIP3 -0.21 0.42 -9999 0 -0.96 45 45
EGLN3 -0.22 0.44 -9999 0 -0.99 51 51
CA9 -0.22 0.42 -9999 0 -0.96 49 49
TERT -0.22 0.42 -9999 0 -0.95 50 50
ENO1 -0.21 0.42 -9999 0 -0.94 50 50
PFKL -0.21 0.42 -9999 0 -0.96 44 44
NCOA1 0.013 0 -9999 0 -10000 0 0
ADM -0.24 0.44 -9999 0 -0.96 56 56
ARNT -0.015 0.066 -9999 0 -10000 0 0
HNF4A -0.027 0.065 -9999 0 -0.33 9 9
ADFP -0.22 0.42 -9999 0 -0.92 57 57
SLC2A1 -0.17 0.38 -9999 0 -0.76 61 61
LEP -0.22 0.42 -9999 0 -0.95 51 51
HIF1A/ARNT/Cbp/p300 -0.32 0.36 -9999 0 -0.86 90 90
EPO -0.14 0.3 -9999 0 -0.98 10 10
CREBBP -0.07 0.18 -9999 0 -0.34 85 85
HIF1A/ARNT/Cbp/p300/HDAC7 -0.29 0.34 -9999 0 -0.82 89 89
PFKFB3 -0.21 0.43 -9999 0 -0.96 47 47
NT5E -0.22 0.43 -9999 0 -0.98 46 46
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 0.013 0 -10000 0 -10000 0 0
EPHB2 0.006 0.077 -10000 0 -0.86 3 3
EFNB1 -0.011 0.15 -10000 0 -0.66 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.24 0.25 -10000 0 -0.55 143 143
Ephrin B2/EPHB1-2 -0.18 0.25 -10000 0 -0.53 129 129
neuron projection morphogenesis -0.22 0.24 -10000 0 -0.52 143 143
Ephrin B1/EPHB1-2/Tiam1 -0.25 0.28 -10000 0 -0.59 143 143
DNM1 -0.03 0.18 -10000 0 -0.83 19 19
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.012 0.044 -10000 0 -0.81 1 1
YES1 -0.001 0.053 -10000 0 -1 1 1
Ephrin B1/EPHB1-2/NCK2 -0.18 0.26 -10000 0 -0.51 143 143
PI3K 0.011 0.068 -10000 0 -1.3 1 1
mol:GDP -0.25 0.27 -10000 0 -0.58 143 143
ITGA2B -0.095 0.29 -10000 0 -0.86 47 47
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.001 0.053 -10000 0 -1 1 1
MAP3K7 -0.004 0.045 -10000 0 -0.86 1 1
FGR -0.003 0.054 -10000 0 -1 1 1
TIAM1 -0.16 0.16 -10000 0 -0.3 210 210
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.049 0.21 -10000 0 -0.54 53 53
LYN -0.001 0.053 -10000 0 -1 1 1
Ephrin B1/EPHB1-2/Src Family Kinases -0.005 0.05 -10000 0 -0.97 1 1
Ephrin B1/EPHB1-2 -0.012 0.048 -10000 0 -0.93 1 1
SRC -0.003 0.054 -10000 0 -1 1 1
ITGB3 -0.015 0.15 -10000 0 -0.86 12 12
EPHB1 -0.28 0.41 -10000 0 -0.86 127 127
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.1 0.26 -10000 0 -0.72 53 53
BLK -0.059 0.098 -10000 0 -1 1 1
HCK -0.004 0.054 -10000 0 -1 1 1
regulation of stress fiber formation 0.19 0.25 0.5 143 -10000 0 143
MAPK8 0.018 0.069 -10000 0 -0.84 2 2
Ephrin B1/EPHB1-2/RGS3 -0.18 0.26 -10000 0 -0.51 143 143
endothelial cell migration 0 0.04 -10000 0 -0.76 1 1
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.013 0.052 -10000 0 -0.97 1 1
regulation of focal adhesion formation 0.19 0.25 0.5 143 -10000 0 143
chemotaxis 0.19 0.25 0.5 143 -10000 0 143
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
Rac1/GTP -0.23 0.25 -10000 0 -0.54 143 143
angiogenesis -0.012 0.048 -10000 0 -0.92 1 1
LCK -0.006 0.057 -10000 0 -1 1 1
Glypican 2 network

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
MDK -0.079 0.14 -9999 0 -0.3 112 112
GPC2 -0.014 0.088 -9999 0 -0.3 33 33
GPC2/Midkine -0.072 0.11 -9999 0 -0.38 16 16
neuron projection morphogenesis -0.072 0.11 -9999 0 -0.37 16 16
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.6 62 62
FYN -0.11 0.34 -10000 0 -0.8 63 63
LAT/GRAP2/SLP76 -0.13 0.27 -10000 0 -0.65 72 72
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.056 0.22 -10000 0 -0.47 71 71
B2M 0.012 0.006 -10000 0 -10000 0 0
IKBKG -0.031 0.05 -10000 0 -0.19 7 7
MAP3K8 0.004 0.089 -10000 0 -0.86 4 4
mol:Ca2+ -0.033 0.052 -10000 0 -0.13 82 82
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.32 -10000 0 -0.72 72 72
TRPV6 -0.19 0.36 -10000 0 -0.82 87 87
CD28 -0.044 0.19 -10000 0 -0.58 36 36
SHC1 -0.11 0.34 -10000 0 -0.78 67 67
receptor internalization -0.14 0.38 -10000 0 -0.81 76 76
PRF1 -0.11 0.34 -10000 0 -0.88 52 52
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.037 0.18 -10000 0 -0.38 64 64
LAT -0.12 0.35 -10000 0 -0.8 67 67
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.097 0.28 -10000 0 -0.74 55 55
CD3E -0.065 0.24 -10000 0 -0.87 30 30
CD3G -0.14 0.33 -10000 0 -0.81 71 71
RASGRP2 0 0.03 -10000 0 -0.19 4 4
RASGRP1 -0.052 0.22 -10000 0 -0.46 74 74
HLA-A 0.01 0.023 -10000 0 -10000 0 0
RASSF5 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.068 -10000 0 -0.12 48 48
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.057 0.09 -10000 0 -0.25 50 50
PRKCA -0.066 0.14 -10000 0 -0.32 73 73
GRAP2 -0.045 0.21 -10000 0 -0.79 27 27
mol:IP3 -0.052 0.24 0.28 68 -0.46 69 137
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.15 0.42 -10000 0 -0.94 66 66
ORAI1 0.091 0.16 0.4 80 -10000 0 80
CSK -0.12 0.35 -10000 0 -0.81 67 67
B7 family/CD28 -0.2 0.35 -10000 0 -0.74 92 92
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.15 0.42 -10000 0 -0.92 73 73
PTPN6 -0.12 0.35 -10000 0 -0.82 66 66
VAV1 -0.12 0.34 -10000 0 -0.78 71 71
Monovalent TCR/CD3 -0.16 0.42 -10000 0 -0.76 90 90
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.36 -10000 0 -0.82 66 66
PAG1 -0.12 0.35 -10000 0 -0.81 67 67
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.15 0.42 -10000 0 -0.97 66 66
CD80 -0.086 0.27 -10000 0 -0.83 44 44
CD86 -0.008 0.092 -10000 0 -0.35 21 21
PDK1/CARD11/BCL10/MALT1 -0.07 0.11 -10000 0 -0.29 56 56
HRAS 0.012 0.016 -10000 0 -0.3 1 1
GO:0035030 -0.11 0.3 -10000 0 -0.58 92 92
CD8A -0.048 0.22 -10000 0 -0.86 26 26
CD8B -0.099 0.28 -10000 0 -0.74 57 57
PTPRC -0.032 0.17 -10000 0 -0.55 29 29
PDK1/PKC theta -0.072 0.27 -10000 0 -0.59 70 70
CSK/PAG1 -0.11 0.34 -10000 0 -0.8 64 64
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.019 -10000 0 -10000 0 0
GRAP2/SLP76 -0.15 0.32 -10000 0 -0.76 74 74
STIM1 0.049 0.083 -10000 0 -10000 0 0
RAS family/GTP 0.007 0.091 -10000 0 -0.18 40 40
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.43 -10000 0 -0.9 76 76
mol:DAG -0.071 0.18 -10000 0 -0.41 73 73
RAP1A/GDP 0.006 0.03 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.029 0.18 -10000 0 -0.65 24 24
cytotoxic T cell degranulation -0.1 0.32 -10000 0 -0.83 52 52
RAP1A/GTP -0.003 0.009 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.076 0.26 -10000 0 -0.57 72 72
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.081 0.3 0.3 64 -0.61 72 136
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.028 0.17 -10000 0 -0.66 23 23
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.26 -10000 0 -0.61 74 74
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.011 0.045 -10000 0 -0.86 1 1
CD8 heterodimer -0.11 0.3 -10000 0 -0.79 57 57
CARD11 -0.079 0.17 -10000 0 -0.33 101 101
PRKCB -0.06 0.13 -10000 0 -0.31 63 63
PRKCE -0.052 0.12 -10000 0 -0.3 57 57
PRKCQ -0.095 0.31 -10000 0 -0.68 71 71
LCP2 0.004 0.052 -10000 0 -10000 0 0
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.042 0.19 -10000 0 -0.4 70 70
IKK complex 0.01 0.069 -10000 0 -0.12 32 32
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.017 0.14 -10000 0 -0.3 52 52
PDPK1 -0.049 0.21 -10000 0 -0.45 69 69
TCR/CD3/MHC I/CD8/Fyn -0.17 0.45 -10000 0 -1 66 66
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.3 0.36 -9999 0 -0.64 174 174
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.056 0.23 -9999 0 -0.76 34 34
SMAD9 -0.22 0.29 -9999 0 -0.62 119 119
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.11 0.21 -9999 0 -0.38 132 132
BMP7/USAG1 -0.35 0.33 -9999 0 -0.66 199 199
SMAD5/SKI -0.094 0.2 -9999 0 -0.55 21 21
SMAD1 0.016 0.047 -9999 0 -10000 0 0
BMP2 -0.015 0.15 -9999 0 -0.86 12 12
SMAD1/SMAD1/SMAD4 -0.002 0.003 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.29 0.41 -9999 0 -0.86 132 132
BMPR1A-1B/BAMBI -0.21 0.28 -9999 0 -0.58 132 132
AHSG -0.011 0.071 -9999 0 -0.3 22 22
CER1 0 0.002 -9999 0 -10000 0 0
BMP2-4/CER1 -0.038 0.14 -9999 0 -0.58 24 24
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.086 0.2 -9999 0 -0.65 25 25
BMP2-4 (homodimer) -0.044 0.16 -9999 0 -0.66 24 24
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.18 0.25 -9999 0 -0.52 132 132
RGMA -0.017 0.16 -9999 0 -0.86 13 13
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.096 0.19 -9999 0 -0.59 23 23
BMP2-4/USAG1 -0.34 0.31 -9999 0 -0.6 213 213
SMAD6/SMURF1/SMAD5 -0.094 0.2 -9999 0 -0.55 21 21
SOSTDC1 -0.44 0.43 -9999 0 -0.86 199 199
BMP7/BMPR2/BMPR1A-1B -0.18 0.25 -9999 0 -0.52 132 132
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.013 0 -9999 0 -10000 0 0
HFE2 0.001 0.031 -9999 0 -0.3 4 4
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.05 0.16 -9999 0 -0.59 31 31
SMAD5/SMAD5/SMAD4 -0.094 0.2 -9999 0 -0.55 21 21
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.1 0.14 -9999 0 -0.5 23 23
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.011 0.044 -9999 0 -10000 0 0
SMAD1/SKI 0.023 0.044 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.047 0.15 -9999 0 -0.6 24 24
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.2 0.36 -9999 0 -0.74 108 108
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.011 0.077 -9999 0 -0.57 7 7
BMPR1A-1B (homodimer) -0.23 0.32 -9999 0 -0.66 132 132
CHRDL1 -0.6 0.39 -9999 0 -0.86 269 269
ENDOFIN/SMAD1 0.023 0.044 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.007 0.01 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI 0 0.072 -9999 0 -0.86 1 1
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.44 0.3 -9999 0 -0.61 274 274
BMP2-4/GREM1 -0.17 0.29 -9999 0 -0.64 96 96
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.18 0.28 -9999 0 -0.58 119 119
SMAD1/SMAD6 0.023 0.044 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.013 0 -9999 0 -10000 0 0
BMP6 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.073 0.16 -9999 0 -0.51 23 23
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.023 0.044 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A -0.003 0.12 -9999 0 -0.86 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.22 0.33 -9999 0 -0.83 70 70
CHRD -0.005 0.12 -9999 0 -0.86 8 8
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.1 0.2 -9999 0 -0.63 23 23
BMP4 -0.018 0.16 -9999 0 -0.72 16 16
FST -0.22 0.38 -9999 0 -0.82 104 104
BMP2-4/NOG -0.083 0.2 -9999 0 -0.58 51 51
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.17 0.23 -9999 0 -0.49 132 132
Glucocorticoid receptor regulatory network

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
PCK2 0.046 0.094 0.33 8 -10000 0 8
SMARCC2 0.013 0.013 -10000 0 -10000 0 0
SMARCC1 0.013 0.013 -10000 0 -10000 0 0
TBX21 -0.16 0.29 -10000 0 -0.87 37 37
SUMO2 0.014 0.012 -10000 0 -10000 0 0
STAT1 (dimer) 0.014 0.051 -10000 0 -0.3 10 10
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.004 0.089 -10000 0 -0.86 4 4
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.35 31 -0.54 4 35
PRL -0.088 0.12 -10000 0 -0.52 1 1
cortisol/GR alpha (dimer)/TIF2 0.27 0.29 0.59 122 -0.56 8 130
RELA -0.043 0.09 -10000 0 -0.31 1 1
FGG 0.25 0.19 0.52 83 -10000 0 83
GR beta/TIF2 0.1 0.21 0.38 32 -0.59 23 55
IFNG -0.49 0.51 -10000 0 -1.1 113 113
apoptosis 0.03 0.24 0.52 41 -0.53 1 42
CREB1 0.012 0.02 -10000 0 -10000 0 0
histone acetylation -0.078 0.16 -10000 0 -0.41 45 45
BGLAP -0.099 0.15 -10000 0 -0.52 11 11
GR/PKAc 0.13 0.1 0.36 19 -10000 0 19
NF kappa B1 p50/RelA -0.084 0.16 -10000 0 -0.47 21 21
SMARCD1 0.013 0.013 -10000 0 -10000 0 0
MDM2 0.12 0.095 0.28 72 -10000 0 72
GATA3 -0.034 0.2 -10000 0 -0.86 22 22
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.2 0.16 -10000 0 -0.49 56 56
GSK3B 0.014 0.012 -10000 0 -10000 0 0
NR1I3 0.057 0.23 0.5 35 -0.78 4 39
CSN2 0.2 0.14 0.45 41 -10000 0 41
BRG1/BAF155/BAF170/BAF60A 0.006 0.043 -10000 0 -10000 0 0
NFATC1 0.001 0.11 -10000 0 -0.86 6 6
POU2F1 0.013 0.016 -10000 0 -10000 0 0
CDKN1A 0.024 0.051 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.012 -10000 0 -10000 0 0
SFN -0.21 0.17 -10000 0 -0.32 254 254
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.052 0.16 0.35 12 -0.48 11 23
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.087 0.45 0.49 34 -0.89 84 118
JUN -0.33 0.31 -10000 0 -0.7 127 127
IL4 -0.13 0.17 -10000 0 -0.66 16 16
CDK5R1 0.01 0.029 -10000 0 -0.3 3 3
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.38 0.43 -10000 0 -0.87 138 138
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.35 24 -0.49 4 28
cortisol/GR alpha (monomer) 0.37 0.3 0.71 134 -10000 0 134
NCOA2 -0.04 0.21 -10000 0 -0.86 23 23
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.27 0.38 -10000 0 -0.88 103 103
AP-1/NFAT1-c-4 -0.57 0.5 -10000 0 -1 170 170
AFP -0.22 0.22 -10000 0 -0.58 77 77
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.48 41 -10000 0 41
TP53 0.032 0.021 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.48 0.4 -10000 0 -0.96 107 107
KRT14 -0.22 0.17 -10000 0 -0.58 17 17
TBP 0.022 0.006 -10000 0 -10000 0 0
CREBBP 0.055 0.061 -10000 0 -10000 0 0
HDAC1 0.01 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.013 -10000 0 -10000 0 0
AP-1 -0.57 0.51 -10000 0 -1 170 170
MAPK14 0.014 0.011 -10000 0 -10000 0 0
MAPK10 0.014 0.012 -10000 0 -10000 0 0
MAPK11 0.014 0.012 -10000 0 -10000 0 0
KRT5 -0.56 0.56 -10000 0 -1.2 127 127
interleukin-1 receptor activity 0.016 0.013 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 0.014 0.052 -10000 0 -0.3 10 10
CGA -0.13 0.16 -10000 0 -0.56 15 15
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.23 0.14 0.37 141 -10000 0 141
MAPK3 0.014 0.012 -10000 0 -10000 0 0
MAPK1 0.014 0.011 -10000 0 -10000 0 0
ICAM1 -0.28 0.27 -10000 0 -0.7 75 75
NFKB1 -0.043 0.09 -10000 0 -0.31 1 1
MAPK8 -0.18 0.18 -10000 0 -0.47 76 76
MAPK9 0.014 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.025 0.24 0.52 41 -0.56 1 42
BAX 0.029 0.028 -10000 0 -10000 0 0
POMC -0.56 0.71 -10000 0 -1.5 112 112
EP300 0.055 0.061 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.33 0.24 0.61 128 -10000 0 128
proteasomal ubiquitin-dependent protein catabolic process 0.088 0.072 0.24 25 -10000 0 25
SGK1 0.098 0.22 -10000 0 -1.4 7 7
IL13 -0.3 0.27 -10000 0 -0.87 41 41
IL6 -0.44 0.57 -10000 0 -1.3 104 104
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.26 0.22 -10000 0 -0.78 29 29
IL2 -0.36 0.28 -10000 0 -0.76 83 83
CDK5 0.012 0.007 -10000 0 -10000 0 0
PRKACB 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.28 0.32 -10000 0 -0.81 65 65
CDK5R1/CDK5 0.006 0.025 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.039 0.12 -10000 0 -0.49 1 1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.57 119 -10000 0 119
SMARCA4 0.013 0.013 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.15 0.42 77 -10000 0 77
NF kappa B1 p50/RelA/Cbp 0.002 0.16 -10000 0 -0.48 7 7
JUN (dimer) -0.33 0.3 -10000 0 -0.7 127 127
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.26 0.43 -10000 0 -1.1 71 71
NR3C1 0.22 0.19 0.51 82 -10000 0 82
NR4A1 -0.33 0.43 -10000 0 -0.78 166 166
TIF2/SUV420H1 -0.04 0.16 -10000 0 -0.66 23 23
MAPKKK cascade 0.03 0.24 0.52 41 -0.53 1 42
cortisol/GR alpha (dimer)/Src-1 0.32 0.24 0.59 132 -10000 0 132
PBX1 0.011 0.045 -10000 0 -0.86 1 1
POU1F1 0.006 0.008 -10000 0 -10000 0 0
SELE -0.36 0.51 -10000 0 -1.2 78 78
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.15 0.42 75 -10000 0 75
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.57 119 -10000 0 119
mol:cortisol 0.21 0.19 0.4 155 -10000 0 155
MMP1 -0.21 0.15 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.12 0.24 -10000 0 -0.48 109 109
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.016 -10000 0 -0.3 1 1
IRS1/Crk -0.12 0.24 -10000 0 -0.48 109 109
IGF-1R heterotetramer/IGF1/PTP1B -0.12 0.23 -10000 0 -0.55 81 81
AKT1 -0.082 0.22 -10000 0 -0.81 9 9
BAD -0.069 0.2 -10000 0 -0.73 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.24 -10000 0 -0.48 109 109
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.23 -10000 0 -0.48 109 109
RAF1 -0.059 0.19 -10000 0 -0.68 9 9
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.13 0.22 -10000 0 -0.45 109 109
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.25 -10000 0 -0.52 109 109
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
RPS6KB1 -0.082 0.22 -10000 0 -0.81 9 9
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.052 0.16 -10000 0 -0.55 9 9
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.43 81 81
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.099 0.18 -10000 0 -0.44 81 81
IGF-1R heterotetramer -0.017 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.14 0.23 -10000 0 -0.48 109 109
Crk/p130 Cas/Paxillin -0.12 0.2 -10000 0 -0.46 81 81
IGF1R -0.017 0.048 -10000 0 -10000 0 0
IGF1 -0.19 0.36 -10000 0 -0.84 86 86
IRS2/Crk -0.11 0.23 -10000 0 -0.45 109 109
PI3K -0.13 0.22 -10000 0 -0.49 81 81
apoptosis 0.051 0.18 0.6 9 -10000 0 9
HRAS/GDP -0.001 0.01 -10000 0 -10000 0 0
PRKCD -0.099 0.24 -10000 0 -0.55 81 81
RAF1/14-3-3 E -0.043 0.17 -10000 0 -0.55 9 9
BAD/14-3-3 -0.055 0.19 -10000 0 -0.65 9 9
PRKCZ -0.082 0.22 -10000 0 -0.81 9 9
Crk/p130 Cas/Paxillin/FAK1 -0.096 0.16 -10000 0 -0.66 9 9
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.11 0.26 -10000 0 -0.59 81 81
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.2 -10000 0 -0.49 81 81
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.24 -10000 0 -0.48 109 109
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.12 0.24 -10000 0 -0.48 109 109
IRS1 -0.14 0.26 -10000 0 -0.52 109 109
IRS2 -0.12 0.24 -10000 0 -0.48 109 109
IGF-1R heterotetramer/IGF1 -0.16 0.28 -10000 0 -0.69 81 81
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.095 0.23 -10000 0 -0.46 81 81
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.099 0.24 -10000 0 -0.55 81 81
SHC1 0.013 0 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.21 0.54 -9999 0 -1.3 57 57
IL23A -0.22 0.55 -9999 0 -1.3 63 63
NF kappa B1 p50/RelA/I kappa B alpha -0.29 0.46 -9999 0 -1.2 65 65
positive regulation of T cell mediated cytotoxicity -0.24 0.6 -9999 0 -1.3 67 67
ITGA3 -0.2 0.5 -9999 0 -1.2 58 58
IL17F -0.1 0.34 -9999 0 -0.75 48 48
IL12B 0.001 0.085 -9999 0 -0.44 9 9
STAT1 (dimer) -0.23 0.56 -9999 0 -1.3 67 67
CD4 -0.19 0.49 -9999 0 -1.1 62 62
IL23 -0.23 0.52 -9999 0 -1.2 63 63
IL23R -0.004 0.097 -9999 0 -10000 0 0
IL1B -0.23 0.57 -9999 0 -1.3 63 63
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.19 0.49 -9999 0 -1.1 60 60
TYK2 0.013 0.022 -9999 0 -10000 0 0
STAT4 -0.034 0.16 -9999 0 -0.44 39 39
STAT3 0.013 0 -9999 0 -10000 0 0
IL18RAP -0.04 0.2 -9999 0 -0.86 22 22
IL12RB1 -0.024 0.12 -9999 0 -0.52 9 9
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
IL12Rbeta1/TYK2 -0.011 0.094 -9999 0 -0.71 3 3
IL23R/JAK2 -0.001 0.12 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.24 0.6 -9999 0 -1.3 67 67
natural killer cell activation 0.001 0.009 -9999 0 -10000 0 0
JAK2 0.021 0.026 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.013 0.004 -9999 0 -10000 0 0
RELA 0.013 0.004 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.21 0.49 -9999 0 -1.1 64 64
ALOX12B -0.21 0.5 -9999 0 -1.1 63 63
CXCL1 -0.22 0.52 -9999 0 -1.2 58 58
T cell proliferation -0.24 0.6 -9999 0 -1.3 67 67
NFKBIA 0.013 0.004 -9999 0 -10000 0 0
IL17A -0.06 0.28 -9999 0 -0.59 39 39
PI3K -0.3 0.47 -9999 0 -1.2 66 66
IFNG -0.021 0.054 -9999 0 -0.13 55 55
STAT3 (dimer) -0.28 0.43 -9999 0 -1.1 64 64
IL18R1 -0.031 0.14 -9999 0 -0.4 39 39
IL23/IL23R/JAK2/TYK2/SOCS3 -0.1 0.32 -9999 0 -0.75 43 43
IL18/IL18R -0.077 0.19 -9999 0 -0.62 35 35
macrophage activation -0.015 0.018 -9999 0 -0.044 65 65
TNF -0.26 0.61 -9999 0 -1.4 74 74
STAT3/STAT4 -0.31 0.48 -9999 0 -1.2 69 69
STAT4 (dimer) -0.25 0.57 -9999 0 -1.3 69 69
IL18 -0.035 0.15 -9999 0 -0.39 44 44
IL19 -0.19 0.49 -9999 0 -1.2 57 57
STAT5A (dimer) -0.23 0.56 -9999 0 -1.3 66 66
STAT1 0.005 0.05 -9999 0 -0.3 10 10
SOCS3 -0.05 0.22 -9999 0 -0.84 28 28
CXCL9 -0.27 0.6 -9999 0 -1.3 77 77
MPO -0.19 0.5 -9999 0 -1.1 61 61
positive regulation of humoral immune response -0.24 0.6 -9999 0 -1.3 67 67
IL23/IL23R/JAK2/TYK2 -0.28 0.71 -9999 0 -1.5 67 67
IL6 -0.34 0.67 -9999 0 -1.4 99 99
STAT5A 0.013 0 -9999 0 -10000 0 0
IL2 0.001 0.017 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 -9999 0 -10000 0 0
CD3E -0.22 0.55 -9999 0 -1.3 62 62
keratinocyte proliferation -0.24 0.6 -9999 0 -1.3 67 67
NOS2 -0.2 0.5 -9999 0 -1.1 63 63
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.042 0.12 -9999 0 -0.51 10 10
EGFR 0.001 0.099 -9999 0 -0.86 5 5
EPHA2 0.011 0.023 -9999 0 -0.3 2 2
USP6 0.01 0.028 -9999 0 -0.3 3 3
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.1 0.24 -9999 0 -0.66 56 56
ARRB2 -0.041 0.15 -9999 0 -0.46 42 42
mol:GTP 0.02 0.012 -9999 0 -10000 0 0
ARRB1 0.011 0.045 -9999 0 -0.86 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.008 0.063 -9999 0 -0.86 2 2
EGF -0.11 0.3 -9999 0 -0.86 51 51
somatostatin receptor activity 0 0 -9999 0 -0.001 101 101
ARAP2 0.011 0.045 -9999 0 -0.86 1 1
mol:GDP -0.12 0.14 -9999 0 -0.31 99 99
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 90 90
ITGA2B -0.095 0.29 -9999 0 -0.86 47 47
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.009 -9999 0 -10000 0 0
ADAP1 0.013 0 -9999 0 -10000 0 0
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.16 0.24 -9999 0 -0.73 51 51
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.15 -9999 0 -0.32 102 102
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.087 0.2 -9999 0 -0.57 56 56
ADRB2 -0.01 0.14 -9999 0 -0.86 10 10
receptor agonist activity 0 0 -9999 0 0 107 107
actin filament binding 0 0 -9999 0 -0.001 98 98
SRC 0.012 0.016 -9999 0 -10000 0 0
ITGB3 -0.015 0.15 -9999 0 -0.86 12 12
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 92 92
ARF6/GDP 0.001 0.069 -9999 0 -0.34 2 2
ARF6/GDP/GULP/ACAP1 -0.19 0.2 -9999 0 -0.52 82 82
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.081 0.21 -9999 0 -0.58 53 53
ACAP1 -0.001 0.081 -9999 0 -0.86 2 2
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.081 0.22 -9999 0 -0.71 42 42
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.1 0.3 -9999 0 -0.86 51 51
CYTH3 0.01 0.035 -9999 0 -0.67 1 1
CYTH2 0.007 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 90 90
endosomal lumen acidification 0 0 -9999 0 -0.001 104 104
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.14 0.33 -9999 0 -0.86 68 68
GNAQ/ARNO 0.008 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 21 21
MET -0.11 0.15 -9999 0 -0.3 154 154
GNA14 -0.2 0.37 -9999 0 -0.86 91 91
GNA15 -0.017 0.099 -9999 0 -0.31 35 35
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 97 97
GNA11 0.006 0.077 -9999 0 -0.86 3 3
LHCGR -0.093 0.27 -9999 0 -0.86 42 42
AGTR1 -0.32 0.42 -9999 0 -0.86 146 146
desensitization of G-protein coupled receptor protein signaling pathway -0.08 0.22 -9999 0 -0.7 42 42
IPCEF1/ARNO -0.064 0.16 -9999 0 -0.46 56 56
alphaIIb/beta3 Integrin -0.1 0.26 -9999 0 -0.72 53 53
Syndecan-1-mediated signaling events

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
TGFB1 0.007 0.042 -9999 0 -10000 0 0
CCL5 -0.043 0.21 -9999 0 -0.72 29 29
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.16 -9999 0 -0.47 39 39
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 -0.089 0.16 -9999 0 -0.52 25 25
Syndecan-1/Syntenin -0.089 0.16 -9999 0 -0.67 14 14
MAPK3 -0.066 0.14 -9999 0 -0.63 12 12
HGF/MET -0.16 0.24 -9999 0 -0.73 51 51
TGFB1/TGF beta receptor Type II 0.007 0.042 -9999 0 -10000 0 0
BSG 0.012 0.016 -9999 0 -10000 0 0
keratinocyte migration -0.088 0.15 -9999 0 -0.51 25 25
Syndecan-1/RANTES -0.12 0.22 -9999 0 -0.75 32 32
Syndecan-1/CD147 -0.09 0.14 -9999 0 -0.68 12 12
Syndecan-1/Syntenin/PIP2 -0.096 0.14 -9999 0 -0.65 14 14
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.094 0.14 -9999 0 -0.62 14 14
MMP7 -0.17 0.22 -9999 0 -0.36 186 186
HGF -0.1 0.3 -9999 0 -0.86 51 51
Syndecan-1/CASK -0.097 0.15 -9999 0 -0.45 39 39
Syndecan-1/HGF/MET -0.21 0.23 -9999 0 -0.67 61 61
regulation of cell adhesion -0.056 0.14 -9999 0 -0.6 12 12
HPSE -0.021 0.14 -9999 0 -0.86 9 9
positive regulation of cell migration -0.1 0.16 -9999 0 -0.47 39 39
SDC1 -0.1 0.16 -9999 0 -0.48 39 39
Syndecan-1/Collagen -0.1 0.16 -9999 0 -0.47 39 39
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.11 0.15 -9999 0 -0.3 154 154
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.086 0.24 -9999 0 -0.54 68 68
MAPK1 -0.066 0.14 -9999 0 -0.63 12 12
homophilic cell adhesion -0.1 0.16 -9999 0 -0.47 39 39
MMP1 -0.14 0.15 -9999 0 -0.3 180 180
TCGA08_retinoblastoma

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
CDKN2B -0.12 0.15 -10000 0 -10000 0 0
CDKN2C 0.026 0.034 -10000 0 -0.29 3 3
CDKN2A -0.12 0.16 -10000 0 -0.3 164 164
CCND2 0.067 0.069 0.16 114 -10000 0 114
RB1 -0.066 0.068 -10000 0 -0.23 1 1
CDK4 0.067 0.068 0.24 1 -10000 0 1
CDK6 0.07 0.073 0.24 1 -0.19 1 2
G1/S progression 0.058 0.075 0.23 1 -10000 0 1
Coregulation of Androgen receptor activity

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
NRIP1 -0.014 0.062 -10000 0 -0.35 10 10
SVIL -0.006 0.03 -10000 0 -10000 0 0
ZNF318 0.06 0.082 -10000 0 -10000 0 0
JMJD2C -0.065 0.069 -10000 0 -0.12 215 215
T-DHT/AR/Ubc9 -0.28 0.3 -10000 0 -0.65 149 149
CARM1 0.011 0.003 -10000 0 -10000 0 0
PRDX1 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.02 0.01 -10000 0 -10000 0 0
CTNNB1 -0.002 0.023 -10000 0 -10000 0 0
AKT1 0.025 0.019 -10000 0 -10000 0 0
PTK2B 0.004 0.015 -10000 0 -10000 0 0
MED1 0.024 0.019 -10000 0 -10000 0 0
MAK 0.048 0.13 -10000 0 -0.83 5 5
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.008 0.053 -10000 0 -0.86 1 1
GSN -0.006 0.03 -10000 0 -10000 0 0
NCOA2 -0.042 0.21 -10000 0 -0.86 23 23
NCOA6 -0.005 0.028 -10000 0 -10000 0 0
DNA-PK 0.057 0.082 0.26 1 -10000 0 1
NCOA4 0.011 0.004 -10000 0 -10000 0 0
PIAS3 -0.002 0.023 -10000 0 -10000 0 0
cell proliferation -0.014 0.15 -10000 0 -1.1 5 5
XRCC5 0.024 0.017 -10000 0 -10000 0 0
UBE3A -0.015 0.046 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.3 0.33 -10000 0 -0.68 154 154
FHL2 -0.16 0.37 -10000 0 -1.4 31 31
RANBP9 -0.005 0.028 -10000 0 -10000 0 0
JMJD1A 0.002 0.037 -10000 0 -0.12 28 28
CDK6 0.012 0.045 -10000 0 -0.85 1 1
TGFB1I1 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.29 0.31 -10000 0 -0.66 151 151
XRCC6 0.024 0.017 -10000 0 -10000 0 0
T-DHT/AR -0.33 0.33 -10000 0 -0.66 172 172
CTDSP1 0.008 0.006 -10000 0 -10000 0 0
CTDSP2 0.045 0.05 -10000 0 -10000 0 0
BRCA1 -0.006 0.03 -10000 0 -10000 0 0
TCF4 0.035 0.034 -10000 0 -10000 0 0
CDKN2A -0.1 0.15 -10000 0 -10000 0 0
SRF 0.026 0.04 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -1.3 3 3
KLK3 -0.43 0.7 -10000 0 -1.6 102 102
TMF1 0.009 0.006 -10000 0 -10000 0 0
HNRNPA1 0.03 0.027 -10000 0 -10000 0 0
AOF2 -0.021 0.033 -10000 0 -0.075 102 102
APPL1 0.051 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.27 0.3 -10000 0 -0.64 149 149
AR -0.37 0.43 -10000 0 -0.9 149 149
UBA3 0.008 0.006 -10000 0 -10000 0 0
PATZ1 0.03 0.027 -10000 0 -10000 0 0
PAWR 0.009 0.006 -10000 0 -10000 0 0
PRKDC 0.024 0.017 -10000 0 -10000 0 0
PA2G4 0.035 0.035 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.25 0.29 -10000 0 -0.6 149 149
RPS6KA3 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.28 0.31 -10000 0 -0.65 149 149
LATS2 0.03 0.027 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.25 0.28 -10000 0 -0.59 149 149
Cyclin D3/CDK11 p58 0 0 -10000 0 -10000 0 0
VAV3 -0.011 0.091 -10000 0 -0.86 4 4
KLK2 -0.78 0.64 -10000 0 -1.3 215 215
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.29 0.33 -10000 0 -0.67 154 154
TMPRSS2 -0.18 0.32 -10000 0 -1.2 28 28
CCND1 0 0.05 -10000 0 -0.3 10 10
PIAS1 -0.015 0.046 -10000 0 -10000 0 0
mol:T-DHT -0.033 0.043 -10000 0 -0.084 132 132
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.034 0.075 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.28 0.31 -10000 0 -0.65 149 149
CMTM2 0.014 0.023 -10000 0 -0.29 2 2
SNURF -0.022 0.17 -10000 0 -0.86 15 15
ZMIZ1 -0.013 0.038 -10000 0 -10000 0 0
CCND3 0.014 0.002 -10000 0 -10000 0 0
TGIF1 0.03 0.027 -10000 0 -10000 0 0
FKBP4 -0.005 0.028 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.13 0.42 -9999 0 -1.4 38 38
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.042 0.11 -9999 0 -0.33 38 38
ATF2/c-Jun -0.23 0.44 -9999 0 -1 88 88
MAPK11 -0.042 0.11 -9999 0 -0.39 16 16
MITF -0.036 0.14 -9999 0 -0.4 38 38
MAPKAPK5 -0.036 0.14 -9999 0 -0.4 38 38
KRT8 -0.036 0.14 -9999 0 -0.4 38 38
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.059 0.17 -9999 0 -0.51 38 38
CEBPB -0.036 0.14 -9999 0 -0.4 38 38
SLC9A1 -0.036 0.14 -9999 0 -0.4 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.072 0.19 -9999 0 -0.44 53 53
p38alpha-beta/MNK1 -0.034 0.14 -9999 0 -0.5 16 16
JUN -0.23 0.44 -9999 0 -1 88 88
PPARGC1A -0.24 0.25 -9999 0 -0.47 200 200
USF1 -0.036 0.14 -9999 0 -0.4 38 38
RAB5/GDP/GDI1 -0.043 0.087 -9999 0 -0.35 16 16
NOS2 -0.057 0.16 -9999 0 -0.54 16 16
DDIT3 -0.039 0.14 -9999 0 -0.41 38 38
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.019 0.11 -9999 0 -0.39 16 16
p38alpha-beta/HBP1 -0.034 0.14 -9999 0 -0.5 16 16
CREB1 -0.049 0.16 -9999 0 -0.43 43 43
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.022 0.12 -9999 0 -0.43 16 16
RPS6KA4 -0.036 0.14 -9999 0 -0.4 38 38
PLA2G4A -0.055 0.2 -9999 0 -0.61 36 36
GDI1 -0.036 0.14 -9999 0 -0.4 38 38
TP53 -0.047 0.17 -9999 0 -0.5 38 38
RPS6KA5 -0.071 0.2 -9999 0 -0.46 60 60
ESR1 -0.072 0.21 -9999 0 -0.53 47 47
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.036 0.14 -9999 0 -0.4 38 38
MEF2A -0.036 0.14 -9999 0 -0.4 38 38
EIF4EBP1 -0.049 0.16 -9999 0 -0.43 44 44
KRT19 -0.11 0.23 -9999 0 -0.57 51 51
ELK4 -0.036 0.14 -9999 0 -0.4 38 38
ATF6 -0.036 0.14 -9999 0 -0.4 38 38
ATF1 -0.049 0.16 -9999 0 -0.44 38 38
p38alpha-beta/MAPKAPK2 -0.034 0.14 -9999 0 -0.5 16 16
p38alpha-beta/MAPKAPK3 -0.034 0.14 -9999 0 -0.5 16 16
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0 0 -9999 0 -10000 0 0
forebrain development -0.33 0.28 -9999 0 -0.56 201 201
GNAO1 -0.017 0.14 -9999 0 -0.86 10 10
SMO/beta Arrestin2 0.012 0.012 -9999 0 -10000 0 0
SMO 0.007 0.007 -9999 0 -10000 0 0
ARRB2 0.007 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.048 0.043 -9999 0 -10000 0 0
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.01 0.006 -9999 0 -10000 0 0
SIN3/HDAC complex 0.008 0.033 -9999 0 -0.52 1 1
GNAI1 0.007 0.045 -9999 0 -0.86 1 1
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.25 0.19 -9999 0 -0.52 105 105
SAP30 0.012 0.045 -9999 0 -0.86 1 1
mol:GDP 0.007 0.007 -9999 0 -10000 0 0
MIM/GLI2A -0.009 0.044 -9999 0 -0.29 1 1
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.01 0.005 -9999 0 -10000 0 0
GLI2 0.032 0.062 -9999 0 -10000 0 0
GLI3 0.042 0.045 -9999 0 -0.31 6 6
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.013 0 -9999 0 -10000 0 0
Gi family/GTP 0.009 0.065 -9999 0 -0.34 11 11
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.03 0.044 -9999 0 -10000 0 0
GLI2/Su(fu) 0.021 0.058 -9999 0 -10000 0 0
FOXA2 -0.69 0.67 -9999 0 -1.4 189 189
neural tube patterning -0.33 0.28 -9999 0 -0.56 201 201
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.017 0.018 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.009 0.044 -9999 0 -0.29 1 1
embryonic limb morphogenesis -0.33 0.28 -9999 0 -0.56 201 201
SUFU 0.016 0.016 -9999 0 -10000 0 0
LGALS3 -0.1 0.15 -9999 0 -0.3 139 139
catabolic process 0.063 0.06 -9999 0 -0.4 1 1
GLI3A/CBP -0.2 0.2 -9999 0 -0.39 201 201
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.34 0.29 -9999 0 -0.57 201 201
RAB23 0.006 0.077 -9999 0 -0.86 3 3
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.034 0.073 -9999 0 -10000 0 0
GNAZ 0.01 0.005 -9999 0 -10000 0 0
RBBP4 0.014 0.001 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.037 0.058 -9999 0 -10000 0 0
STK36 0.008 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.015 0.055 -9999 0 -0.28 4 4
PTCH1 -0.29 0.26 -9999 0 -0.62 105 105
MIM/GLI1 -0.47 0.39 -9999 0 -0.77 196 196
CREBBP -0.2 0.2 -9999 0 -0.39 201 201
Su(fu)/SIN3/HDAC complex 0.057 0.017 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.1 0.22 -10000 0 -0.59 66 66
cell-cell adhesion 0.14 0.19 0.56 8 -10000 0 8
Ephrin B/EPHB2/RasGAP -0.013 0.068 -10000 0 -0.49 7 7
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.094 0.076 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.2 0.28 -10000 0 -0.58 127 127
HRAS/GDP -0.13 0.18 -10000 0 -0.5 10 10
Ephrin B/EPHB1/GRB7 -0.19 0.25 -10000 0 -0.53 130 130
Endophilin/SYNJ1 0.025 0.072 -10000 0 -0.46 7 7
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.17 0.24 -10000 0 -0.5 130 130
endothelial cell migration -0.001 0.025 -10000 0 -0.49 1 1
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.033 0.11 -10000 0 -0.3 56 56
PAK1 0.033 0.073 -10000 0 -0.46 7 7
HRAS 0.012 0.016 -10000 0 -0.3 1 1
RRAS 0.025 0.073 -10000 0 -0.47 7 7
DNM1 -0.029 0.18 -10000 0 -0.83 19 19
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.14 0.24 -10000 0 -0.48 130 130
lamellipodium assembly -0.14 0.19 -10000 0 -0.56 8 8
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.091 0.18 -10000 0 -0.34 127 127
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.006 0.077 -10000 0 -0.86 3 3
EPHB3 -0.18 0.15 -10000 0 -10000 0 0
EPHB1 -0.28 0.41 -10000 0 -0.86 127 127
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.06 0.18 -10000 0 -0.47 8 8
Ephrin B/EPHB2 -0.014 0.07 -10000 0 -0.5 7 7
Ephrin B/EPHB3 -0.079 0.08 -10000 0 -0.6 4 4
JNK cascade -0.14 0.25 -10000 0 -0.48 129 129
Ephrin B/EPHB1 -0.18 0.24 -10000 0 -0.51 130 130
RAP1/GDP -0.045 0.16 -10000 0 -0.47 3 3
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.009 0.11 -10000 0 -0.42 19 19
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.18 0.26 -10000 0 -0.54 129 129
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.2 -10000 0 -0.53 13 13
Rap1/GTP -0.14 0.19 -10000 0 -0.57 8 8
axon guidance -0.1 0.22 -10000 0 -0.59 66 66
MAPK3 -0.066 0.16 -10000 0 -0.55 1 1
MAPK1 -0.066 0.16 -10000 0 -0.55 1 1
Rac1/GDP -0.036 0.17 -10000 0 -0.45 6 6
actin cytoskeleton reorganization -0.1 0.14 -10000 0 -0.57 2 2
CDC42/GDP -0.036 0.17 -10000 0 -0.42 8 8
PI3K -0.001 0.026 -10000 0 -0.5 1 1
EFNA5 -0.14 0.33 -10000 0 -0.84 66 66
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.028 0.054 -10000 0 -0.34 7 7
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.14 0.19 -10000 0 -0.54 9 9
PTK2 0.037 0.052 -10000 0 -10000 0 0
MAP4K4 -0.14 0.25 -10000 0 -0.49 129 129
SRC 0.012 0.016 -10000 0 -10000 0 0
KALRN 0.013 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.057 0.18 -10000 0 -0.56 2 2
MAP2K1 -0.077 0.17 -10000 0 -0.4 8 8
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.18 0.25 -10000 0 -0.53 129 129
cell migration -0.072 0.19 -10000 0 -0.43 8 8
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.025 0.073 -10000 0 -0.47 7 7
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.035 0.19 -10000 0 -0.47 56 56
HRAS/GTP -0.15 0.21 -10000 0 -0.6 9 9
Ephrin B1/EPHB1-2 -0.18 0.26 -10000 0 -0.54 129 129
cell adhesion mediated by integrin 0.012 0.07 0.53 4 -10000 0 4
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.16 0.22 -10000 0 -0.46 132 132
RAC1-CDC42/GTP -0.19 0.21 -10000 0 -0.51 96 96
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.045 0.16 -10000 0 -0.47 3 3
ruffle organization -0.1 0.22 -10000 0 -0.57 8 8
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.009 0.13 -10000 0 -0.49 23 23
Ephrin B/EPHB2/KALRN -0.013 0.068 -10000 0 -0.49 7 7
ROCK1 -0.068 0.077 -10000 0 -10000 0 0
RAS family/GDP -0.08 0.11 -10000 0 -0.54 2 2
Rac1/GTP -0.15 0.2 -10000 0 -0.6 8 8
Ephrin B/EPHB1/Src/Paxillin -0.096 0.18 -10000 0 -0.35 130 130
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.019 0.14 -10000 0 -0.45 15 15
TBX21 -0.12 0.44 -10000 0 -1.1 48 48
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.015 0.02 -10000 0 -10000 0 0
IL12RB1 -0.022 0.12 -10000 0 -0.48 11 11
GADD45B -0.1 0.39 -10000 0 -0.99 46 46
IL12RB2 -0.013 0.15 -10000 0 -0.74 14 14
GADD45G -0.075 0.34 -10000 0 -0.89 37 37
natural killer cell activation 0.002 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.032 0.15 -10000 0 -0.38 44 44
IL2RA -0.04 0.18 -10000 0 -0.86 16 16
IFNG -0.11 0.28 -10000 0 -0.73 60 60
STAT3 (dimer) -0.072 0.32 -10000 0 -0.78 45 45
HLA-DRB5 -0.052 0.14 -10000 0 -0.86 2 2
FASLG -0.14 0.47 -10000 0 -1.2 52 52
NF kappa B2 p52/RelB -0.17 0.32 -10000 0 -0.93 46 46
CD4 0 0.055 -10000 0 -0.3 12 12
SOCS1 0.01 0.032 -10000 0 -0.3 4 4
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.1 0.28 -10000 0 -0.73 56 56
CD3E -0.068 0.24 -10000 0 -0.74 38 38
CD3G -0.15 0.33 -10000 0 -0.82 71 71
IL12Rbeta2/JAK2 0.002 0.12 -10000 0 -0.66 11 11
CCL3 -0.11 0.43 -10000 0 -1.2 35 35
CCL4 -0.15 0.52 -10000 0 -1.4 47 47
HLA-A 0.01 0.024 -10000 0 -0.32 1 1
IL18/IL18R -0.04 0.21 -10000 0 -0.6 37 37
NOS2 -0.09 0.35 -10000 0 -0.87 42 42
IL12/IL12R/TYK2/JAK2/SPHK2 -0.018 0.14 -10000 0 -0.45 15 15
IL1R1 -0.086 0.37 -10000 0 -0.98 39 39
IL4 0.002 0.022 -10000 0 -10000 0 0
JAK2 0.015 0.02 -10000 0 -10000 0 0
EntrezGene:6957 -0.007 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.24 0.54 -10000 0 -1.1 79 79
RAB7A -0.044 0.29 -10000 0 -0.7 37 37
lysosomal transport -0.039 0.28 -10000 0 -0.65 39 39
FOS -0.42 0.66 -10000 0 -1.3 123 123
STAT4 (dimer) -0.081 0.35 -10000 0 -0.83 46 46
STAT5A (dimer) -0.22 0.36 -10000 0 -0.89 67 67
GZMA -0.1 0.41 -10000 0 -1.1 37 37
GZMB -0.1 0.39 -10000 0 -1 41 41
HLX 0.006 0.045 -10000 0 -10000 0 0
LCK -0.11 0.42 -10000 0 -1.1 46 46
TCR/CD3/MHC II/CD4 -0.19 0.34 -10000 0 -0.74 74 74
IL2/IL2R -0.08 0.23 -10000 0 -0.73 33 33
MAPK14 -0.073 0.35 -10000 0 -0.8 52 52
CCR5 -0.092 0.38 -10000 0 -1 37 37
IL1B -0.05 0.23 -10000 0 -0.78 32 32
STAT6 -0.004 0.11 -10000 0 -0.25 12 12
STAT4 -0.034 0.16 -10000 0 -0.44 39 39
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.005 0.05 -10000 0 -0.3 10 10
NFKB1 0.013 0 -10000 0 -10000 0 0
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B 0.001 0.08 -10000 0 -0.44 9 9
CD8A -0.048 0.22 -10000 0 -0.86 26 26
CD8B -0.1 0.28 -10000 0 -0.73 57 57
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.019 0.14 0.45 15 -10000 0 15
IL2RB -0.018 0.14 -10000 0 -0.54 21 21
proteasomal ubiquitin-dependent protein catabolic process -0.069 0.32 -10000 0 -0.75 46 46
IL2RG -0.052 0.2 -10000 0 -0.51 47 47
IL12 -0.053 0.21 -10000 0 -0.66 39 39
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.033 0.18 -10000 0 -0.66 24 24
IL2 0.004 0.006 -10000 0 -10000 0 0
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.071 0.26 -10000 0 -0.82 39 39
IL12/IL12R/TYK2/JAK2 -0.12 0.47 -10000 0 -1.1 48 48
MAP2K3 -0.075 0.35 -10000 0 -0.79 51 51
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.081 0.36 -10000 0 -0.82 52 52
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.033 0.12 -10000 0 -0.34 47 47
IL18RAP -0.037 0.2 -10000 0 -0.86 22 22
IL12Rbeta1/TYK2 -0.006 0.093 -10000 0 -0.67 3 3
EOMES -0.14 0.41 -10000 0 -1.5 30 30
STAT1 (dimer) -0.13 0.36 -10000 0 -0.78 67 67
T cell proliferation -0.054 0.27 -10000 0 -0.61 43 43
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.028 0.14 -10000 0 -0.4 39 39
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.24 -10000 0 -0.67 51 51
ATF2 -0.068 0.33 -10000 0 -0.75 50 50
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.043 0.12 -9999 0 -0.51 14 14
alphaM/beta2 Integrin/GPIbA -0.053 0.14 -9999 0 -0.55 20 20
alphaM/beta2 Integrin/proMMP-9 -0.096 0.2 -9999 0 -0.6 42 42
PLAUR -0.086 0.14 -9999 0 -0.3 121 121
HMGB1 0.001 0.024 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.036 0.1 -9999 0 -0.68 4 4
AGER -0.078 0.25 -9999 0 -0.88 33 33
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.008 0.077 -9999 0 -0.3 25 25
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.13 0.21 -9999 0 -0.66 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.086 0.24 -9999 0 -0.54 68 68
CYR61 -0.26 0.4 -9999 0 -0.86 119 119
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.073 0.094 -9999 0 -0.46 6 6
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.006 0.12 -9999 0 -0.65 11 11
MYH2 -0.1 0.12 -9999 0 -0.41 32 32
MST1R -0.005 0.11 -9999 0 -0.86 6 6
leukocyte activation during inflammatory response -0.04 0.093 -9999 0 -0.59 4 4
APOB -0.007 0.069 -9999 0 -0.3 20 20
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.001 0.093 -9999 0 -0.62 7 7
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.015 0.14 -9999 0 -0.59 17 17
alphaM/beta2 Integrin/CTGF -0.12 0.23 -9999 0 -0.62 61 61
alphaM/beta2 Integrin -0.097 0.11 -9999 0 -0.37 34 34
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.094 0.15 -9999 0 -0.3 131 131
phagocytosis triggered by activation of immune response cell surface activating receptor -0.096 0.11 -9999 0 -0.36 34 34
cell adhesion -0.053 0.14 -9999 0 -0.55 20 20
NFKB1 -0.15 0.31 -9999 0 -0.86 39 39
THY1 0.01 0.028 -9999 0 -0.3 3 3
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.012 0.046 -9999 0 -0.32 2 2
alphaM/beta2 Integrin/LRP/tPA -0.036 0.1 -9999 0 -0.56 8 8
IL6 -0.27 0.48 -9999 0 -1.1 86 86
ITGB2 -0.024 0.093 -9999 0 -0.32 28 28
elevation of cytosolic calcium ion concentration -0.13 0.16 -9999 0 -0.52 31 31
alphaM/beta2 Integrin/JAM2/JAM3 -0.035 0.11 -9999 0 -0.68 6 6
JAM2 0.003 0.09 -9999 0 -0.86 4 4
alphaM/beta2 Integrin/ICAM1 -0.076 0.14 -9999 0 -0.54 16 16
alphaM/beta2 Integrin/uPA/Plg -0.092 0.12 -9999 0 -0.5 17 17
RhoA/GTP -0.11 0.13 -9999 0 -0.43 34 34
positive regulation of phagocytosis -0.072 0.12 -9999 0 -0.48 11 11
Ron/MSP -0.015 0.092 -9999 0 -0.66 7 7
alphaM/beta2 Integrin/uPAR/uPA -0.13 0.16 -9999 0 -0.52 31 31
alphaM/beta2 Integrin/uPAR -0.084 0.13 -9999 0 -0.53 18 18
PLAU -0.12 0.15 -9999 0 -0.3 167 167
PLAT 0.003 0.075 -9999 0 -0.42 9 9
actin filament polymerization -0.1 0.12 -9999 0 -0.4 32 32
MST1 0.01 0.047 -9999 0 -0.58 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.04 0.094 -9999 0 -0.6 4 4
TNF -0.2 0.4 -9999 0 -1 59 59
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.1 0.13 -9999 0 -0.53 18 18
fibrinolysis -0.091 0.12 -9999 0 -0.49 17 17
HCK -0.007 0.076 -9999 0 -0.3 24 24
dendritic cell antigen processing and presentation -0.096 0.11 -9999 0 -0.36 34 34
VTN -0.085 0.27 -9999 0 -0.8 46 46
alphaM/beta2 Integrin/CYR61 -0.22 0.29 -9999 0 -0.63 120 120
LPA -0.003 0.046 -9999 0 -0.3 9 9
LRP1 0.011 0.045 -9999 0 -0.86 1 1
cell migration -0.09 0.2 -9999 0 -0.6 40 40
FN1 -0.21 0.14 -9999 0 -0.3 273 273
alphaM/beta2 Integrin/Thy1 -0.037 0.1 -9999 0 -0.48 10 10
MPO 0.001 0.091 -9999 0 -0.67 6 6
KNG1 -0.01 0.068 -9999 0 -10000 0 0
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.096 0.12 -9999 0 -0.45 19 19
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0.022 -9999 0 -10000 0 0
CTGF -0.12 0.31 -9999 0 -0.86 57 57
alphaM/beta2 Integrin/Hck -0.046 0.12 -9999 0 -0.52 16 16
ITGAM -0.024 0.1 -9999 0 -0.35 26 26
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.05 0.13 -9999 0 -0.53 20 20
HP -0.071 0.16 -9999 0 -0.33 93 93
leukocyte adhesion -0.1 0.17 -9999 0 -0.63 22 22
SELP -0.006 0.12 -9999 0 -0.65 11 11
Syndecan-4-mediated 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
PTK2 -0.075 0.058 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.12 0.17 -9999 0 -0.66 29 29
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.6 55 55
Syndecan-4/ADAM12 -0.16 0.18 -9999 0 -0.66 29 29
CCL5 -0.043 0.21 -9999 0 -0.72 29 29
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG 0.002 0.025 -9999 0 -0.3 1 1
ADAM12 -0.067 0.14 -9999 0 -0.3 97 97
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.063 0.045 -9999 0 -0.23 2 2
Syndecan-4/Laminin alpha1 -0.16 0.21 -9999 0 -0.7 36 36
Syndecan-4/CXCL12/CXCR4 -0.17 0.22 -9999 0 -0.64 54 54
Syndecan-4/Laminin alpha3 -0.14 0.19 -9999 0 -0.66 35 35
MDK -0.079 0.14 -9999 0 -0.3 112 112
Syndecan-4/FZD7 -0.13 0.18 -9999 0 -0.65 31 31
Syndecan-4/Midkine -0.16 0.18 -9999 0 -0.66 29 29
FZD7 0.004 0.089 -9999 0 -0.86 4 4
Syndecan-4/FGFR1/FGF -0.12 0.16 -9999 0 -0.61 30 30
THBS1 -0.011 0.083 -9999 0 -0.3 29 29
integrin-mediated signaling pathway -0.17 0.18 -9999 0 -0.67 29 29
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.6 55 55
Syndecan-4/TACI -0.24 0.26 -9999 0 -0.63 100 100
CXCR4 0.01 0.032 -9999 0 -0.3 4 4
cell adhesion -0.073 0.1 -9999 0 -0.46 22 22
Syndecan-4/Dynamin -0.12 0.17 -9999 0 -0.66 29 29
Syndecan-4/TSP1 -0.13 0.18 -9999 0 -0.66 29 29
Syndecan-4/GIPC -0.12 0.17 -9999 0 -0.66 29 29
Syndecan-4/RANTES -0.15 0.22 -9999 0 -0.78 34 34
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.052 0.23 -9999 0 -0.84 29 29
LAMA3 -0.023 0.16 -9999 0 -0.6 22 22
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.001 0.2 -9999 0 -0.78 22 22
Syndecan-4/alpha-Actinin -0.12 0.17 -9999 0 -0.66 29 29
TFPI -0.04 0.21 -9999 0 -0.86 23 23
F2 -0.001 0.033 -9999 0 -0.31 4 4
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.21 -9999 0 -0.68 39 39
ACTN1 0.012 0.016 -9999 0 -10000 0 0
TNC -0.12 0.16 -9999 0 -0.86 3 3
Syndecan-4/CXCL12 -0.18 0.23 -9999 0 -0.67 55 55
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.086 0.28 -9999 0 -0.86 43 43
TNFRSF13B -0.19 0.36 -9999 0 -0.82 91 91
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.011 0.045 -9999 0 -0.86 1 1
Syndecan-4/PI-4-5-P2 -0.13 0.17 -9999 0 -0.67 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.21 0.14 -9999 0 -0.3 245 245
cell migration -0.021 0.017 -9999 0 -10000 0 0
PRKCD 0.008 0.015 -9999 0 -10000 0 0
vasculogenesis -0.13 0.17 -9999 0 -0.63 29 29
SDC4 -0.14 0.18 -9999 0 -0.71 29 29
Syndecan-4/Tenascin C -0.18 0.19 -9999 0 -0.71 29 29
Syndecan-4/PI-4-5-P2/PKC alpha -0.05 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.12 0.17 -9999 0 -0.66 29 29
MMP9 -0.087 0.24 -9999 0 -0.54 67 67
Rac1/GTP -0.075 0.11 -9999 0 -0.47 22 22
cytoskeleton organization -0.12 0.17 -9999 0 -0.63 29 29
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.15 0.21 -9999 0 -0.66 45 45
IL6-mediated signaling events

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
BCL2L1 -0.05 0.2 -9999 0 -0.62 20 20
CRP -0.055 0.2 -9999 0 -0.69 12 12
cell cycle arrest -0.069 0.23 -9999 0 -0.73 21 21
TIMP1 -0.14 0.2 -9999 0 -0.59 25 25
IL6ST -0.078 0.26 -9999 0 -0.86 39 39
Rac1/GDP -0.082 0.24 -9999 0 -0.59 44 44
AP1 -0.21 0.34 -9999 0 -0.7 111 111
GAB2 0.013 0.001 -9999 0 -10000 0 0
TNFSF11 -0.092 0.21 -9999 0 -0.65 19 19
HSP90B1 0.023 0.041 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.098 0.3 -9999 0 -0.82 43 43
AKT1 0.055 0.022 -9999 0 -10000 0 0
FOXO1 0.061 0.021 -9999 0 -10000 0 0
MAP2K6 -0.099 0.28 -9999 0 -0.72 46 46
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.072 0.22 -9999 0 -0.7 23 23
MITF -0.085 0.25 -9999 0 -0.62 43 43
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.013 0 -9999 0 -10000 0 0
A2M 0.024 0.006 -9999 0 -10000 0 0
CEBPB 0.021 0.002 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.025 0.078 -9999 0 -10000 0 0
STAT3 -0.081 0.24 -9999 0 -0.79 21 21
STAT1 -0.011 0.021 -9999 0 -10000 0 0
CEBPD -0.051 0.2 -9999 0 -0.63 18 18
PIK3CA 0.012 0.045 -9999 0 -0.86 1 1
PI3K -0.002 0.034 -9999 0 -0.66 1 1
JUN -0.19 0.37 -9999 0 -0.86 88 88
PIAS3/MITF -0.074 0.24 -9999 0 -0.59 41 41
MAPK11 -0.098 0.3 -9999 0 -0.82 43 43
STAT3 (dimer)/FOXO1 -0.001 0.19 -9999 0 -0.6 11 11
GRB2/SOS1/GAB family -0.11 0.19 -9999 0 -0.7 19 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.25 -9999 0 -0.49 79 79
GRB2 0.013 0 -9999 0 -10000 0 0
JAK2 0.013 0 -9999 0 -10000 0 0
LBP -0.06 0.19 -9999 0 -0.6 11 11
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.013 0.005 -9999 0 -10000 0 0
MYC -0.062 0.25 -9999 0 -0.85 19 19
FGG -0.058 0.2 -9999 0 -0.63 20 20
macrophage differentiation -0.069 0.23 -9999 0 -0.73 21 21
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.18 0.28 -9999 0 -0.57 116 116
JUNB -0.058 0.23 -9999 0 -0.78 18 18
FOS -0.22 0.39 -9999 0 -0.86 103 103
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.095 0.27 -9999 0 -0.56 64 64
STAT1/PIAS1 -0.076 0.23 -9999 0 -0.53 46 46
GRB2/SOS1/GAB family/SHP2/PI3K 0.036 0.028 -9999 0 -0.32 1 1
STAT3 (dimer) -0.078 0.23 -9999 0 -0.76 21 21
PRKCD -0.06 0.22 -9999 0 -0.68 20 20
IL6R -0.01 0.14 -9999 0 -0.86 10 10
SOCS3 -0.12 0.4 -9999 0 -1.1 42 42
gp130 (dimer)/JAK1/JAK1/LMO4 -0.043 0.18 -9999 0 -0.57 39 39
Rac1/GTP -0.1 0.23 -9999 0 -0.59 43 43
HCK -0.007 0.076 -9999 0 -0.3 24 24
MAPKKK cascade 0.012 0.06 -9999 0 -10000 0 0
bone resorption -0.088 0.21 -9999 0 -0.61 20 20
IRF1 -0.05 0.2 -9999 0 -0.64 17 17
mol:GDP -0.093 0.25 -9999 0 -0.62 46 46
SOS1 0.013 0.001 -9999 0 -10000 0 0
VAV1 -0.096 0.26 -9999 0 -0.63 46 46
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.3 -9999 0 -0.78 45 45
PTPN11 -0.008 0.018 -9999 0 -10000 0 0
IL6/IL6RA -0.17 0.3 -9999 0 -0.68 91 91
gp130 (dimer)/TYK2/TYK2/LMO4 -0.048 0.18 -9999 0 -0.57 39 39
gp130 (dimer)/JAK2/JAK2/LMO4 -0.048 0.18 -9999 0 -0.57 39 39
IL6 -0.2 0.36 -9999 0 -0.86 84 84
PIAS3 0.013 0 -9999 0 -10000 0 0
PTPRE -0.098 0.15 -9999 0 -0.31 55 55
PIAS1 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.094 0.25 -9999 0 -0.46 96 96
LMO4 0.011 0.01 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.094 0.22 -9999 0 -0.77 21 21
MCL1 0.06 0.02 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.098 0.22 -9999 0 -0.41 112 112
MAP3K8 0.001 0.089 -9999 0 -0.86 4 4
FOS -0.06 0.16 -9999 0 -0.5 22 22
PRKCA -0.04 0.2 -9999 0 -0.86 22 22
PTPN7 -0.042 0.16 -9999 0 -0.41 48 48
HRAS 0.011 0.016 -9999 0 -0.3 1 1
PRKCB -0.031 0.11 -9999 0 -0.31 48 48
NRAS 0.012 0.002 -9999 0 -10000 0 0
RAS family/GTP 0 0.007 -9999 0 -10000 0 0
MAPK3 -0.031 0.12 -9999 0 -0.58 9 9
MAP2K1 -0.03 0.15 -9999 0 -0.56 23 23
ELK1 0.007 0.011 -9999 0 -10000 0 0
BRAF -0.049 0.13 -9999 0 -0.56 23 23
mol:GTP -0.002 0.003 -9999 0 -0.006 103 103
MAPK1 -0.031 0.12 -9999 0 -0.44 16 16
RAF1 -0.049 0.13 -9999 0 -0.56 23 23
KRAS 0.012 0.002 -9999 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 -0.036 0.11 -10000 0 -0.3 56 56
GNB1/GNG2 -0.046 0.067 -10000 0 -0.2 39 39
AKT1 -0.017 0.1 -10000 0 -0.21 32 32
EGF -0.11 0.3 -10000 0 -0.86 51 51
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.006 0.068 -10000 0 -0.59 1 1
mol:Ca2+ -0.049 0.14 -10000 0 -0.31 57 57
LYN 0.007 0.067 -10000 0 -0.59 1 1
RhoA/GTP -0.032 0.045 -10000 0 -0.13 17 17
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.05 0.16 -10000 0 -0.35 55 55
GNG2 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.024 0.11 -10000 0 -0.54 4 4
G beta5/gamma2 -0.062 0.092 -10000 0 -0.27 39 39
PRKCH -0.057 0.16 -10000 0 -0.37 54 54
DNM1 -0.029 0.18 -10000 0 -0.83 19 19
TXA2/TP beta/beta Arrestin3 -0.017 0.067 -10000 0 -0.31 18 18
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.022 0.17 -10000 0 -0.86 15 15
G12 family/GTP -0.081 0.11 -10000 0 -0.31 55 55
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.013 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.1 0.37 10 -10000 0 10
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.21 0.38 -10000 0 -0.86 98 98
mol:IP3 -0.066 0.18 -10000 0 -0.39 57 57
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.095 0.23 -10000 0 -0.54 57 57
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.12 0.2 -10000 0 -0.41 113 113
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0 0.07 -10000 0 -0.59 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.004 0.089 -10000 0 -0.86 4 4
PRKCB1 -0.066 0.17 -10000 0 -0.39 57 57
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.092 0.23 -10000 0 -0.54 58 58
LCK -0.002 0.086 -10000 0 -0.53 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.017 0.079 -10000 0 -0.84 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.025 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.077 -10000 0 -0.84 1 1
MAPK14 -0.024 0.11 -10000 0 -0.23 54 54
TGM2/GTP -0.079 0.2 -10000 0 -0.44 59 59
MAPK11 -0.024 0.11 -10000 0 -0.23 54 54
ARHGEF1 -0.019 0.088 -10000 0 -0.18 32 32
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.063 0.18 -10000 0 -0.4 58 58
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.059 0.15 -10000 0 -0.3 62 62
cAMP biosynthetic process -0.064 0.16 -10000 0 -0.37 55 55
Gq family/GTP/EBP50 -0.045 0.12 -10000 0 -0.33 15 15
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.007 0.067 -10000 0 -0.59 1 1
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.021 0.1 -10000 0 -0.39 3 3
VCAM1 -0.043 0.14 -10000 0 -0.3 58 58
TP beta/Gq family/GDP/G beta5/gamma2 -0.024 0.11 -10000 0 -0.54 4 4
platelet activation -0.032 0.15 -10000 0 -0.31 55 55
PGI2/IP -0.007 0.069 -10000 0 -0.67 4 4
PRKACA -0.003 0.1 -10000 0 -0.43 18 18
Gq family/GDP/G beta5/gamma2 -0.026 0.11 -10000 0 -0.5 4 4
TXA2/TP beta/beta Arrestin2 -0.034 0.14 -10000 0 -0.68 18 18
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.009 0.097 -10000 0 -0.4 18 18
mol:DAG -0.075 0.19 -10000 0 -0.44 57 57
EGFR 0.001 0.099 -10000 0 -0.86 5 5
TXA2/TP alpha -0.089 0.22 -10000 0 -0.5 55 55
Gq family/GTP -0.078 0.13 -10000 0 -0.31 94 94
YES1 0.007 0.067 -10000 0 -0.59 1 1
GNAI2/GTP -0.015 0.07 -10000 0 -0.72 1 1
PGD2/DP -0.027 0.13 -10000 0 -0.67 15 15
SLC9A3R1 0.011 0.023 -10000 0 -0.3 2 2
FYN 0.007 0.067 -10000 0 -0.59 1 1
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.017 0.099 -10000 0 -0.31 35 35
PGK/cGMP -0.15 0.26 -10000 0 -0.58 98 98
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.029 0.086 -10000 0 -0.56 4 4
NOS3 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.073 0.18 -10000 0 -0.39 70 70
PRKCB -0.067 0.16 -10000 0 -0.37 60 60
PRKCE -0.06 0.17 -10000 0 -0.38 56 56
PRKCD -0.06 0.17 -10000 0 -0.39 56 56
PRKCG -0.065 0.17 -10000 0 -0.4 56 56
muscle contraction -0.081 0.21 -10000 0 -0.5 58 58
PRKCZ -0.05 0.16 -10000 0 -0.35 55 55
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.017 0.079 -10000 0 -0.86 1 1
PRKCQ -0.06 0.17 -10000 0 -0.37 60 60
MAPKKK cascade -0.082 0.2 -10000 0 -0.47 58 58
SELE -0.063 0.18 -10000 0 -0.43 56 56
TP beta/GNAI2/GDP/G beta/gamma -0.016 0.076 -10000 0 -0.83 1 1
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.2 0.37 -10000 0 -0.86 91 91
chemotaxis -0.1 0.26 -10000 0 -0.62 58 58
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 0.006 0.077 -10000 0 -0.86 3 3
Rac1/GTP 0 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.032 0.16 -9999 0 -0.51 30 30
NF kappa B1 p50/RelA/I kappa B alpha -0.052 0.12 -9999 0 -0.62 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.064 0.15 -9999 0 -0.65 20 20
AP1 -0.27 0.37 -9999 0 -0.88 90 90
ILK -0.035 0.16 -9999 0 -0.54 30 30
bone resorption -0.054 0.14 -9999 0 -0.67 7 7
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.053 0.14 -9999 0 -0.49 30 30
ITGAV 0.011 0.045 -9999 0 -0.85 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.014 0.095 -9999 0 -0.66 8 8
alphaV/beta3 Integrin/Osteopontin -0.07 0.17 -9999 0 -0.6 30 30
MAP3K1 -0.032 0.17 -9999 0 -0.55 30 30
JUN -0.19 0.37 -9999 0 -0.86 88 88
MAPK3 -0.031 0.16 -9999 0 -0.51 30 30
MAPK1 -0.031 0.16 -9999 0 -0.51 30 30
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.023 0.16 -9999 0 -0.52 31 31
ITGB3 -0.014 0.15 -9999 0 -0.85 12 12
NFKBIA -0.024 0.16 -9999 0 -0.49 30 30
FOS -0.22 0.39 -9999 0 -0.86 103 103
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.097 0.18 -9999 0 -0.72 5 5
NF kappa B1 p50/RelA -0.057 0.12 -9999 0 -0.6 6 6
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.022 0.12 -9999 0 -0.7 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.032 0.17 -9999 0 -0.55 30 30
VAV3 -0.026 0.17 -9999 0 -0.52 33 33
MAP3K14 -0.039 0.17 -9999 0 -0.55 30 30
ROCK2 -0.005 0.12 -9999 0 -0.86 8 8
SPP1 -0.078 0.21 -9999 0 -0.43 78 78
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.054 0.14 -9999 0 -0.47 33 33
MMP2 -0.18 0.3 -9999 0 -0.68 80 80
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0.016 -9999 0 -0.3 1 1
EGFR 0.001 0.099 -9999 0 -0.86 5 5
EGF/EGFR -0.081 0.18 -9999 0 -0.48 62 62
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.074 0.17 -9999 0 -0.49 56 56
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.007 0.055 -9999 0 -0.86 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.86 51 51
EGF/EGFR dimer/SHC -0.087 0.2 -9999 0 -0.57 56 56
mol:GDP -0.073 0.17 -9999 0 -0.48 56 56
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.001 0.1 -9999 0 -0.76 6 6
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.067 0.16 -9999 0 -0.45 56 56
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.069 0.16 -9999 0 -0.46 56 56
FRAP1 -0.037 0.18 -9999 0 -0.47 56 56
EGF/EGFR dimer -0.1 0.24 -9999 0 -0.66 56 56
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.013 0.085 -9999 0 -0.66 6 6
FAS signaling pathway (CD95)

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
SPTAN1 0.021 0.072 0.3 22 -10000 0 22
RFC1 0.021 0.072 0.3 22 -10000 0 22
PRKDC 0.021 0.072 0.3 22 -10000 0 22
RIPK1 0.014 0.005 -10000 0 -10000 0 0
CASP7 -0.014 0.047 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.031 0.1 0.26 1 -0.39 25 26
MAP2K4 -0.032 0.16 -10000 0 -0.54 14 14
mol:ceramide -0.028 0.15 -10000 0 -0.51 25 25
GSN 0.021 0.072 0.3 22 -10000 0 22
FASLG/FAS/FADD/FAF1/Caspase 8 -0.024 0.13 -10000 0 -0.49 25 25
FAS 0.01 0.006 -10000 0 -10000 0 0
BID -0.033 0.08 0.32 3 -10000 0 3
MAP3K1 -0.002 0.099 -10000 0 -0.29 14 14
MAP3K7 0.01 0.006 -10000 0 -10000 0 0
RB1 0.021 0.072 0.3 22 -10000 0 22
CFLAR 0.014 0.005 -10000 0 -10000 0 0
HGF/MET -0.14 0.21 -10000 0 -0.63 52 52
ARHGDIB 0.017 0.075 0.3 21 -10000 0 21
FADD 0.01 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.021 0.072 -10000 0 -0.3 22 22
NFKB1 -0.056 0.091 -10000 0 -0.29 14 14
MAPK8 -0.064 0.22 -10000 0 -0.46 80 80
DFFA 0.021 0.072 0.3 22 -10000 0 22
DNA fragmentation during apoptosis 0.021 0.072 0.3 22 -10000 0 22
FAS/FADD/MET -0.061 0.073 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.005 0.097 -10000 0 -0.39 18 18
FAF1 0.01 0.007 -10000 0 -10000 0 0
PARP1 0.021 0.072 0.3 22 -10000 0 22
DFFB 0.021 0.072 0.3 22 -10000 0 22
CHUK -0.048 0.08 -10000 0 -10000 0 0
FASLG -0.062 0.22 -10000 0 -0.63 43 43
FAS/FADD 0 0.001 -10000 0 -10000 0 0
HGF -0.1 0.3 -10000 0 -0.86 51 51
LMNA 0.019 0.065 0.27 22 -10000 0 22
CASP6 0.021 0.072 0.3 22 -10000 0 22
CASP10 0.01 0.006 -10000 0 -10000 0 0
CASP3 0.025 0.087 0.35 25 -10000 0 25
PTPN13 0.011 0.045 -10000 0 -0.86 1 1
CASP8 0.009 0.049 0.46 3 -10000 0 3
IL6 -0.29 0.59 -10000 0 -1.4 84 84
MET -0.11 0.15 -10000 0 -0.3 154 154
ICAD/CAD 0.02 0.067 0.28 22 -10000 0 22
FASLG/FAS/FADD/FAF1/Caspase 10 -0.029 0.15 -10000 0 -0.52 25 25
activation of caspase activity by cytochrome c -0.033 0.08 0.32 3 -10000 0 3
PAK2 0.021 0.072 0.3 22 -10000 0 22
BCL2 -0.037 0.2 -10000 0 -0.86 22 22
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.042 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.049 0.13 0.41 25 -10000 0 25
IL27/IL27R/JAK1 -0.098 0.18 -10000 0 -0.61 26 26
TBX21 -0.074 0.21 -10000 0 -0.65 26 26
IL12B -0.002 0.075 -10000 0 -0.42 9 9
IL12A -0.057 0.2 -10000 0 -0.67 36 36
IL6ST -0.078 0.27 -10000 0 -0.86 39 39
IL27RA/JAK1 0.014 0.025 -10000 0 -10000 0 0
IL27 0.001 0.036 -10000 0 -0.3 5 5
TYK2 0.012 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.074 0.16 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.049 0.13 0.41 25 -10000 0 25
T cell proliferation during immune response 0.049 0.13 0.41 25 -10000 0 25
MAPKKK cascade -0.049 0.13 -10000 0 -0.41 25 25
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.005 0.05 -10000 0 -0.3 10 10
IL12RB1 -0.025 0.12 -10000 0 -0.86 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.07 0.2 -10000 0 -0.63 20 20
IL27/IL27R/JAK2/TYK2 -0.05 0.14 -10000 0 -0.42 25 25
positive regulation of T cell mediated cytotoxicity -0.049 0.13 -10000 0 -0.41 25 25
STAT1 (dimer) -0.091 0.23 0.52 14 -0.81 10 24
JAK2 0.014 0.007 -10000 0 -10000 0 0
JAK1 0.013 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.039 0.13 -10000 0 -0.52 6 6
T cell proliferation -0.16 0.24 -10000 0 -0.54 89 89
IL12/IL12R/TYK2/JAK2 -0.049 0.15 -10000 0 -0.68 8 8
IL17A -0.075 0.16 -10000 0 -10000 0 0
mast cell activation 0.049 0.13 0.41 25 -10000 0 25
IFNG -0.017 0.047 -10000 0 -0.13 48 48
T cell differentiation -0.005 0.008 -10000 0 -0.022 46 46
STAT3 (dimer) -0.039 0.13 -10000 0 -0.52 6 6
STAT5A (dimer) -0.039 0.13 -10000 0 -0.52 6 6
STAT4 (dimer) -0.064 0.15 -10000 0 -0.51 20 20
STAT4 -0.034 0.16 -10000 0 -0.44 39 39
T cell activation -0.011 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.044 0.16 -10000 0 -0.53 27 27
GATA3 -0.058 0.36 -10000 0 -1.5 22 22
IL18 -0.022 0.11 -10000 0 -0.28 44 44
positive regulation of mast cell cytokine production -0.039 0.13 -10000 0 -0.51 6 6
IL27/EBI3 -0.093 0.11 -10000 0 -0.42 6 6
IL27RA 0.006 0.026 -10000 0 -10000 0 0
IL6 -0.2 0.36 -10000 0 -0.86 84 84
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.001 0.013 -10000 0 -10000 0 0
IL1B -0.039 0.17 -10000 0 -0.58 32 32
EBI3 -0.14 0.16 -10000 0 -0.3 182 182
TNF -0.069 0.22 -10000 0 -0.62 48 48
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.077 0.093 -10000 0 -10000 0 0
CRKL -0.029 0.11 -10000 0 -0.33 22 22
mol:PIP3 -0.018 0.038 0.71 1 -10000 0 1
AKT1 0.001 0.038 0.46 1 -0.56 1 2
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 -0.02 0.1 -10000 0 -10000 0 0
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
HGF/MET/SHIP2 -0.14 0.21 -10000 0 -0.64 51 51
MAP3K5 -0.019 0.11 -10000 0 -0.49 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.19 -10000 0 -0.58 51 51
AP1 -0.3 0.45 -10000 0 -0.92 120 120
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.27 0.4 -10000 0 -0.85 120 120
STAT3 (dimer) -0.037 0.13 -10000 0 -0.39 22 22
GAB1/CRKL/SHP2/PI3K -0.038 0.086 -10000 0 -0.4 1 1
INPP5D -0.01 0.081 -10000 0 -0.3 28 28
CBL/CRK -0.02 0.1 -10000 0 -10000 0 0
PTPN11 0.013 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.011 0.045 -10000 0 -0.86 1 1
ELK1 -0.051 0.061 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.037 0.071 -10000 0 -0.25 22 22
PAK1 0.01 0.035 0.43 1 -0.52 1 2
HGF/MET/RANBP10 -0.14 0.21 -10000 0 -0.64 51 51
HRAS -0.055 0.16 -10000 0 -0.44 51 51
DOCK1 -0.021 0.11 -10000 0 -0.45 1 1
GAB1 -0.039 0.12 -10000 0 -0.31 51 51
CRK -0.029 0.11 -10000 0 -0.33 22 22
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.21 -10000 0 -0.62 51 51
JUN -0.19 0.37 -10000 0 -0.86 88 88
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.069 0.1 -10000 0 -0.3 51 51
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis -0.007 0.13 -10000 0 -10000 0 0
GRB2/SHC -0.053 0.085 -10000 0 -0.3 22 22
FOS -0.22 0.39 -10000 0 -0.86 103 103
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.051 0.061 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.14 0.21 -10000 0 -0.64 51 51
cell migration -0.052 0.084 -10000 0 -0.3 22 22
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.077 0.093 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.049 0.14 -10000 0 -0.38 51 51
MET/MUC20 -0.082 0.099 -10000 0 -0.2 154 154
RAP1B -0.011 0.1 -10000 0 -10000 0 0
RAP1A -0.011 0.1 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.14 0.21 -10000 0 -0.64 51 51
RAF1 -0.044 0.15 -10000 0 -0.46 22 22
STAT3 -0.038 0.13 -10000 0 -0.4 22 22
cell proliferation -0.044 0.17 -10000 0 -0.47 51 51
RPS6KB1 -0.015 0.039 -10000 0 -10000 0 0
MAPK3 -0.051 0.055 -10000 0 -10000 0 0
MAPK1 -0.051 0.055 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 0.001 0.11 -10000 0 -0.48 6 6
SRC -0.038 0.13 -10000 0 -0.39 22 22
PI3K -0.054 0.088 -10000 0 -0.48 1 1
MET/Glomulin -0.062 0.09 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.033 0.14 -10000 0 -0.42 22 22
MET -0.11 0.15 -10000 0 -0.3 154 154
MAP4K1 -0.027 0.12 -10000 0 -0.55 4 4
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.033 0.14 -10000 0 -0.42 22 22
BAD 0.01 0.035 0.43 1 -0.52 1 2
MAP2K4 -0.009 0.1 -10000 0 -0.44 5 5
SHP2/GRB2/SOS1/GAB1 -0.054 0.09 -10000 0 -10000 0 0
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS -0.047 0.1 -10000 0 -0.32 22 22
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.1 0.3 -10000 0 -0.86 51 51
RASA1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.056 0.095 -10000 0 -0.33 22 22
PDPK1 -0.008 0.041 0.53 1 -0.6 1 2
HGF/MET/SHIP -0.15 0.21 -10000 0 -0.64 51 51
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.01 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0 0.009 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.016 0.065 -9999 0 -0.58 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.004 0.017 -9999 0 -0.3 1 1
GRK1 -0.071 0.26 -9999 0 -0.86 36 36
CNG Channel -0.028 0.09 -9999 0 -0.56 7 7
mol:Na + -0.026 0.093 -9999 0 -0.48 13 13
mol:ADP -0.07 0.25 -9999 0 -0.85 36 36
RGS9-1/Gbeta5/R9AP -0.1 0.23 -9999 0 -0.59 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.026 0.096 -9999 0 -0.49 13 13
CNGB1 -0.002 0.064 -9999 0 -0.3 17 17
RDH5 -0.18 0.15 -9999 0 -0.3 238 238
SAG 0.003 0.005 -9999 0 -10000 0 0
mol:Ca2+ 0.013 0.099 -9999 0 -0.64 2 2
Na + (4 Units) -0.023 0.086 -9999 0 -0.62 2 2
RGS9 -0.085 0.27 -9999 0 -0.83 44 44
GNB1/GNGT1 -0.003 0.022 -9999 0 -10000 0 0
GNAT1/GDP -0.091 0.2 -9999 0 -0.52 66 66
GUCY2D -0.01 0.12 -9999 0 -0.86 6 6
GNGT1 -0.004 0.034 -9999 0 -0.3 5 5
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.004 0.068 -9999 0 -0.5 3 3
mol:11-cis-retinal -0.18 0.15 -9999 0 -0.3 238 238
mol:cGMP -0.017 0.08 -9999 0 -0.51 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.12 0.094 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 -0.002 0.1 -9999 0 -0.61 9 9
Metarhodopsin II -0.052 0.16 -9999 0 -0.54 36 36
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.018 0.085 -9999 0 -0.54 9 9
RGS9BP -0.047 0.22 -9999 0 -0.86 26 26
Metarhodopsin II/Transducin 0.011 0.012 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.05 -9999 0 -0.55 3 3
PDE6A/B -0.011 0.044 -9999 0 -10000 0 0
mol:Pi -0.1 0.22 -9999 0 -0.59 66 66
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.002 0.017 -9999 0 -10000 0 0
PDE6B 0.013 0 -9999 0 -10000 0 0
PDE6A -0.007 0.072 -9999 0 -10000 0 0
PDE6G -0.015 0.11 -9999 0 -0.36 28 28
RHO 0.006 0.017 -9999 0 -0.3 1 1
PDE6 -0.1 0.2 -9999 0 -0.5 68 68
GUCA1A 0.004 0.028 -9999 0 -0.3 3 3
GC2/GCAP Family -0.005 0.05 -9999 0 -0.55 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.006 0.077 -9999 0 -0.86 3 3
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.02 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.045 0.11 -9999 0 -0.58 3 3
NFATC4 -0.005 0.12 -9999 0 -0.59 2 2
ERBB2IP 0.013 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.013 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.051 0.14 -9999 0 -0.43 45 45
JUN 0.003 0.094 -9999 0 -0.28 6 6
HRAS 0.012 0.016 -9999 0 -0.3 1 1
DOCK7 -0.018 0.14 -9999 0 -0.4 45 45
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.062 0.17 -9999 0 -0.52 45 45
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.024 0.064 -9999 0 -0.29 1 1
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.032 0.16 -9999 0 -0.46 45 45
RAF1 -0.008 0.13 -9999 0 -0.56 3 3
ErbB2/ErbB3/neuregulin 2 -0.076 0.19 -9999 0 -0.55 52 52
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.022 0.081 -9999 0 -0.28 2 2
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.14 0.34 -9999 0 -0.68 92 92
FOS -0.12 0.29 -9999 0 -0.52 120 120
NRAS 0.012 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.051 0.14 -9999 0 -0.43 45 45
MAPK3 -0.09 0.26 -9999 0 -0.51 89 89
MAPK1 -0.09 0.26 -9999 0 -0.51 89 89
JAK2 -0.018 0.14 -9999 0 -0.4 45 45
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.024 0.14 -9999 0 -0.39 45 45
NRG1 -0.075 0.26 -9999 0 -0.84 38 38
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.011 0.13 -9999 0 -0.35 46 46
MAPK9 -0.024 0.064 -9999 0 -0.29 1 1
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.013 0.13 -9999 0 -0.86 9 9
SHC1 0.012 0.003 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.003 -9999 0 -10000 0 0
RNF41 0.027 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.034 0.092 -9999 0 -0.44 1 1
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.061 0.21 -9999 0 -0.39 78 78
myelination 0.005 0.12 -9999 0 -0.53 2 2
PPP3CB -0.016 0.13 -9999 0 -0.37 45 45
KRAS 0.012 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.039 0.11 -9999 0 -0.92 1 1
NRG2 -0.088 0.28 -9999 0 -0.82 46 46
mol:GDP -0.023 0.14 -9999 0 -0.39 45 45
SOS1 0.012 0.001 -9999 0 -10000 0 0
MAP2K2 -0.011 0.14 -9999 0 -0.43 18 18
SRC 0.012 0.016 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.018 0.14 -9999 0 -0.4 45 45
MAP2K1 -0.083 0.24 -9999 0 -0.62 24 24
heart morphogenesis -0.051 0.14 -9999 0 -0.43 45 45
RAS family/GDP -0.039 0.11 -9999 0 -0.68 2 2
GRB2 0.012 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.009 -9999 0 -10000 0 0
CHRNE 0.011 0.032 -9999 0 -0.13 10 10
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.051 0.14 -9999 0 -0.43 45 45
CDC42 0.013 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.002 0.11 -9999 0 -0.86 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.15 0.16 -9999 0 -0.29 218 218
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.01 0.032 -9999 0 -10000 0 0
p38 alpha/TAB1 -0.048 0.067 -9999 0 -0.3 2 2
PRKG1 -0.21 0.38 -9999 0 -0.86 98 98
DUSP8 0.001 0.086 -9999 0 -0.86 3 3
PGK/cGMP/p38 alpha -0.16 0.21 -9999 0 -0.49 100 100
apoptosis -0.047 0.065 -9999 0 -0.29 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.13 0.32 -9999 0 -0.86 62 62
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.011 0.045 -9999 0 -0.86 1 1
RAC1 0.013 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 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.063 0.12 -9999 0 -0.38 6 6
BLK -0.26 0.39 -9999 0 -0.86 113 113
HCK -0.007 0.076 -9999 0 -0.3 24 24
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.009 0.05 -9999 0 -0.48 3 3
TRAF6/MEKK3 -0.001 0.028 -9999 0 -0.54 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.029 0.09 -9999 0 -0.32 2 2
positive regulation of innate immune response -0.062 0.13 -9999 0 -0.41 5 5
LCK -0.012 0.11 -9999 0 -0.4 23 23
p38alpha-beta/MKP7 -0.053 0.13 -9999 0 -0.46 2 2
p38alpha-beta/MKP5 -0.054 0.13 -9999 0 -0.54 3 3
PGK/cGMP -0.17 0.29 -9999 0 -0.67 98 98
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.2 -9999 0 -0.5 56 56
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.49 0.43 -9999 0 -0.86 218 218
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.033 0.12 -10000 0 -0.52 18 18
ER alpha/Gai/GDP/Gbeta gamma 0.008 0.14 -10000 0 -0.49 24 24
AKT1 -0.009 0.19 -10000 0 -0.86 18 18
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.011 0.19 -10000 0 -0.87 18 18
mol:Ca2+ -0.1 0.23 -10000 0 -0.5 92 92
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.057 0.17 -10000 0 -0.61 29 29
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.007 0.18 0.81 18 -10000 0 18
RhoA/GTP -0.026 0.091 -10000 0 -0.44 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.034 0.13 -10000 0 -0.6 17 17
regulation of stress fiber formation -0.021 0.1 0.44 1 -10000 0 1
E2/ERA-ERB (dimer) -0.041 0.14 -10000 0 -0.61 18 18
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.034 0.12 -10000 0 -0.54 17 17
pseudopodium formation 0.021 0.1 -10000 0 -0.44 1 1
E2/ER alpha (dimer)/PELP1 -0.038 0.12 -10000 0 -0.58 17 17
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.013 0 -10000 0 -10000 0 0
GNAO1 -0.013 0.14 -10000 0 -0.86 10 10
HRAS 0.012 0.016 -10000 0 -0.3 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.016 0.14 -10000 0 -0.61 17 17
E2/ER beta (dimer) -0.004 0.049 -10000 0 -0.67 2 2
mol:GDP -0.034 0.13 -10000 0 -0.6 18 18
mol:NADP 0.016 0.14 -10000 0 -0.61 17 17
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.11 0.24 -10000 0 -0.53 92 92
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.12 0.25 -10000 0 -0.55 92 92
PLCB2 -0.12 0.25 -10000 0 -0.55 91 91
IGF1 -0.18 0.36 -10000 0 -0.82 86 86
mol:L-citrulline 0.016 0.14 -10000 0 -0.61 17 17
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.022 0.13 -10000 0 -0.81 10 10
JNK cascade -0.004 0.048 -10000 0 -0.67 2 2
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.008 0.063 -10000 0 -0.86 2 2
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.049 0.19 -10000 0 -0.51 45 45
Gq family/GDP/Gbeta gamma -0.055 0.16 -10000 0 -0.63 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.08 -10000 0 -0.34 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.034 0.13 -10000 0 -0.6 17 17
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.045 0.14 -10000 0 -0.67 17 17
STRN -0.017 0.16 -10000 0 -0.86 13 13
GNAL -0.095 0.29 -10000 0 -0.86 47 47
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.016 0.043 -10000 0 -0.58 2 2
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.011 0.045 -10000 0 -0.86 1 1
HBEGF -0.002 0.16 -10000 0 -0.52 22 22
cAMP biosynthetic process -0.091 0.2 -10000 0 -0.52 61 61
SRC 0.016 0.14 -10000 0 -0.51 17 17
PI3K -0.002 0.034 -10000 0 -0.66 1 1
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.029 0.11 -10000 0 -0.52 18 18
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.098 0.18 -10000 0 -0.54 28 28
Gs family/GTP -0.093 0.2 -10000 0 -0.53 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0.007 -10000 0 -10000 0 0
vasodilation 0.017 0.14 -10000 0 -0.58 17 17
mol:DAG -0.11 0.24 -10000 0 -0.53 92 92
Gs family/GDP/Gbeta gamma -0.073 0.16 -10000 0 -0.43 61 61
MSN 0.02 0.11 -10000 0 -0.48 1 1
Gq family/GTP -0.15 0.25 -10000 0 -0.58 91 91
mol:PI-3-4-5-P3 -0.009 0.18 -10000 0 -0.82 18 18
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.017 0.14 0.58 17 -10000 0 17
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.031 0.12 -10000 0 -0.55 18 18
NOS3 0.014 0.15 -10000 0 -0.65 17 17
GNA11 0.006 0.077 -10000 0 -0.86 3 3
MAPKKK cascade 0.006 0.18 -10000 0 -0.59 29 29
E2/ER alpha (dimer)/PELP1/Src -0.037 0.14 -10000 0 -0.64 17 17
ruffle organization 0.021 0.1 -10000 0 -0.44 1 1
ROCK2 0.012 0.12 -10000 0 -0.44 8 8
GNA14 -0.2 0.37 -10000 0 -0.86 91 91
GNA15 -0.017 0.099 -10000 0 -0.31 35 35
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.026 0.19 -10000 0 -0.52 42 42
MMP2 0.018 0.14 -10000 0 -0.49 20 20
Syndecan-2-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
Syndecan-2/Fibronectin -0.11 0.1 -9999 0 -0.68 5 5
EPHB2 0.006 0.077 -9999 0 -0.86 3 3
Syndecan-2/TACI -0.13 0.26 -9999 0 -0.59 88 88
LAMA1 -0.052 0.23 -9999 0 -0.84 29 29
Syndecan-2/alpha2 ITGB1 -0.069 0.11 -9999 0 -0.5 17 17
HRAS 0.012 0.016 -9999 0 -0.3 1 1
Syndecan-2/CASK -0.008 0.066 -9999 0 -0.58 5 5
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.032 0.074 -9999 0 -0.5 7 7
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.007 0.06 -9999 0 -0.52 5 5
LAMA3 -0.023 0.16 -9999 0 -0.6 22 22
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.063 -9999 0 -0.86 2 2
Syndecan-2/MMP2 0.01 0.092 -9999 0 -0.57 9 9
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.077 0.093 -9999 0 -10000 0 0
dendrite morphogenesis 0.013 0.086 -9999 0 -0.57 8 8
Syndecan-2/GM-CSF -0.1 0.097 -9999 0 -0.6 5 5
determination of left/right symmetry 0.012 0.078 -9999 0 -0.66 5 5
Syndecan-2/PKC delta 0.017 0.068 -9999 0 -0.57 5 5
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.078 0.09 -9999 0 -0.55 5 5
MAPK1 -0.078 0.09 -9999 0 -0.55 5 5
Syndecan-2/RACK1 -0.007 0.057 -9999 0 -0.5 5 5
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.078 -9999 0 -0.66 5 5
ITGA2 -0.11 0.15 -9999 0 -0.3 154 154
MAPK8 0.025 0.081 -9999 0 -0.57 7 7
Syndecan-2/alpha2/beta1 Integrin -0.087 0.15 -9999 0 -0.54 31 31
Syndecan-2/Kininogen -0.004 0.076 -9999 0 -0.58 5 5
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.031 0.058 -9999 0 -0.46 5 5
Syndecan-2/CASK/Protein 4.1 -0.007 0.06 -9999 0 -0.53 5 5
extracellular matrix organization 0.014 0.071 -9999 0 -0.57 5 5
actin cytoskeleton reorganization -0.11 0.1 -9999 0 -0.68 5 5
Syndecan-2/Caveolin-2/Ras -0.01 0.079 -9999 0 -0.6 6 6
Syndecan-2/Laminin alpha3 -0.006 0.13 -9999 0 -0.57 17 17
Syndecan-2/RasGAP -0.006 0.054 -9999 0 -0.47 5 5
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.013 0.086 -9999 0 -0.57 8 8
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.057 -9999 0 -0.45 5 5
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.19 0.36 -9999 0 -0.82 91 91
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.077 0.093 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.017 0.068 -9999 0 -0.57 5 5
TGFB1 0.007 0.042 -9999 0 -10000 0 0
CASP3 0.027 0.063 -9999 0 -0.52 5 5
FN1 -0.21 0.14 -9999 0 -0.3 273 273
Syndecan-2/IL8 -0.036 0.12 -9999 0 -0.57 13 13
SDC2 0.012 0.078 -9999 0 -0.66 5 5
KNG1 -0.01 0.068 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.017 0.068 -9999 0 -0.57 5 5
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.19 0.14 -9999 0 -0.3 251 251
Syndecan-2/TGFB1 0.014 0.072 -9999 0 -0.57 5 5
Syndecan-2/Syntenin/PI-4-5-P2 -0.007 0.06 -9999 0 -0.53 5 5
Syndecan-2/Ezrin -0.007 0.059 -9999 0 -0.52 5 5
PRKACA 0.027 0.063 -9999 0 -0.52 5 5
angiogenesis -0.036 0.12 -9999 0 -0.57 13 13
MMP2 0.001 0.093 -9999 0 -0.62 7 7
IL8 -0.079 0.17 -9999 0 -0.86 8 8
calcineurin-NFAT signaling pathway -0.13 0.26 -9999 0 -0.58 88 88
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.046 0.15 -9999 0 -0.55 31 31
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.042 -9999 0 -10000 0 0
AP1 -0.27 0.39 -9999 0 -0.74 137 137
mol:PIP3 -0.045 0.14 -9999 0 -0.68 7 7
AKT1 -0.029 0.097 -9999 0 -0.56 3 3
PTK2B -0.001 0.085 -9999 0 -0.27 31 31
RHOA 0.03 0.047 -9999 0 -0.27 1 1
PIK3CB 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.003 0.073 -9999 0 -10000 0 0
MAGI3 0.011 0.044 -9999 0 -0.85 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.016 0.14 -9999 0 -0.46 31 31
HRAS/GDP -0.001 0.01 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.091 -9999 0 -0.52 3 3
NF kappa B1 p50/RelA -0.052 0.12 -9999 0 -0.54 8 8
endothelial cell migration -0.029 0.2 -9999 0 -0.65 32 32
ADCY4 -0.016 0.2 -9999 0 -0.64 31 31
ADCY5 -0.052 0.22 -9999 0 -0.67 35 35
ADCY6 -0.016 0.2 -9999 0 -0.64 31 31
ADCY7 -0.016 0.2 -9999 0 -0.64 31 31
ADCY1 -0.019 0.2 -9999 0 -0.64 31 31
ADCY2 -0.041 0.22 -9999 0 -0.68 32 32
ADCY3 -0.016 0.2 -9999 0 -0.64 31 31
ADCY8 -0.055 0.2 -9999 0 -0.67 31 31
ADCY9 -0.016 0.2 -9999 0 -0.64 31 31
GSK3B 0.007 0.081 -9999 0 -0.31 7 7
arachidonic acid secretion -0.009 0.18 -9999 0 -0.59 31 31
GNG2 0.013 0.001 -9999 0 -10000 0 0
TRIP6 0.026 0.008 -9999 0 -10000 0 0
GNAO1 -0.041 0.21 -9999 0 -0.63 39 39
HRAS 0.012 0.016 -9999 0 -0.3 1 1
NFKBIA 0.009 0.077 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.03 0.1 -9999 0 -0.98 4 4
JUN -0.19 0.37 -9999 0 -0.86 88 88
LPA/LPA2/NHERF2 -0.001 0.006 -9999 0 -10000 0 0
TIAM1 -0.04 0.12 -9999 0 -1.2 4 4
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
mol:IP3 0.003 0.074 -9999 0 -10000 0 0
PLCB3 0.03 0.007 -9999 0 -10000 0 0
FOS -0.22 0.39 -9999 0 -0.86 103 103
positive regulation of mitosis -0.009 0.18 -9999 0 -0.59 31 31
LPA/LPA1-2-3 -0.053 0.16 -9999 0 -0.56 31 31
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation 0.002 0.11 -9999 0 -0.36 31 31
GNAZ -0.023 0.18 -9999 0 -0.59 32 32
EGFR/PI3K-beta/Gab1 -0.047 0.14 -9999 0 -0.73 7 7
positive regulation of dendritic cell cytokine production -0.052 0.16 -9999 0 -0.56 31 31
LPA/LPA2/MAGI-3 -0.002 0.032 -9999 0 -0.62 1 1
ARHGEF1 -0.003 0.16 -9999 0 -0.51 31 31
GNAI2 -0.023 0.18 -9999 0 -0.59 32 32
GNAI3 -0.023 0.18 -9999 0 -0.59 32 32
GNAI1 -0.025 0.18 -9999 0 -0.59 33 33
LPA/LPA3 -0.01 0.043 -9999 0 -0.26 1 1
LPA/LPA2 -0.001 0.008 -9999 0 -10000 0 0
LPA/LPA1 -0.059 0.19 -9999 0 -0.68 32 32
HB-EGF/EGFR -0.056 0.17 -9999 0 -0.57 34 34
HBEGF -0.06 0.19 -9999 0 -0.64 31 31
mol:DAG 0.003 0.074 -9999 0 -10000 0 0
cAMP biosynthetic process -0.029 0.2 -9999 0 -0.6 39 39
NFKB1 0.013 0 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -10000 0 0
GNB1 0.013 0.001 -9999 0 -10000 0 0
LYN 0.009 0.077 -9999 0 -10000 0 0
GNAQ 0.018 0.028 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.004 0.066 -9999 0 -0.3 18 18
LPAR1 -0.055 0.24 -9999 0 -0.87 31 31
IL8 -0.13 0.2 -9999 0 -0.49 47 47
PTK2 -0.013 0.16 -9999 0 -0.52 31 31
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.018 0.14 -9999 0 -0.46 31 31
EGFR 0.001 0.099 -9999 0 -0.86 5 5
PLCG1 -0.017 0.084 -9999 0 -0.3 7 7
PLD2 -0.013 0.16 -9999 0 -0.52 31 31
G12/G13 -0.047 0.15 -9999 0 -0.55 31 31
PI3K-beta -0.034 0.11 -9999 0 -0.44 20 20
cell migration -0.016 0.059 -9999 0 -0.28 4 4
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.001 0.12 -9999 0 -0.37 31 31
HRAS/GTP -0.024 0.19 -9999 0 -0.61 31 31
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.086 0.24 -9999 0 -0.54 68 68
PRKCE 0.006 0.077 -9999 0 -0.86 3 3
PRKCD 0.01 0.071 -9999 0 -10000 0 0
Gi(beta/gamma) -0.009 0.19 -9999 0 -0.6 31 31
mol:LPA 0.003 0.016 -9999 0 -0.22 1 1
TRIP6/p130 Cas/FAK1/Paxillin -0.032 0.14 -9999 0 -0.48 25 25
MAPKKK cascade -0.009 0.18 -9999 0 -0.59 31 31
contractile ring contraction involved in cytokinesis 0.029 0.047 -9999 0 -0.26 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.094 0.2 -9999 0 -0.46 91 91
GNA15 0.006 0.057 -9999 0 -0.45 1 1
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.008 0.093 -9999 0 -0.55 3 3
GNA11 0.014 0.05 -9999 0 -0.44 3 3
Rac1/GTP -0.031 0.11 -9999 0 -1.1 4 4
MMP2 -0.029 0.2 -9999 0 -0.65 32 32
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.062 0.18 -9999 0 -0.58 34 34
MAP4K1 -0.024 0.14 -9999 0 -0.86 7 7
MAP3K8 0.004 0.089 -9999 0 -0.86 4 4
PRKCB -0.028 0.11 -9999 0 -0.31 48 48
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.009 0.12 -9999 0 -0.54 6 6
JUN -0.1 0.24 -9999 0 -0.51 90 90
MAP3K7 0.009 0.12 -9999 0 -0.54 6 6
GRAP2 -0.045 0.21 -9999 0 -0.79 27 27
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.016 0.11 -9999 0 -0.52 6 6
LAT 0.003 0.09 -9999 0 -0.74 5 5
LCP2 0.004 0.052 -9999 0 -10000 0 0
MAPK8 0.011 0.076 -9999 0 -0.71 3 3
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0 0.12 -9999 0 -0.39 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.058 0.17 -9999 0 -0.56 32 32
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.075 -9999 0 -0.66 5 5
alphaV beta3 Integrin -0.02 0.11 -9999 0 -0.62 12 12
PTK2 0.009 0.16 -9999 0 -0.57 12 12
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.026 0.1 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -10000 0 0
CDKN1B -0.076 0.2 -9999 0 -0.64 41 41
VEGFA 0.008 0.063 -9999 0 -0.86 2 2
ILK -0.076 0.2 -9999 0 -0.64 41 41
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.07 0.18 -9999 0 -0.59 41 41
PTK2B 0.017 0.12 -9999 0 -0.55 16 16
alphaV/beta3 Integrin/JAM-A -0.071 0.18 -9999 0 -0.51 52 52
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.02 0.11 -9999 0 -0.62 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.16 0.26 -9999 0 -0.56 109 109
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.004 0.12 -9999 0 -0.56 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.021 0.11 -9999 0 -0.62 12 12
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.22 0.26 -9999 0 -0.65 79 79
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
alphaV/beta3 Integrin/Osteopontin -0.071 0.17 -9999 0 -0.62 30 30
RPS6KB1 -0.19 0.25 -9999 0 -0.6 79 79
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.095 0.17 -9999 0 -0.81 12 12
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.095 0.17 -9999 0 -0.81 12 12
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.039 0.16 -9999 0 -0.67 22 22
cell adhesion -0.03 0.11 -9999 0 -0.57 12 12
ANGPTL3 0.006 0.017 -9999 0 -0.3 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.066 -9999 0 -0.57 5 5
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.045 -9999 0 -0.86 1 1
ITGB3 -0.015 0.15 -9999 0 -0.86 12 12
IGF1 -0.18 0.36 -9999 0 -0.82 86 86
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.019 0.11 -9999 0 -0.61 12 12
apoptosis 0.011 0.044 -9999 0 -0.85 1 1
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.02 0.11 -9999 0 -0.62 12 12
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.033 0.12 -9999 0 -0.61 15 15
CSF1 0.004 0.089 -9999 0 -0.86 4 4
PIK3C2A -0.076 0.2 -9999 0 -0.64 41 41
PI4 Kinase/Pyk2 -0.064 0.16 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.025 0.12 -9999 0 -0.59 16 16
FAK1/Vinculin 0.018 0.13 -9999 0 -0.53 5 5
alphaV beta3/Integrin/ppsTEM5 -0.02 0.11 -9999 0 -0.62 12 12
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.085 0.27 -9999 0 -0.8 46 46
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.013 0 -9999 0 -10000 0 0
F11R 0.024 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.038 0.12 -9999 0 -0.62 12 12
alphaV/beta3 Integrin/TGFBR2 -0.021 0.12 -9999 0 -0.61 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.007 0.06 -9999 0 -0.52 5 5
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.018 0.1 -9999 0 -0.57 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.21 0.14 -9999 0 -0.3 273 273
alphaV/beta3 Integrin/Pyk2 -0.023 0.12 -9999 0 -0.55 16 16
SDC1 0.01 0.028 -9999 0 -0.3 3 3
VAV3 0.029 0.081 -9999 0 -0.49 9 9
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.07 0.26 -9999 0 -0.86 36 36
FAK1/Paxillin 0.018 0.13 -9999 0 -0.53 5 5
cell migration 0.028 0.12 -9999 0 -0.47 5 5
ITGAV 0.011 0.045 -9999 0 -0.86 1 1
PI3K -0.065 0.16 -9999 0 -0.46 52 52
SPP1 -0.079 0.21 -9999 0 -0.43 78 78
KDR 0.006 0.077 -9999 0 -0.86 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.011 0.044 -9999 0 -0.85 1 1
COL4A3 -0.017 0.16 -9999 0 -0.86 13 13
angiogenesis -0.087 0.19 -9999 0 -0.62 30 30
Rac1/GTP -0.011 0.068 -9999 0 -0.44 9 9
EDIL3 -0.013 0.11 -9999 0 -0.36 26 26
cell proliferation -0.021 0.11 -9999 0 -0.61 13 13
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.01 0.21 -10000 0 -0.94 16 16
NCK1/PAK1/Dok-R -0.028 0.09 -10000 0 -0.42 17 17
NCK1/Dok-R -0.065 0.23 -10000 0 -1.1 16 16
PIK3CA 0.01 0.045 -10000 0 -0.86 1 1
mol:beta2-estradiol -0.003 0.047 0.25 12 -10000 0 12
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.013 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.005 0.058 0.26 3 -0.32 4 7
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.057 0.21 -10000 0 -1 16 16
FN1 -0.21 0.14 -10000 0 -0.3 273 273
PLD2 0.002 0.26 -10000 0 -1.2 16 16
PTPN11 0.013 0 -10000 0 -10000 0 0
GRB14 -0.022 0.17 -10000 0 -0.86 15 15
ELK1 0.017 0.23 -10000 0 -1 16 16
GRB7 -0.033 0.11 -10000 0 -0.3 56 56
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.098 0.23 -10000 0 -1.2 16 16
CDKN1A -0.011 0.17 -10000 0 -0.64 15 15
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.065 0.23 -10000 0 -1.1 16 16
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.026 0.16 -10000 0 -0.68 16 16
PLG -0.006 0.26 -10000 0 -1.2 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.008 0.2 -10000 0 -0.9 16 16
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0.002 -10000 0 -10000 0 0
ANGPT2 -0.11 0.23 -10000 0 -0.82 17 17
BMX -0.011 0.27 -10000 0 -1.2 17 17
ANGPT1 -0.039 0.29 -10000 0 -1.5 14 14
tube development -0.017 0.18 -10000 0 -0.72 16 16
ANGPT4 -0.063 0.24 -10000 0 -0.86 31 31
response to hypoxia 0 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.024 0.28 -10000 0 -1.2 16 16
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 0.012 0.002 -10000 0 -10000 0 0
STAT5A (dimer) -0.02 0.2 -10000 0 -0.82 16 16
mol:L-citrulline 0.026 0.16 -10000 0 -0.68 16 16
AGTR1 -0.32 0.42 -10000 0 -0.85 146 146
MAPK14 -0.01 0.25 -10000 0 -1.2 16 16
Tie2/SHP2 -0.019 0.098 -10000 0 -1.2 2 2
TEK 0.022 0.12 -10000 0 -1.4 2 2
RPS6KB1 0.01 0.21 -10000 0 -0.9 16 16
Angiotensin II/AT1 -0.25 0.33 -10000 0 -0.67 146 146
Tie2/Ang1/GRB2 -0.004 0.26 -10000 0 -1.2 16 16
MAPK3 0.012 0.24 -10000 0 -1.1 16 16
MAPK1 0.012 0.24 -10000 0 -1.1 16 16
Tie2/Ang1/GRB7 -0.024 0.27 -10000 0 -1.2 16 16
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.26 -10000 0 -1.1 17 17
PI3K -0.004 0.24 -10000 0 -1.1 16 16
FES -0.009 0.25 -10000 0 -1.2 16 16
Crk/Dok-R -0.065 0.23 -10000 0 -1.1 16 16
Tie2/Ang1/ABIN2 -0.004 0.26 -10000 0 -1.2 16 16
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.014 0.19 -10000 0 -0.83 16 16
STAT5A 0.013 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.01 0.21 -10000 0 -0.9 16 16
Tie2/Ang2 -0.038 0.23 -10000 0 -1 16 16
Tie2/Ang1 -0.009 0.27 -10000 0 -1.3 16 16
FOXO1 0.021 0.2 -10000 0 -0.83 16 16
ELF1 0.019 0.045 -10000 0 -0.85 1 1
ELF2 -0.001 0.25 -10000 0 -1.1 16 16
mol:Choline 0.005 0.24 -10000 0 -1.1 16 16
cell migration -0.022 0.055 -10000 0 -10000 0 0
FYN -0.023 0.2 -10000 0 -0.82 16 16
DOK2 0 0.08 -10000 0 -0.39 12 12
negative regulation of cell cycle -0.007 0.16 -10000 0 -0.58 15 15
ETS1 0.015 0.044 -10000 0 -10000 0 0
PXN 0.022 0.17 -10000 0 -0.73 16 16
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.022 0.18 -10000 0 -0.78 16 16
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.089 0.28 -10000 0 -0.8 48 48
MAPKKK cascade 0.005 0.24 -10000 0 -1.1 16 16
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.007 0.26 -10000 0 -1.2 16 16
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.028 0.15 -10000 0 -0.6 16 16
mol:Phosphatidic acid 0.005 0.24 -10000 0 -1.1 16 16
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.026 0.16 -10000 0 -0.68 16 16
Rac1/GTP -0.05 0.17 -10000 0 -0.83 16 16
MMP2 -0.004 0.26 -10000 0 -1.2 16 16
BCR signaling 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
JUN -0.1 0.18 -9999 0 -0.46 48 48
IKBKB -0.016 0.067 -9999 0 -0.28 4 4
AKT1 -0.036 0.1 -9999 0 -0.27 17 17
IKBKG -0.014 0.07 -9999 0 -0.3 4 4
CALM1 -0.029 0.082 -9999 0 -0.36 2 2
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
MAP3K1 -0.066 0.18 -9999 0 -0.66 13 13
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.038 0.086 -9999 0 -0.38 2 2
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.08 0.14 -9999 0 -0.28 89 89
LYN 0.013 0 -9999 0 -10000 0 0
BLNK 0.013 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
BCR complex -0.16 0.24 -9999 0 -0.52 103 103
CD22 -0.14 0.23 -9999 0 -0.7 37 37
CAMK2G -0.02 0.078 -9999 0 -0.33 2 2
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.01 0.081 -9999 0 -0.3 28 28
SHC/GRB2/SOS1 -0.092 0.15 -9999 0 -10000 0 0
GO:0007205 -0.039 0.087 -9999 0 -0.39 2 2
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.029 0.083 -9999 0 -0.36 2 2
NFATC1 -0.063 0.16 -9999 0 -0.54 15 15
B-cell antigen/BCR complex -0.16 0.24 -9999 0 -0.52 103 103
PAG1/CSK 0 0 -9999 0 -10000 0 0
NFKBIB 0.003 0.026 -9999 0 -0.1 1 1
HRAS -0.032 0.096 -9999 0 -0.35 2 2
NFKBIA 0.003 0.026 -9999 0 -0.1 1 1
NF-kappa-B/RelA/I kappa B beta 0.009 0.022 -9999 0 -10000 0 0
RasGAP/Csk -0.13 0.2 -9999 0 -0.53 64 64
mol:GDP -0.035 0.08 -9999 0 -0.35 2 2
PTEN 0.011 0.045 -9999 0 -0.86 1 1
CD79B -0.032 0.11 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.009 0.021 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.078 0.18 -9999 0 -0.45 51 51
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.045 0.084 -9999 0 -0.39 2 2
CSK 0.013 0 -9999 0 -10000 0 0
FOS -0.15 0.23 -9999 0 -0.5 105 105
CHUK -0.014 0.07 -9999 0 -0.3 4 4
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.063 0.091 -9999 0 -0.51 6 6
PTPN6 -0.13 0.21 -9999 0 -0.65 37 37
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.004 0.034 -9999 0 -0.13 13 13
VAV2 -0.13 0.19 -9999 0 -0.87 9 9
ubiquitin-dependent protein catabolic process 0.008 0.025 -9999 0 -0.095 1 1
BTK -0.004 0.12 -9999 0 -1.2 3 3
CD19 -0.14 0.2 -9999 0 -0.5 52 52
MAP4K1 -0.024 0.14 -9999 0 -0.86 7 7
CD72 0.01 0.032 -9999 0 -0.3 4 4
PAG1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.048 0.16 -9999 0 -0.54 13 13
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.03 0.086 -9999 0 -0.33 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.053 0.16 -9999 0 -0.45 48 48
RAF1 -0.022 0.092 -9999 0 -10000 0 0
RasGAP/p62DOK/SHIP -0.13 0.2 -9999 0 -0.51 64 64
CD79A -0.18 0.3 -9999 0 -0.5 142 142
re-entry into mitotic cell cycle -0.078 0.14 -9999 0 -0.28 89 89
RASA1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.004 0.081 -9999 0 -10000 0 0
MAPK1 -0.004 0.081 -9999 0 -10000 0 0
CD72/SHP1 -0.097 0.21 -9999 0 -0.7 24 24
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.05 0.16 -9999 0 -0.54 15 15
actin cytoskeleton organization -0.08 0.18 -9999 0 -0.7 9 9
NF-kappa-B/RelA 0.023 0.042 -9999 0 -10000 0 0
Calcineurin -0.03 0.057 -9999 0 -10000 0 0
PI3K -0.12 0.16 -9999 0 -0.57 21 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.049 0.083 -9999 0 -0.35 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.095 0.24 -9999 0 -1 14 14
DAPP1 -0.12 0.25 -9999 0 -1.3 11 11
cytokine secretion -0.059 0.15 -9999 0 -0.5 15 15
mol:DAG -0.045 0.084 -9999 0 -0.39 2 2
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.013 0.087 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.16 0.24 -9999 0 -0.62 64 64
mol:PI-3-4-5-P3 -0.09 0.12 -9999 0 -0.4 18 18
ETS1 -0.01 0.074 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.11 0.17 -9999 0 -0.49 51 51
B-cell antigen/BCR complex/LYN -0.12 0.2 -9999 0 -0.52 55 55
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.011 0.045 -9999 0 -0.86 1 1
RAC1 -0.085 0.19 -9999 0 -0.77 9 9
B-cell antigen/BCR complex/LYN/SYK -0.14 0.23 -9999 0 -0.6 55 55
CARD11 -0.071 0.12 -9999 0 -0.58 7 7
FCGR2B -0.029 0.18 -9999 0 -0.77 20 20
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex 0.001 0.034 -9999 0 -0.14 1 1
PTPRC -0.03 0.17 -9999 0 -0.55 29 29
PDPK1 -0.039 0.099 -9999 0 -0.27 17 17
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.013 0 -9999 0 -10000 0 0
POU2F2 0.009 0.023 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.02 0.015 -10000 0 -10000 0 0
HSPA8 0.008 0.045 -10000 0 -0.86 1 1
SMAD3/SMAD4/ER alpha -0.053 0.14 -10000 0 -0.62 17 17
AKT1 0.009 0.008 -10000 0 -10000 0 0
GSC -0.21 0.56 -10000 0 -1.6 56 56
NKX2-5 0.001 0.031 -10000 0 -0.29 4 4
muscle cell differentiation 0.026 0.046 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.003 0.079 -10000 0 -10000 0 0
SMAD4 -0.015 0.059 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.011 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.11 0.079 -10000 0 -0.57 4 4
SMAD3/SMAD4/VDR 0.01 0.045 -10000 0 -10000 0 0
MYC 0.004 0.13 -10000 0 -0.86 8 8
CDKN2B -0.074 0.14 -10000 0 -10000 0 0
AP1 -0.28 0.53 -10000 0 -1 120 120
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.032 0.042 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.066 -10000 0 -10000 0 0
SP3 0.016 0.002 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.005 0.058 -10000 0 -0.29 9 9
SMAD3/SMAD4/GR -0.018 0.046 -10000 0 -10000 0 0
GATA3 -0.038 0.2 -10000 0 -0.85 22 22
SKI/SIN3/HDAC complex/NCoR1 0.041 0.023 -10000 0 -10000 0 0
MEF2C/TIF2 -0.047 0.13 -10000 0 -0.52 14 14
endothelial cell migration -0.009 0.11 1.4 1 -10000 0 1
MAX 0.013 0.006 -10000 0 -10000 0 0
RBBP7 0.011 0.004 -10000 0 -10000 0 0
RBBP4 0.011 0.004 -10000 0 -10000 0 0
RUNX2 -0.078 0.15 -10000 0 -0.31 107 107
RUNX3 -0.01 0.11 -10000 0 -0.4 21 21
RUNX1 -0.13 0.16 -10000 0 -0.3 178 178
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.006 -10000 0 -10000 0 0
VDR 0.012 0.016 -10000 0 -10000 0 0
CDKN1A 0.024 0.07 -10000 0 -10000 0 0
KAT2B 0.015 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.037 0.088 -10000 0 -10000 0 0
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.011 0.004 -10000 0 -10000 0 0
SERPINE1 0.008 0.11 -10000 0 -1.5 1 1
SMAD3/SMAD4/ATF2 -0.031 0.099 -10000 0 -0.63 8 8
SMAD3/SMAD4/ATF3 -0.17 0.28 -10000 0 -0.66 91 91
SAP30 0.009 0.045 -10000 0 -0.86 1 1
Cbp/p300/PIAS3 0.033 0.045 -10000 0 -10000 0 0
JUN -0.27 0.53 -10000 0 -0.98 120 120
SMAD3/SMAD4/IRF7 -0.017 0.045 -10000 0 -10000 0 0
TFE3 0.018 0.006 -10000 0 -10000 0 0
COL1A2 -0.004 0.11 -10000 0 -1.2 1 1
mesenchymal cell differentiation 0.067 0.095 0.52 3 -10000 0 3
DLX1 -0.044 0.22 -10000 0 -0.86 25 25
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.24 0.42 -10000 0 -0.92 103 103
SMAD3/SMAD4/Max -0.018 0.046 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.008 0.021 -10000 0 -10000 0 0
ZBTB17 0.02 0.011 -10000 0 -10000 0 0
LAMC1 0.023 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.018 0.045 -10000 0 -10000 0 0
IRF7 0.014 0.004 -10000 0 -10000 0 0
ESR1 -0.05 0.19 -10000 0 -0.51 45 45
HNF4A -0.004 0.046 -10000 0 -0.3 9 9
MEF2C 0.007 0.085 -10000 0 -10000 0 0
SMAD2-3/SMAD4 -0.033 0.055 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.024 0.031 -10000 0 -10000 0 0
IGHV3OR16-13 -0.017 0.022 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.017 0.01 -10000 0 -10000 0 0
SKIL 0.013 0 -10000 0 -10000 0 0
HDAC1 0.011 0.004 -10000 0 -10000 0 0
HDAC2 0.011 0.004 -10000 0 -10000 0 0
SNIP1 0.011 0.005 -10000 0 -10000 0 0
GCN5L2 0.006 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.013 0.045 -10000 0 -10000 0 0
MSG1/HSC70 -0.16 0.098 -10000 0 -0.69 5 5
SMAD2 -0.003 0.04 -10000 0 -10000 0 0
SMAD3 -0.006 0.048 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.064 -10000 0 -0.4 3 3
SMAD2/SMAD2/SMAD4 0.012 0.025 -10000 0 -10000 0 0
NCOR1 0.011 0.004 -10000 0 -10000 0 0
NCOA2 -0.04 0.21 -10000 0 -0.86 23 23
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.019 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.01 0.075 -10000 0 -10000 0 0
IFNB1 0.014 0.056 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.004 0.086 -10000 0 -10000 0 0
CITED1 -0.24 0.14 -10000 0 -0.3 307 307
SMAD2-3/SMAD4/ARC105 -0.024 0.045 -10000 0 -10000 0 0
RBL1 -0.003 0.12 -10000 0 -0.86 7 7
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.005 0.078 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.082 0.099 -10000 0 -0.61 4 4
SMAD7 -0.12 0.28 -10000 0 -0.61 74 74
MYC/MIZ-1 0.015 0.11 -10000 0 -0.67 8 8
SMAD3/SMAD4 0.062 0.1 0.31 32 -10000 0 32
IL10 -0.032 0.2 -10000 0 -0.63 31 31
PIASy/HDAC complex 0.007 0.009 -10000 0 -10000 0 0
PIAS3 0.015 0.006 -10000 0 -10000 0 0
CDK2 0.018 0.011 -10000 0 -10000 0 0
IL5 -0.022 0.15 -10000 0 -0.53 22 22
CDK4 0.018 0.012 -10000 0 -10000 0 0
PIAS4 0.007 0.009 -10000 0 -10000 0 0
ATF3 -0.2 0.37 -10000 0 -0.86 91 91
SMAD3/SMAD4/SP1 -0.019 0.053 -10000 0 -10000 0 0
FOXG1 -0.013 0.11 -10000 0 -0.47 16 16
FOXO3 0.017 0.015 -10000 0 -10000 0 0
FOXO1 0.017 0.015 -10000 0 -10000 0 0
FOXO4 0.017 0.015 -10000 0 -10000 0 0
heart looping 0.007 0.085 -10000 0 -10000 0 0
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.059 0.16 -10000 0 -0.63 25 25
MYOD1 -0.002 0.031 -10000 0 -0.3 4 4
SMAD3/SMAD4/HNF4 -0.025 0.054 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.057 0.15 -10000 0 -0.57 26 26
SnoN/SIN3/HDAC complex/NCoR1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.076 0.097 -10000 0 -0.55 4 4
SMAD3/SMAD4/SP1-3 -0.009 0.045 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.014 0.021 -10000 0 -10000 0 0
SIN3B 0.011 0.004 -10000 0 -10000 0 0
SIN3A 0.011 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.029 0.08 -10000 0 -10000 0 0
ITGB5 0.034 0.061 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.26 0.3 -10000 0 -0.63 149 149
AR -0.33 0.42 -10000 0 -0.86 149 149
negative regulation of cell growth -0.041 0.13 -10000 0 -0.53 2 2
SMAD3/SMAD4/MYOD -0.024 0.05 -10000 0 -10000 0 0
E2F5 0.013 0 -10000 0 -10000 0 0
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.019 0.057 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.064 -10000 0 -10000 0 0
TFDP1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.3 0.54 -10000 0 -1 117 117
SMAD3/SMAD4/RUNX2 -0.067 0.096 -10000 0 -0.52 3 3
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.005 0.12 -10000 0 -0.86 8 8
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.002 0.034 -9999 0 -0.66 1 1
Necdin/E2F1 -0.063 0.1 -9999 0 -0.81 2 2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.038 0.12 -9999 0 -0.52 18 18
NGF (dimer)/p75(NTR)/BEX1 -0.3 0.3 -9999 0 -0.6 184 184
NT-4/5 (dimer)/p75(NTR) -0.077 0.19 -9999 0 -0.69 29 29
IKBKB 0.013 0 -9999 0 -10000 0 0
AKT1 -0.005 0.13 -9999 0 -0.52 19 19
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.02 0.16 -9999 0 -0.72 17 17
MGDIs/NGR/p75(NTR)/LINGO1 -0.049 0.13 -9999 0 -0.6 16 16
FURIN 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.064 0.16 -9999 0 -0.59 28 28
LINGO1 0 0.062 -9999 0 -0.3 16 16
Sortilin/TRAF6/NRIF -0.001 0.022 -9999 0 -0.43 1 1
proBDNF (dimer) -0.02 0.16 -9999 0 -0.72 17 17
NTRK1 0 0.054 -9999 0 -0.3 12 12
RTN4R 0.013 0 -9999 0 -10000 0 0
neuron apoptosis -0.016 0.15 -9999 0 -0.52 23 23
IRAK1 0.013 0 -9999 0 -10000 0 0
SHC1 -0.024 0.14 -9999 0 -0.6 18 18
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.042 0.12 -9999 0 -0.55 18 18
MAGEH1 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.045 0.13 -9999 0 -0.55 20 20
Mammalian IAPs/DIABLO -0.029 0.12 -9999 0 -0.52 19 19
proNGF (dimer) 0.005 0.078 -9999 0 -0.85 3 3
MAGED1 0.013 0 -9999 0 -10000 0 0
APP 0.013 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.021 0.16 -9999 0 -0.85 12 12
ZNF274 0.013 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.039 0.12 -9999 0 -0.52 18 18
NGF 0.005 0.079 -9999 0 -0.86 3 3
cell cycle arrest 0.042 0.17 -9999 0 -0.5 18 18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.007 0.092 -9999 0 -0.56 2 2
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.066 0.17 -9999 0 -0.62 29 29
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.048 0.14 -9999 0 -0.6 18 18
PSENEN 0.013 0 -9999 0 -10000 0 0
mol:ceramide -0.013 0.13 -9999 0 -0.54 18 18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.019 0.076 -9999 0 -0.45 2 2
p75(NTR)/beta APP -0.052 0.14 -9999 0 -0.66 16 16
BEX1 -0.38 0.43 -9999 0 -0.86 170 170
mol:GDP -0.034 0.14 -9999 0 -0.61 18 18
NGF (dimer) -0.091 0.13 -9999 0 -0.54 24 24
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.043 0.12 -9999 0 -0.55 16 16
PIK3R1 0.013 0 -9999 0 -10000 0 0
RAC1/GTP -0.041 0.12 -9999 0 -0.53 18 18
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.048 0.14 -9999 0 -0.6 18 18
RHOB 0.011 0.045 -9999 0 -0.86 1 1
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.06 0.088 -9999 0 -10000 0 0
NT3 (dimer) -0.052 0.21 -9999 0 -0.63 38 38
TP53 -0.011 0.14 -9999 0 -0.48 29 29
PRDM4 -0.013 0.13 -9999 0 -0.55 18 18
BDNF (dimer) -0.13 0.17 -9999 0 -0.57 33 33
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
SORT1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.038 0.11 -9999 0 -0.51 18 18
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.044 0.13 -9999 0 -0.56 19 19
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 0.018 0.13 -9999 0 -0.46 17 17
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 -0.013 0.13 -9999 0 -0.55 18 18
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.048 0.14 -9999 0 -0.6 18 18
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.099 0.21 -9999 0 -0.7 37 37
MAPK8 0.017 0.14 -9999 0 -0.47 17 17
MAPK9 0.018 0.13 -9999 0 -0.63 3 3
APAF1 0.013 0 -9999 0 -10000 0 0
NTF3 -0.052 0.21 -9999 0 -0.64 38 38
NTF4 -0.021 0.16 -9999 0 -0.86 12 12
NDN 0.008 0.063 -9999 0 -0.86 2 2
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.036 0.11 -9999 0 -0.5 18 18
p75 CTF/Sortilin/TRAF6/NRIF -0.003 0.053 -9999 0 -1 1 1
RhoA-B-C/GTP -0.047 0.13 -9999 0 -0.6 18 18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.053 0.14 -9999 0 -0.51 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.058 0.15 -9999 0 -0.55 29 29
PRKACB 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.026 0.13 -9999 0 -0.66 14 14
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.038 0.19 -9999 0 -0.68 28 28
BIRC2 0.013 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.068 0.18 -9999 0 -0.5 18 18
BAD 0.026 0.13 -9999 0 -0.45 17 17
RIPK2 0.013 0 -9999 0 -10000 0 0
NGFR -0.064 0.2 -9999 0 -0.86 16 16
CYCS -0.004 0.13 -9999 0 -0.51 18 18
ADAM17 0.011 0.045 -9999 0 -0.86 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.044 0.13 -9999 0 -0.56 19 19
BCL2L11 0.026 0.13 -9999 0 -0.45 17 17
BDNF (dimer)/p75(NTR) -0.077 0.18 -9999 0 -0.68 28 28
PI3K -0.043 0.13 -9999 0 -0.56 19 19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.042 0.12 -9999 0 -0.55 18 18
NDNL2 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.058 0.16 -9999 0 -0.69 18 18
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.042 0.12 -9999 0 -0.55 18 18
TRAF6 0.011 0.045 -9999 0 -0.86 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
PLG 0 0.022 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.024 0.16 -9999 0 -0.52 30 30
SQSTM1 0.013 0 -9999 0 -10000 0 0
NGFRAP1 0.013 0 -9999 0 -10000 0 0
CASP3 0.028 0.12 -9999 0 -0.42 17 17
E2F1 -0.085 0.14 -9999 0 -0.3 119 119
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.014 0.065 -9999 0 -0.56 3 3
NGF (dimer)/TRKA -0.012 0.068 -9999 0 -0.66 3 3
MMP7 -0.17 0.22 -9999 0 -0.36 186 186
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.04 0.12 -9999 0 -0.52 19 19
MMP3 -0.039 0.11 -9999 0 -0.3 55 55
APAF-1/Caspase 9 -0.043 0.12 -9999 0 -0.7 5 5
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0.016 -9999 0 -0.3 1 1
LAT2 -0.017 0.099 -9999 0 -0.33 5 5
AP1 -0.21 0.29 -9999 0 -0.6 123 123
mol:PIP3 -0.018 0.16 -9999 0 -0.45 23 23
IKBKB 0.003 0.092 -9999 0 -0.28 10 10
AKT1 -0.016 0.14 -9999 0 -0.5 4 4
IKBKG 0.003 0.092 -9999 0 -0.29 8 8
MS4A2 -0.068 0.13 -9999 0 -0.3 94 94
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
MAP3K1 0.012 0.097 -9999 0 -0.42 5 5
mol:Ca2+ -0.009 0.12 -9999 0 -0.34 23 23
LYN 0.01 0.007 -9999 0 -10000 0 0
CBLB -0.011 0.088 -9999 0 -0.33 3 3
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.087 0.2 -9999 0 -0.53 62 62
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.01 0.081 -9999 0 -0.3 28 28
PLD2 -0.049 0.15 -9999 0 -0.48 27 27
PTPN13 0.002 0.085 -9999 0 -0.5 1 1
PTPN11 0.012 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.018 0.1 -9999 0 -0.32 3 3
SYK 0.01 0.007 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.063 0.13 -9999 0 -0.44 33 33
LAT -0.017 0.1 -9999 0 -0.45 7 7
PAK2 0.003 0.1 -9999 0 -0.46 6 6
NFATC2 -0.12 0.26 -9999 0 -0.78 48 48
HRAS -0.006 0.11 -9999 0 -0.51 6 6
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.03 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.1 0.17 -9999 0 -0.52 43 43
Antigen/IgE/Fc epsilon R1 -0.091 0.16 -9999 0 -0.48 43 43
mol:GDP -0.013 0.12 -9999 0 -0.54 7 7
JUN -0.19 0.37 -9999 0 -0.86 88 88
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.22 0.39 -9999 0 -0.86 103 103
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.044 0.078 -9999 0 -0.34 4 4
CHUK 0.003 0.092 -9999 0 -0.29 8 8
KLRG1 -0.023 0.11 -9999 0 -0.4 12 12
VAV1 -0.022 0.11 -9999 0 -0.49 6 6
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.011 0.088 -9999 0 -0.33 3 3
negative regulation of mast cell degranulation -0.023 0.11 -9999 0 -0.39 12 12
BTK -0.042 0.097 -9999 0 -0.51 7 7
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.051 0.19 -9999 0 -0.53 37 37
GAB2/PI3K/SHP2 -0.063 0.12 -9999 0 -0.53 5 5
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.019 0.095 -9999 0 -0.3 27 27
RAF1 0.018 0.021 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.21 -9999 0 -0.6 45 45
FCER1G -0.009 0.08 -9999 0 -0.3 26 26
FCER1A -0.076 0.23 -9999 0 -0.57 57 57
Antigen/IgE/Fc epsilon R1/Fyn -0.081 0.15 -9999 0 -0.5 33 33
MAPK3 0.029 0.017 -9999 0 -10000 0 0
MAPK1 0.029 0.017 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.016 0.057 -9999 0 -0.61 2 2
DUSP1 -0.13 0.32 -9999 0 -0.86 62 62
NF-kappa-B/RelA -0.018 0.041 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.005 0.083 -9999 0 -10000 0 0
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.039 0.094 -9999 0 -0.51 6 6
FER -0.014 0.094 -9999 0 -0.39 5 5
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.074 0.18 -9999 0 -0.55 46 46
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.01 0.12 -9999 0 -0.54 7 7
cytokine secretion -0.014 0.03 -9999 0 -10000 0 0
SPHK1 -0.014 0.09 -9999 0 -0.33 3 3
PTK2 -0.005 0.085 -9999 0 -10000 0 0
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.065 0.14 -9999 0 -0.46 32 32
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.011 0.15 -9999 0 -0.43 22 22
MAP2K2 0.025 0.018 -9999 0 -10000 0 0
MAP2K1 0.025 0.018 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.047 0.091 -9999 0 -0.41 11 11
MAP2K4 0.02 0.007 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.22 -9999 0 -0.64 42 42
mol:Choline -0.049 0.15 -9999 0 -0.48 27 27
SHC/Grb2/SOS1 -0.031 0.065 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.003 0.081 -9999 0 -10000 0 0
HCLS1 -0.013 0.093 -9999 0 -0.36 4 4
PRKCB -0.01 0.12 -9999 0 -0.37 16 16
FCGR2B -0.029 0.18 -9999 0 -0.77 20 20
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.024 0.11 -9999 0 -0.4 12 12
LCP2 0.004 0.052 -9999 0 -10000 0 0
PLA2G4A -0.042 0.16 -9999 0 -0.53 26 26
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.049 0.15 -9999 0 -0.48 27 27
IKK complex 0.018 0.074 -9999 0 -0.23 1 1
WIPF1 0.013 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.017 0.089 -9999 0 -0.51 12 12
RGS9BP -0.047 0.22 -9999 0 -0.86 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.071 0.26 -9999 0 -0.86 36 36
mol:Na + -0.019 0.052 -9999 0 -10000 0 0
mol:ADP -0.048 0.2 -9999 0 -0.67 36 36
GNAT2 0.009 0.023 -9999 0 -0.3 2 2
RGS9-1/Gbeta5/R9AP -0.1 0.23 -9999 0 -0.59 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.012 -9999 0 -10000 0 0
GRK7 0.007 0.006 -9999 0 -10000 0 0
CNGB3 0.003 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.059 -9999 0 -10000 0 0
Cone PDE6 -0.09 0.2 -9999 0 -0.51 66 66
Cone Metarhodopsin II -0.052 0.16 -9999 0 -0.54 36 36
Na + (4 Units) -0.022 0.053 -9999 0 -10000 0 0
GNAT2/GDP -0.09 0.2 -9999 0 -0.51 66 66
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.014 -9999 0 -10000 0 0
Cone Transducin -0.018 0.094 -9999 0 -0.53 12 12
SLC24A2 -0.009 0.061 -9999 0 -0.3 16 16
GNB3/GNGT2 -0.022 0.12 -9999 0 -0.66 12 12
GNB3 -0.015 0.15 -9999 0 -0.86 12 12
GNAT2/GTP -0.001 0.015 -9999 0 -10000 0 0
CNGA3 -0.023 0.099 -9999 0 -0.3 44 44
ARR3 0.004 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.019 0.052 -9999 0 -10000 0 0
mol:Pi -0.1 0.22 -9999 0 -0.59 66 66
Cone CNG Channel -0.014 0.039 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.009 0.061 -9999 0 -0.3 16 16
RGS9 -0.085 0.27 -9999 0 -0.83 44 44
PDE6C 0.004 0.006 -9999 0 -10000 0 0
GNGT2 0.011 0.023 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.004 0.006 -9999 0 -10000 0 0
IL1-mediated signaling events

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.029 0.067 -9999 0 -0.32 6 6
IRAK/TOLLIP 0.029 0.004 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.13 0.27 -9999 0 -0.7 63 63
IL1A -0.059 0.24 -9999 0 -0.8 33 33
IL1B -0.031 0.19 -9999 0 -0.66 29 29
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.023 -9999 0 -0.45 1 1
IL1R2 -0.094 0.26 -9999 0 -0.62 64 64
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.023 0.056 -9999 0 -0.3 1 1
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.006 0.077 -9999 0 -0.86 3 3
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.066 0.023 -9999 0 -10000 0 0
JUN -0.073 0.22 -9999 0 -0.45 92 92
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.065 0.14 -9999 0 -0.5 28 28
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.078 0.15 -9999 0 -0.54 30 30
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.07 0.14 -9999 0 -0.5 30 30
IL1 beta fragment/IL1R1/IL1RAP -0.077 0.15 -9999 0 -0.56 28 28
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.029 0.079 -9999 0 -0.49 8 8
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.042 0.11 -9999 0 -0.66 8 8
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.011 0.045 -9999 0 -0.86 1 1
PI3K -0.002 0.034 -9999 0 -0.66 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.086 -9999 0 -0.35 6 6
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.077 0.15 -9999 0 -0.56 28 28
IL1 beta/IL1R2 -0.11 0.24 -9999 0 -0.63 61 61
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.024 -9999 0 -0.47 1 1
NF kappa B1 p50/RelA -0.055 0.12 -9999 0 -0.58 6 6
IRAK3 0.011 0.045 -9999 0 -0.86 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.068 0.14 -9999 0 -0.52 30 30
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.019 0.11 -9999 0 -0.35 30 30
IL1 alpha/IL1R1/IL1RAP -0.089 0.16 -9999 0 -0.59 30 30
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.013 0 -9999 0 -10000 0 0
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.001 0.026 -9999 0 -0.5 1 1
IL1RAP -0.076 0.14 -9999 0 -0.3 109 109
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.052 0.12 -9999 0 -0.52 9 9
CASP1 0.006 0.069 -9999 0 -0.52 5 5
IL1RN/IL1R2 -0.12 0.23 -9999 0 -0.64 52 52
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.069 0.14 -9999 0 -0.53 28 28
TMEM189-UBE2V1 0.004 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.08 -9999 0 -0.34 3 3
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
IL1RN -0.051 0.16 -9999 0 -0.37 63 63
TRAF6/TAK1/TAB1/TAB2 -0.001 0.025 -9999 0 -0.49 1 1
MAP2K6 0.024 0.067 -9999 0 -0.46 7 7
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.25 0.4 -10000 0 -0.86 116 116
HRAS 0.012 0.016 -10000 0 -0.3 1 1
EGFR 0.001 0.099 -10000 0 -0.86 5 5
AKT 0.017 0.025 -10000 0 -10000 0 0
FOXO3 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.013 0 -10000 0 -10000 0 0
FOXO4 0.013 0 -10000 0 -10000 0 0
MET -0.11 0.15 -10000 0 -0.3 154 154
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
PIK3CG -0.009 0.13 -10000 0 -0.75 11 11
PIK3R3 0.011 0.045 -10000 0 -0.86 1 1
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.063 0.1 -10000 0 -0.28 37 37
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.024 0.022 -10000 0 -10000 0 0
PI3K -0.041 0.098 0.23 1 -0.23 41 42
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.024 0.026 0.2 1 -10000 0 1
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.011 0.045 -10000 0 -0.86 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.013 0.014 -9999 0 -10000 0 0
REL -0.018 0.18 -9999 0 -0.85 16 16
HDAC7 -0.022 0.12 -9999 0 -0.57 7 7
JUN -0.19 0.36 -9999 0 -0.86 88 88
EP300 0.012 0.001 -9999 0 -10000 0 0
KAT2B 0.011 0.004 -9999 0 -10000 0 0
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 0 0.087 -9999 0 -0.67 6 6
FOXO1 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.035 0.12 -9999 0 -0.59 8 8
MAP2K6 -0.007 0.11 -9999 0 -0.86 6 6
BRM/BAF57 -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 0.008 0.007 -9999 0 -10000 0 0
SMARCA2 0.009 0.006 -9999 0 -10000 0 0
PDE9A 0.012 0.053 -9999 0 -10000 0 0
NCOA2 -0.047 0.21 -9999 0 -0.86 23 23
CEBPA 0.005 0.089 -9999 0 -0.86 4 4
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.059 0.13 -9999 0 -0.5 5 5
NR0B1 -0.002 0.038 -9999 0 -10000 0 0
EGR1 -0.18 0.36 -9999 0 -0.86 84 84
RXRs/9cRA -0.12 0.056 -9999 0 -0.53 2 2
AR/RACK1/Src -0.11 0.14 -9999 0 -0.62 7 7
AR/GR -0.12 0.18 -9999 0 -0.36 96 96
GNB2L1 0.006 0.007 -9999 0 -10000 0 0
PKN1 0.011 0.004 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.006 0.005 -9999 0 -10000 0 0
MAPK8 0.007 0.051 -9999 0 -0.66 2 2
T-DHT/AR/TIF2/CARM1 -0.1 0.19 -9999 0 -0.66 27 27
SRC 0.005 0.083 -9999 0 -0.5 8 8
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.39 0.57 -9999 0 -1.3 102 102
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.044 0.12 -9999 0 -0.61 8 8
TMPRSS2 -0.059 0.32 -9999 0 -1.3 24 24
RXRG -0.26 0.11 -9999 0 -0.86 2 2
mol:9cRA -0.002 0.002 -9999 0 -10000 0 0
RXRA 0.012 0.001 -9999 0 -10000 0 0
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.006 0.007 -9999 0 -10000 0 0
NR2C2 0.005 0.077 -9999 0 -0.86 3 3
KLK2 -0.48 0.43 -9999 0 -0.84 216 216
AR -0.14 0.2 -9999 0 -0.38 151 151
SENP1 0.012 0.002 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.022 0.014 -9999 0 -10000 0 0
SRY 0.009 0.014 -9999 0 -10000 0 0
GATA2 0.012 0.016 -9999 0 -0.3 1 1
MYST2 0.014 0.002 -9999 0 -10000 0 0
HOXB13 -0.016 0.057 -9999 0 -0.31 11 11
T-DHT/AR/RACK1/Src -0.068 0.12 -9999 0 -0.6 8 8
positive regulation of transcription 0.012 0.016 -9999 0 -0.3 1 1
DNAJA1 0.013 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.004 -9999 0 -10000 0 0
NCOA1 0.012 0.009 -9999 0 -10000 0 0
SPDEF -0.024 0.097 -9999 0 -0.3 40 40
T-DHT/AR/TIF2 -0.037 0.12 -9999 0 -0.41 22 22
T-DHT/AR/Hsp90 -0.046 0.11 -9999 0 -0.61 8 8
GSK3B 0.009 0.006 -9999 0 -10000 0 0
NR2C1 0.014 0.003 -9999 0 -10000 0 0
mol:T-DHT 0.003 0.086 -9999 0 -0.54 8 8
SIRT1 0.012 0.001 -9999 0 -10000 0 0
ZMIZ2 0.022 0.015 -9999 0 -10000 0 0
POU2F1 0.03 0.02 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.064 0.11 -9999 0 -0.61 8 8
CREBBP 0.011 0.004 -9999 0 -10000 0 0
SMARCE1 0.009 0.006 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.013 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.019 0.1 -10000 0 -0.49 6 6
PTP1B/AKT1 -0.002 0.065 -10000 0 -0.41 2 2
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.01 0.071 -10000 0 -0.39 3 3
EGFR 0 0.1 -10000 0 -0.86 5 5
EGF/EGFR -0.085 0.19 -10000 0 -0.52 56 56
CSF1 0.004 0.089 -10000 0 -0.86 4 4
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.013 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.093 0.13 -10000 0 -0.51 19 19
Insulin Receptor/Insulin -0.014 0.043 -10000 0 -10000 0 0
HCK -0.007 0.076 -10000 0 -0.3 24 24
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.002 0.067 -10000 0 -0.42 2 2
EGF -0.11 0.3 -10000 0 -0.86 51 51
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.018 0.11 -10000 0 -0.49 4 4
TXN 0.011 0.017 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.063 0.15 -10000 0 -0.5 38 38
cell migration 0.01 0.071 0.39 3 -10000 0 3
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.043 0.19 -10000 0 -0.86 18 18
ITGA2B -0.095 0.29 -10000 0 -0.86 47 47
CSF1R 0.009 0.035 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin -0.037 0.15 -10000 0 -0.67 18 18
FGR 0.01 0.032 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.002 0.067 -10000 0 -0.42 2 2
Crk/p130 Cas -0.016 0.05 -10000 0 -0.4 2 2
DOK1 0.007 0.063 -10000 0 -0.38 2 2
JAK2 -0.007 0.084 -10000 0 -0.39 6 6
Jak2/Leptin Receptor/Leptin -0.066 0.16 -10000 0 -0.61 27 27
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.01 0.071 -10000 0 -0.4 3 3
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.18 0.21 -10000 0 -0.86 16 16
SRC 0.012 0.029 -10000 0 -10000 0 0
ITGB3 -0.016 0.15 -10000 0 -0.86 12 12
CAT1/PTP1B -0.093 0.15 -10000 0 -0.4 38 38
CAPN1 0.013 0.004 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.014 0.045 -10000 0 -0.63 1 1
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.066 0.17 -10000 0 -0.65 27 27
negative regulation of transcription -0.006 0.084 -10000 0 -0.38 7 7
FCGR2A -0.007 0.085 -10000 0 -0.32 23 23
FER 0.007 0.064 -10000 0 -0.87 2 2
alphaIIb/beta3 Integrin -0.1 0.26 -10000 0 -0.72 53 53
BLK -0.26 0.39 -10000 0 -0.86 113 113
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.013 0.004 -10000 0 -10000 0 0
LEPR 0 0.1 -10000 0 -0.85 5 5
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.13 0.19 -10000 0 -0.49 37 37
PRL 0.001 0.017 -10000 0 -0.29 1 1
SOCS3 -0.098 0.39 -10000 0 -1.5 27 27
SPRY2 0.011 0.017 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.056 0.17 -10000 0 -0.59 36 36
CSF1/CSF1R -0.023 0.075 -10000 0 -0.49 6 6
Ras protein signal transduction 0.02 0.023 -10000 0 -10000 0 0
IRS1 -0.07 0.26 -10000 0 -0.86 36 36
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.009 0.067 -10000 0 -0.3 19 19
STAT5B -0.005 0.07 -10000 0 -0.36 3 3
STAT5A -0.005 0.07 -10000 0 -0.36 3 3
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.067 -10000 0 -0.42 2 2
CSN2 -0.006 0.052 -10000 0 -10000 0 0
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
LAT 0.001 0.072 -10000 0 -0.55 5 5
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.012 0.11 -10000 0 -0.4 23 23
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.12 0.15 -10000 0 -0.3 156 156
Aurora C signaling

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
INCENP 0.013 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.033 0.061 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.009 0.017 -9999 0 -10000 0 0
AURKB -0.056 0.13 -9999 0 -0.3 84 84
AURKC 0.005 0.05 -9999 0 -0.3 10 10
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.036 0.038 -9999 0 -10000 0 0
VDR 0.012 0.016 -9999 0 -10000 0 0
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.051 0.1 -9999 0 -0.34 33 33
RXRs/LXRs/DNA/Oxysterols -0.042 0.15 -9999 0 -0.45 43 43
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.024 0.074 -9999 0 -0.34 15 15
RXRs/NUR77 -0.27 0.27 -9999 0 -0.66 116 116
RXRs/PPAR -0.048 0.061 -9999 0 -0.4 7 7
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.01 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.013 0.082 -9999 0 -0.51 10 10
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.012 0.016 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.013 0.081 -9999 0 -0.5 10 10
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.051 0.031 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.024 0.074 -9999 0 -0.34 15 15
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.01 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.11 0.078 -9999 0 -0.58 2 2
NR1H4 0 0.035 -9999 0 -0.3 5 5
RXRs/LXRs/DNA -0.087 0.086 -9999 0 -0.56 2 2
NR1H2 0.015 0.012 -9999 0 -10000 0 0
NR1H3 0.015 0.014 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.095 0.064 -9999 0 -0.53 2 2
NR4A1 -0.25 0.4 -9999 0 -0.85 116 116
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.042 0.045 -9999 0 -0.31 2 2
RXRG -0.26 0.11 -9999 0 -0.38 34 34
RXR alpha/CCPG 0 0.003 -9999 0 -10000 0 0
RXRA 0.015 0.012 -9999 0 -10000 0 0
RXRB 0.014 0.014 -9999 0 -10000 0 0
THRB 0.001 0.099 -9999 0 -0.86 5 5
PPARG -0.002 0.1 -9999 0 -0.61 9 9
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.13 0.41 -9999 0 -1.3 43 43
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.041 0.15 -9999 0 -0.44 43 43
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.01 0.14 -9999 0 -0.86 10 10
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.46 129 129
SREBF1 -0.031 0.14 -9999 0 -0.63 1 1
RXRs/RXRs/DNA/9cRA -0.11 0.078 -9999 0 -0.58 2 2
ABCA1 -0.031 0.14 -9999 0 -0.63 1 1
RARs/THRs -0.019 0.095 -9999 0 -0.49 15 15
RXRs/FXR -0.11 0.066 -9999 0 -0.56 2 2
BCL2 -0.038 0.2 -9999 0 -0.86 22 22
Effects of Botulinum toxin

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
STX1A 0.012 0 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.001 0.01 -9999 0 -10000 0 0
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.015 0.067 -9999 0 -0.25 10 10
RAB3GAP2/RIMS1/UNC13B 0 0.007 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.011 0.016 -9999 0 -0.3 1 1
mol:ACh -0.008 0.041 -9999 0 -0.16 22 22
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.015 0.067 -9999 0 -0.25 10 10
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.017 0.096 -9999 0 -0.32 33 33
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.12 0.17 -9999 0 -0.41 57 57
SNAP25 -0.033 0.097 -9999 0 -0.39 22 22
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.18 0.24 -9999 0 -0.38 183 183
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.063 0.086 -10000 0 -0.35 19 19
NT3 (dimer)/TRKC -0.094 0.21 -10000 0 -0.71 34 34
NT3 (dimer)/TRKB -0.088 0.19 -10000 0 -0.61 40 40
SHC/Grb2/SOS1/GAB1/PI3K 0.038 0.019 -10000 0 -0.34 1 1
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.02 0.16 -10000 0 -0.72 17 17
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 0 0.054 -10000 0 -0.3 12 12
NTRK2 0.006 0.077 -10000 0 -0.86 3 3
NTRK3 -0.059 0.18 -10000 0 -0.4 66 66
NT-4/5 (dimer)/TRKB -0.069 0.17 -10000 0 -0.61 31 31
neuron apoptosis 0.042 0.097 0.45 10 -10000 0 10
SHC 2-3/Grb2 -0.045 0.11 -10000 0 -0.49 10 10
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.03 0.095 -10000 0 -0.68 4 4
SHC3 -0.049 0.11 -10000 0 -0.62 8 8
STAT3 (dimer) 0.017 0.025 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.089 0.19 -10000 0 -0.62 37 37
RIN/GDP -0.01 0.066 -10000 0 -0.28 3 3
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.033 0.099 -10000 0 -0.46 16 16
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.025 0.045 -10000 0 -10000 0 0
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.013 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.021 0.16 -10000 0 -0.85 12 12
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.019 0.087 -10000 0 -0.58 8 8
TRKA/NEDD4-2 -0.006 0.033 -10000 0 -10000 0 0
ELMO1 -0.34 0.43 -10000 0 -0.86 152 152
RhoG/GTP/ELMO1/DOCK1 -0.24 0.29 -10000 0 -0.59 152 152
NGF 0.005 0.079 -10000 0 -0.86 3 3
HRAS 0.012 0.016 -10000 0 -0.3 1 1
DOCK1 0.011 0.045 -10000 0 -0.86 1 1
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.029 0.18 -10000 0 -0.83 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.22 0.24 -10000 0 -0.49 165 165
mol:GDP -0.017 0.095 -10000 0 -0.41 4 4
NGF (dimer) 0.005 0.078 -10000 0 -0.85 3 3
RhoG/GDP -0.27 0.33 -10000 0 -0.67 152 152
RIT1/GDP -0.005 0.066 -10000 0 -0.29 2 2
TIAM1 -0.16 0.16 -10000 0 -0.3 210 210
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.025 0.13 -10000 0 -0.65 14 14
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.052 0.21 -10000 0 -0.63 38 38
RAP1/GDP -0.019 0.045 -10000 0 -10000 0 0
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.02 0.16 -10000 0 -0.72 17 17
ubiquitin-dependent protein catabolic process -0.01 0.057 -10000 0 -0.57 3 3
Schwann cell development -0.043 0.033 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.074 0.17 -10000 0 -0.7 13 13
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.04 -10000 0 -10000 0 0
STAT3 0.017 0.025 -10000 0 -10000 0 0
axon guidance -0.07 0.16 -10000 0 -0.65 13 13
MAPK3 0.015 0.085 -10000 0 -0.52 8 8
MAPK1 0.015 0.085 -10000 0 -0.52 8 8
CDC42/GDP -0.005 0.066 -10000 0 -0.27 3 3
NTF3 -0.052 0.21 -10000 0 -0.64 38 38
NTF4 -0.021 0.16 -10000 0 -0.86 12 12
NGF (dimer)/TRKA/FAIM -0.01 0.057 -10000 0 -0.58 3 3
PI3K -0.002 0.034 -10000 0 -0.66 1 1
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.12 0.12 -10000 0 -0.5 22 22
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.057 0.19 -10000 0 -0.62 33 33
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.044 -10000 0 -10000 0 0
Rac1/GDP -0.005 0.066 -10000 0 -0.29 2 2
NGF (dimer)/TRKA/GRIT -0.01 0.059 -10000 0 -0.58 3 3
neuron projection morphogenesis -0.001 0.1 -10000 0 -0.69 1 1
NGF (dimer)/TRKA/NEDD4-2 -0.01 0.057 -10000 0 -0.58 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.064 0.2 -10000 0 -0.86 16 16
NGF (dimer)/TRKA/GIPC/GAIP 0.013 0.092 -10000 0 -0.36 20 20
RAS family/GTP/PI3K 0.031 0.024 -10000 0 -0.43 1 1
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.063 -10000 0 -0.62 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.006 0.033 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.023 0.12 -10000 0 -0.6 14 14
NGF (dimer)/TRKA/p62/Atypical PKCs -0.007 0.047 -10000 0 -0.49 3 3
MATK -0.002 0.1 -10000 0 -0.61 9 9
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.016 0.044 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.036 0.11 -10000 0 -0.47 19 19
Rac1/GTP -0.19 0.15 -10000 0 -0.36 153 153
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex -0.002 0.079 -9999 0 -10000 0 0
STMN1 -0.019 0.089 -9999 0 -0.38 1 1
Aurora B/RasGAP/Survivin -0.025 0.11 -9999 0 -0.57 1 1
Chromosomal passenger complex/Cul3 protein complex 0.008 0.068 -9999 0 -0.29 9 9
BIRC5 -0.021 0.1 -9999 0 -0.32 39 39
DES -0.39 0.3 -9999 0 -0.62 234 234
Aurora C/Aurora B/INCENP -0.01 0.073 -9999 0 -10000 0 0
Aurora B/TACC1 -0.018 0.071 -9999 0 -10000 0 0
Aurora B/PP2A -0.024 0.086 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.024 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.054 0.15 -9999 0 -0.37 57 57
Cul3 protein complex -0.016 0.085 -9999 0 -0.57 8 8
KIF2C -0.002 0.041 -9999 0 -10000 0 0
PEBP1 0.01 0.005 -9999 0 -10000 0 0
KIF20A -0.048 0.12 -9999 0 -0.3 74 74
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.024 0.086 -9999 0 -10000 0 0
SEPT1 0.009 0.035 -9999 0 -0.3 5 5
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.007 0.042 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
H3F3B -0.005 0.052 -9999 0 -10000 0 0
AURKB -0.047 0.13 -9999 0 -0.3 84 84
AURKC 0.005 0.05 -9999 0 -0.3 10 10
CDCA8 0.009 0.029 -9999 0 -0.31 3 3
cytokinesis -0.068 0.078 -9999 0 -0.41 3 3
Aurora B/Septin1 -0.028 0.097 -9999 0 -0.4 6 6
AURKA 0.012 0.002 -9999 0 -10000 0 0
INCENP 0.011 0.006 -9999 0 -10000 0 0
KLHL13 -0.014 0.13 -9999 0 -0.55 18 18
BUB1 -0.11 0.15 -9999 0 -0.3 147 147
hSgo1/Aurora B/Survivin -0.028 0.12 -9999 0 -0.43 16 16
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.031 0.071 -9999 0 -0.34 3 3
SGOL1 -0.002 0.066 -9999 0 -0.3 18 18
CENPA -0.008 0.069 -9999 0 -0.24 6 6
NCAPG -0.026 0.1 -9999 0 -0.3 47 47
Aurora B/HC8 Proteasome -0.024 0.086 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.024 0.086 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.04 0.12 -9999 0 -0.3 65 65
NPM1 -0.01 0.045 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.086 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.035 0.079 -9999 0 -0.34 11 11
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.01 0.045 -9999 0 -10000 0 0
MYLK -0.005 0.052 -9999 0 -10000 0 0
KIF23 -0.006 0.074 -9999 0 -10000 0 0
VIM -0.018 0.088 -9999 0 -10000 0 0
RACGAP1 0.012 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.01 0.045 -9999 0 -10000 0 0
Chromosomal passenger complex -0.015 0.08 -9999 0 -0.23 22 22
Chromosomal passenger complex/EVI5 0.013 0.12 -9999 0 -0.41 4 4
TACC1 0.013 0 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.016 0.053 -9999 0 -0.58 3 3
ADCY5 -0.07 0.22 -9999 0 -0.58 56 56
ADCY6 0.016 0.053 -9999 0 -0.58 3 3
ADCY7 0.016 0.053 -9999 0 -0.58 3 3
ADCY1 0.007 0.086 -9999 0 -0.6 7 7
ADCY2 -0.045 0.19 -9999 0 -0.6 37 37
ADCY3 0.016 0.053 -9999 0 -0.58 3 3
ADCY8 -0.11 0.096 -9999 0 -0.72 3 3
PRKCE 0.007 0.061 -9999 0 -0.67 3 3
ADCY9 0.016 0.053 -9999 0 -0.58 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.056 0.11 -9999 0 -0.37 25 25
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.014 0.089 -10000 0 -10000 0 0
epithelial cell differentiation -0.044 0.099 -10000 0 -0.5 8 8
ITCH 0.024 0.021 -10000 0 -10000 0 0
WWP1 -0.003 0.08 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.001 0.099 -10000 0 -0.86 5 5
PRL 0.001 0.016 -10000 0 -0.3 1 1
neuron projection morphogenesis -0.002 0.15 -10000 0 -0.55 8 8
PTPRZ1 -0.019 0.15 -10000 0 -0.86 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.063 0.14 -10000 0 -0.62 8 8
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.05 0.18 -10000 0 -0.56 37 37
ADAM17 0.022 0.049 -10000 0 -0.85 1 1
ErbB4/ErbB4 -0.013 0.1 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.051 0.18 -10000 0 -0.59 29 29
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.072 0.16 -10000 0 -0.53 37 37
GRIN2B -0.035 0.17 -10000 0 -0.5 37 37
ErbB4/ErbB2/betacellulin -0.033 0.098 -10000 0 -0.66 7 7
STAT1 0.005 0.05 -10000 0 -0.3 10 10
HBEGF 0 0.062 -10000 0 -0.3 16 16
PRLR -0.043 0.19 -10000 0 -0.58 36 36
E4ICDs/ETO2 -0.007 0.087 -10000 0 -10000 0 0
axon guidance -0.001 0.083 -10000 0 -10000 0 0
NEDD4 0.024 0.021 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.042 0.15 -10000 0 -0.67 18 18
CBFA2T3 0.012 0.016 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF -0.028 0.056 -10000 0 -0.67 1 1
MAPK3 -0.011 0.15 -10000 0 -0.57 8 8
STAT1 (dimer) -0.011 0.091 -10000 0 -10000 0 0
MAPK1 -0.011 0.15 -10000 0 -0.57 8 8
JAK2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.072 0.16 -10000 0 -0.53 37 37
NRG1 -0.039 0.21 -10000 0 -0.68 37 37
NRG3 -0.054 0.23 -10000 0 -0.86 29 29
NRG2 -0.088 0.28 -10000 0 -0.82 46 46
NRG4 0.007 0.039 -10000 0 -0.3 6 6
heart development -0.001 0.083 -10000 0 -10000 0 0
neural crest cell migration -0.072 0.16 -10000 0 -0.52 37 37
ERBB2 0.029 0.037 -10000 0 -0.65 1 1
WWOX/E4ICDs -0.007 0.086 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.041 0.091 -10000 0 -0.59 5 5
apoptosis 0.059 0.14 0.47 29 -10000 0 29
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.074 0.2 -10000 0 -0.59 43 43
ErbB4/ErbB2/epiregulin -0.075 0.083 -10000 0 -0.67 1 1
ErbB4/ErbB4/betacellulin/betacellulin -0.017 0.12 -10000 0 -0.69 7 7
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.058 0.12 -10000 0 -0.51 18 18
MDM2 -0.002 0.088 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.067 0.16 -10000 0 -0.53 37 37
STAT5A 0.008 0.078 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.079 0.17 -10000 0 -0.54 41 41
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.034 0.064 -10000 0 -10000 0 0
STAT5A (dimer) -0.047 0.11 -10000 0 -0.54 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.076 -10000 0 -10000 0 0
LRIG1 0.006 0.077 -10000 0 -0.86 3 3
EREG -0.13 0.15 -10000 0 -0.3 176 176
BTC -0.003 0.12 -10000 0 -0.86 7 7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.083 -10000 0 -10000 0 0
ERBB4 -0.013 0.1 -10000 0 -10000 0 0
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.011 0.021 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.026 0.055 -10000 0 -0.54 1 1
glial cell differentiation 0.034 0.063 -10000 0 -10000 0 0
WWOX 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.023 0.18 -10000 0 -0.47 40 40
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.046 0.14 -9999 0 -0.45 38 38
Syndecan-3/Neurocan -0.045 0.14 -9999 0 -0.49 34 34
POMC -0.17 0.35 -9999 0 -0.84 80 80
EGFR 0.001 0.099 -9999 0 -0.86 5 5
Syndecan-3/EGFR -0.007 0.056 -9999 0 -0.49 5 5
AGRP -0.003 0.056 -9999 0 -0.3 13 13
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.067 0.25 -9999 0 -0.82 36 36
long-term memory 0 0.003 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.038 0.082 -9999 0 -0.49 8 8
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin -0.001 0.01 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
limb bud formation 0 0.004 -9999 0 -10000 0 0
MC4R 0.001 0.038 -9999 0 -0.3 6 6
SRC 0.012 0.016 -9999 0 -10000 0 0
PTN -0.075 0.26 -9999 0 -0.84 39 39
FGFR/FGF/Syndecan-3 0 0.004 -9999 0 -10000 0 0
neuron projection morphogenesis -0.082 0.17 -9999 0 -0.44 71 71
Syndecan-3/AgRP -0.004 0.021 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.005 0.023 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 0 0.004 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.037 0.081 -9999 0 -0.48 8 8
IL8 -0.079 0.17 -9999 0 -0.86 8 8
Syndecan-3/Fyn/Cortactin 0 0.003 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0.004 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.14 0.27 -9999 0 -0.67 78 78
Gamma Secretase 0 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG -0.018 0.17 -9999 0 -0.51 41 41
VEGFR1 homodimer/NRP1/VEGFR 121 -0.003 0.038 -9999 0 -0.53 2 2
CaM/Ca2+ -0.011 0.16 -9999 0 -0.48 41 41
HIF1A 0.021 0 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.005 0.16 -9999 0 -0.92 1 1
PLCG1 -0.018 0.17 -9999 0 -0.52 41 41
NOS3 0.012 0.16 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.013 0.15 -9999 0 -10000 0 0
FLT1 0.032 0 -9999 0 -10000 0 0
PGF -0.082 0.27 -9999 0 -0.84 42 42
VEGFR1 homodimer/NRP2/VEGFR121 -0.014 0.05 -9999 0 -0.52 2 2
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
eNOS/Hsp90 0.019 0.15 -9999 0 -10000 0 0
endothelial cell proliferation -0.039 0.2 -9999 0 -0.54 41 41
mol:Ca2+ -0.018 0.17 -9999 0 -0.51 41 41
MAPK3 -0.028 0.2 -9999 0 -0.48 59 59
MAPK1 -0.028 0.2 -9999 0 -0.54 22 22
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.082 0.27 -9999 0 -0.84 42 42
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.012 0.15 -9999 0 -0.86 11 11
VEGFA homodimer 0.008 0.063 -9999 0 -0.85 2 2
VEGFR1 homodimer/VEGFA homodimer 0.03 0.044 -9999 0 -0.57 2 2
platelet activating factor biosynthetic process -0.02 0.19 -9999 0 -0.87 4 4
PI3K -0.054 0.15 -9999 0 -0.48 42 42
PRKCA -0.038 0.21 -9999 0 -0.51 59 59
PRKCB -0.027 0.17 -9999 0 -0.48 42 42
VEGFR1 homodimer/PLGF homodimer -0.032 0.19 -9999 0 -0.57 41 41
VEGFA 0.008 0.063 -9999 0 -0.86 2 2
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.018 0.17 -9999 0 -0.51 41 41
RASA1 0.042 0 -9999 0 -10000 0 0
NRP2 -0.017 0.092 -9999 0 -10000 0 0
VEGFR1 homodimer 0.032 0 -9999 0 -10000 0 0
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.006 0.17 -9999 0 -0.84 2 2
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.053 0.15 -9999 0 -0.48 42 42
mol:L-citrulline 0.013 0.15 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.003 0.035 -9999 0 -0.48 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.003 0.038 -9999 0 -0.52 2 2
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.05 0.14 -9999 0 -10000 0 0
PDPK1 -0.004 0.16 -9999 0 -0.93 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.003 0.038 -9999 0 -0.52 2 2
mol:NADP 0.013 0.15 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.003 0.035 -9999 0 -0.48 2 2
VEGFR1 homodimer/NRP2 0.017 0.051 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.008 0.079 -10000 0 -0.77 4 4
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.012 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 -0.003 0.12 -10000 0 -0.86 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.008 0.063 -10000 0 -0.86 2 2
AP1 -0.16 0.27 -10000 0 -0.5 130 130
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 0.004 0.089 -10000 0 -0.86 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.041 0.05 -10000 0 -0.34 1 1
NICD/RBPSUH -0.008 0.079 -10000 0 -0.77 4 4
WIF1 -0.033 0.1 -10000 0 -0.3 47 47
NOTCH1 -0.008 0.081 -10000 0 -0.79 4 4
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.01 0.081 -10000 0 -10000 0 0
DKK1 -0.035 0.12 -10000 0 -0.32 54 54
beta catenin/beta TrCP1 0.036 0.04 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0.002 0.028 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.003 0.035 -10000 0 -0.36 1 1
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.22 0.39 -10000 0 -0.86 103 103
JUN -0.19 0.37 -10000 0 -0.86 88 88
MAP3K7 0.011 0.003 -10000 0 -10000 0 0
CTNNB1 0.03 0.043 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.038 0.13 -10000 0 -0.6 16 16
HNF1A 0.012 0.002 -10000 0 -10000 0 0
CTBP1 0.012 0.002 -10000 0 -10000 0 0
MYC -0.007 0.22 -10000 0 -1.5 8 8
NKD1 -0.02 0.16 -10000 0 -0.75 16 16
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.017 0.099 -10000 0 -0.58 11 11
apoptosis -0.16 0.27 -10000 0 -0.5 130 130
Delta 1/NOTCHprecursor -0.008 0.076 -10000 0 -0.74 4 4
DLL1 0.012 0.016 -10000 0 -0.3 1 1
PPARD 0.024 0.015 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC 0.002 0.028 -10000 0 -10000 0 0
DVL1 0 0.001 -10000 0 -10000 0 0
CSNK2A1 0.013 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.034 0.079 -10000 0 -0.65 2 2
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0.002 -10000 0 -10000 0 0
NLK 0.014 0.007 -10000 0 -10000 0 0
CCND1 0.018 0.042 -10000 0 -10000 0 0
WNT1 0.008 0.028 -10000 0 -0.3 3 3
Axin1/APC/beta catenin 0.047 0.033 -10000 0 -10000 0 0
DKK2 -0.031 0.18 -10000 0 -0.66 25 25
NOTCH1 precursor/DVL1 -0.004 0.069 -10000 0 -0.66 4 4
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.017 0.1 -10000 0 -0.59 11 11
PPP2R5D 0.014 0.07 0.38 13 -10000 0 13
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.016 0.042 -10000 0 -10000 0 0
RBPJ 0.012 0.016 -10000 0 -0.3 1 1
CREBBP 0.016 0.004 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.034 0.35 -9999 0 -0.93 11 11
PLK1 0.04 0.072 -9999 0 -10000 0 0
BIRC5 0.018 0.13 -9999 0 -1.6 1 1
HSPA1B 0.033 0.35 -9999 0 -0.93 11 11
MAP2K1 0.03 0.037 -9999 0 -10000 0 0
BRCA2 0.027 0.37 -9999 0 -0.99 15 15
FOXM1 0.021 0.39 -9999 0 -1.1 13 13
XRCC1 0.034 0.35 -9999 0 -0.93 11 11
FOXM1B/p19 -0.1 0.31 -9999 0 -0.91 19 19
Cyclin D1/CDK4 0.021 0.33 -9999 0 -0.86 11 11
CDC2 0.026 0.37 -9999 0 -0.96 13 13
TGFA 0.005 0.34 -9999 0 -0.86 12 12
SKP2 0.031 0.36 -9999 0 -0.94 12 12
CCNE1 0.015 0.01 -9999 0 -10000 0 0
CKS1B 0.034 0.35 -9999 0 -0.93 11 11
RB1 -0.055 0.097 -9999 0 -10000 0 0
FOXM1C/SP1 0.019 0.37 -9999 0 -1 14 14
AURKB -0.005 0.12 -9999 0 -10000 0 0
CENPF 0.027 0.36 -9999 0 -0.96 12 12
CDK4 0.018 0.015 -9999 0 -10000 0 0
MYC 0.03 0.35 -9999 0 -0.9 17 17
CHEK2 0.03 0.037 -9999 0 -10000 0 0
ONECUT1 0.017 0.35 -9999 0 -0.9 12 12
CDKN2A -0.13 0.15 -9999 0 -10000 0 0
LAMA4 0.034 0.35 -9999 0 -0.93 11 11
FOXM1B/HNF6 0.009 0.37 -9999 0 -1 12 12
FOS -0.21 0.66 -9999 0 -1.2 104 104
SP1 0.014 0.003 -9999 0 -10000 0 0
CDC25B 0.033 0.35 -9999 0 -0.92 12 12
response to radiation 0.013 0.034 -9999 0 -10000 0 0
CENPB 0.034 0.35 -9999 0 -0.93 11 11
CENPA 0.018 0.38 -9999 0 -0.99 16 16
NEK2 0.023 0.36 -9999 0 -0.96 13 13
HIST1H2BA 0.025 0.35 -9999 0 -0.94 11 11
CCNA2 0.007 0.053 -9999 0 -0.31 2 2
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.021 0.38 -9999 0 -1 12 12
CCNB2 0.03 0.36 -9999 0 -0.97 11 11
CCNB1 0.029 0.36 -9999 0 -0.96 12 12
ETV5 0.032 0.35 -9999 0 -0.94 11 11
ESR1 -0.014 0.43 -9999 0 -1.1 27 27
CCND1 0.023 0.34 -9999 0 -0.88 11 11
GSK3A 0.029 0.03 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.033 0.052 -9999 0 -10000 0 0
CDK2 0.015 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.016 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.13 0.23 -9999 0 -0.93 15 15
GAS1 -0.15 0.62 -9999 0 -1.2 83 83
MMP2 0.026 0.37 -9999 0 -1.1 13 13
RB1/FOXM1C 0.031 0.34 -9999 0 -0.92 11 11
CREBBP 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
induction of apoptosis 0 0 -9999 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.021 0.012 -9999 0 -10000 0 0
CDKN1A -0.007 0.035 -9999 0 -10000 0 0
KAT2B 0.013 0 -9999 0 -10000 0 0
BAX 0.013 0 -9999 0 -10000 0 0
FOXO3 0 0 -9999 0 -10000 0 0
FOXO1 0.013 0 -9999 0 -10000 0 0
FOXO4 0.024 0 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
TAT 0.008 0.017 -9999 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -9999 0 -10000 0 0
MYOD1 0.011 0.021 -9999 0 -10000 0 0
PPARGC1A -0.36 0.43 -9999 0 -0.86 163 163
FHL2 -0.058 0.24 -9999 0 -0.86 31 31
response to nutrient levels 0 0 -9999 0 -10000 0 0
KU70/SIRT1 0.002 0.011 -9999 0 -10000 0 0
HIST2H4A 0.021 0.012 -9999 0 -10000 0 0
SIRT1/FOXO3a 0.001 0.008 -9999 0 -10000 0 0
SIRT1 0.002 0.012 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.002 0.011 -9999 0 -10000 0 0
SIRT1/Histone H1b -0.005 0.048 -9999 0 -0.32 8 8
apoptosis -0.002 0.011 -9999 0 -10000 0 0
SIRT1/PGC1A -0.25 0.29 -9999 0 -0.58 163 163
p53/SIRT1 0.006 0.031 -9999 0 -10000 0 0
SIRT1/FOXO4 0.002 0.012 -9999 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.042 0.15 -9999 0 -0.53 31 31
HIST1H1E 0.014 0.059 -9999 0 -0.38 8 8
SIRT1/p300 0.002 0.011 -9999 0 -10000 0 0
muscle cell differentiation 0 0.018 -9999 0 -10000 0 0
TP53 0.002 0.012 -9999 0 -10000 0 0
KU70/SIRT1/BAX 0.002 0.011 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
MEF2D 0.013 0 -9999 0 -10000 0 0
HIV-1 Tat/SIRT1 0.001 0.014 -9999 0 -10000 0 0
ACSS2 0.022 0.004 -9999 0 -10000 0 0
SIRT1/PCAF/MYOD 0 0.018 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.006 0.098 -9999 0 -0.42 17 17
CCNA2 0.005 0.05 -9999 0 -10000 0 0
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
JAK3 -0.059 0.13 -9999 0 -0.3 89 89
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.022 0.14 -9999 0 -0.59 13 13
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.021 0 -9999 0 -10000 0 0
IL2RA -0.03 0.23 -9999 0 -1 17 17
IL2RB -0.017 0.14 -9999 0 -0.54 21 21
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.051 0.2 -9999 0 -0.51 47 47
G1/S transition of mitotic cell cycle 0.04 0.041 -9999 0 -0.62 1 1
PTPN11 0.014 0 -9999 0 -10000 0 0
CCND2 0.032 0 -9999 0 -10000 0 0
LCK -0.011 0.11 -9999 0 -0.39 23 23
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.005 0.006 -9999 0 -10000 0 0
CDK6 0.011 0.045 -9999 0 -0.86 1 1
CCND3 0.032 0.12 -9999 0 -0.67 5 5
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.063 0.17 -10000 0 -0.5 47 47
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.007 0.052 -10000 0 -10000 0 0
GNB1/GNG2 0 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.068 0.18 -10000 0 -0.55 47 47
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.015 0.04 0.12 47 -10000 0 47
GNAL -0.095 0.29 -10000 0 -0.86 47 47
GNG2 0.013 0 -10000 0 -10000 0 0
CRH -0.013 0.076 -10000 0 -0.3 25 25
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.035 -10000 0 -0.47 2 2
MAPK11 0.009 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0.001 0.099 -9999 0 -0.86 5 5
CDKN1A -0.017 0.093 -9999 0 -10000 0 0
PRL-3/alpha Tubulin -0.014 0.049 -9999 0 -10000 0 0
mol:Ca2+ -0.015 0.11 -9999 0 -0.68 8 8
AGT -0.019 0.14 -9999 0 -0.48 25 25
CCNA2 -0.074 0.22 -9999 0 -0.61 5 5
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.13 0.28 -9999 0 -0.66 84 84
CDK2/Cyclin E1 -0.034 0.062 -9999 0 -10000 0 0
MAPK3 0.009 0.055 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.009 0.055 -9999 0 -10000 0 0
PTP4A1 -0.083 0.23 -9999 0 -0.51 84 84
PTP4A3 -0.009 0.08 -9999 0 -0.3 27 27
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.009 0.055 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -10000 0 0
RAC1 -0.019 0.095 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.078 0.22 -9999 0 -0.61 4 4
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.01 0.036 -9999 0 -10000 0 0
RHOC -0.019 0.095 -9999 0 -10000 0 0
RHOA -0.019 0.095 -9999 0 -10000 0 0
cell motility -0.018 0.1 -9999 0 -0.27 9 9
PRL-1/alpha Tubulin -0.072 0.21 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.022 0.094 -9999 0 -0.72 5 5
ROCK1 -0.018 0.1 -9999 0 -0.27 9 9
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.082 0.23 -9999 0 -0.51 84 84
ATF5 -0.001 0.064 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.001 0.096 0.52 10 -10000 0 10
PI3K Class IB/PDE3B -0.001 0.096 -10000 0 -0.52 10 10
PDE3B -0.001 0.096 -10000 0 -0.52 10 10
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.5 27 27
ITGA4 0.006 0.047 -9999 0 -0.3 9 9
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.64 11 11
alpha4/beta1 Integrin -0.005 0.029 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.003 0.079 -9999 0 -0.37 5 5
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0.013 0 -9999 0 -10000 0 0
AKT2 0.013 0 -9999 0 -10000 0 0
STXBP4 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.036 0.074 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
TBC1D4 -0.056 0.22 -9999 0 -0.66 44 44
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
SNARE/Synip 0 0 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
ASIP -0.022 0.096 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
GYS1 0.034 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
TRIP10 0.013 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.033 0.096 -9999 0 -10000 0 0
VAMP2 0.013 0 -9999 0 -10000 0 0
SLC2A4 0.037 0.078 -9999 0 -10000 0 0
STX4 0.013 0 -9999 0 -10000 0 0
GSK3B 0.027 0 -9999 0 -10000 0 0
SFN -0.21 0.17 -9999 0 -0.32 254 254
LNPEP -0.012 0.15 -9999 0 -0.86 11 11
YWHAE 0.013 0 -9999 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.058 0.15 -9999 0 -0.46 46 46
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.049 0.12 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.008 0.023 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.06 -9999 0 -10000 0 0
CaM/Ca2+ -0.054 0.14 -9999 0 -0.42 46 46
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.019 0.16 -9999 0 -0.43 46 46
AKT1 -0.002 0.14 -9999 0 -10000 0 0
MAP2K1 -0.004 0.15 -9999 0 -0.46 2 2
MAP3K11 -0.015 0.16 -9999 0 -0.43 46 46
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.071 -9999 0 -0.66 1 1
Rap1/GTP -0.04 0.1 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.061 0.16 -9999 0 -0.48 46 46
CEBPB 0.017 0.17 -9999 0 -0.78 2 2
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.055 0.14 -9999 0 -10000 0 0
STAT1 -0.018 0.16 -9999 0 -0.42 46 46
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.1 0.28 -9999 0 -0.84 47 47
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
STAT1 (dimer)/PIAS1 -0.045 0.14 -9999 0 -0.42 2 2
CEBPB/PTGES2/Cbp/p300 -0.035 0.08 -9999 0 -0.43 2 2
mol:Ca2+ -0.058 0.15 -9999 0 -0.45 46 46
MAPK3 0.01 0.14 -9999 0 -0.49 2 2
STAT1 (dimer) -0.031 0.08 -9999 0 -10000 0 0
MAPK1 0.01 0.14 -9999 0 -0.49 2 2
JAK2 0.009 0.014 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.014 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.013 0.18 -9999 0 -0.66 19 19
SMAD7 0.041 0.055 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.048 0.12 -9999 0 -10000 0 0
PI3K -0.053 0.13 -9999 0 -0.47 1 1
IFNG -0.1 0.28 -9999 0 -0.84 47 47
apoptosis 0.011 0.13 -9999 0 -0.44 19 19
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.003 0.062 -9999 0 -10000 0 0
CAMK2B 0.002 0.099 -9999 0 -0.86 5 5
FRAP1 0.002 0.14 -9999 0 -10000 0 0
PRKCD 0.001 0.14 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.024 0.06 -9999 0 -10000 0 0
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0 -9999 0 -10000 0 0
IRF1 0.03 0.12 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.053 0.13 -9999 0 -10000 0 0
SOCS1 0.004 0.027 -9999 0 -10000 0 0
mol:GDP -0.046 0.12 -9999 0 -10000 0 0
CASP1 0.039 0.063 -9999 0 -0.36 2 2
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.041 0.057 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.051 0.13 -9999 0 -0.45 1 1
RAP1/GDP -0.04 0.1 -9999 0 -10000 0 0
CBL -0.016 0.15 -9999 0 -0.43 46 46
MAP3K1 -0.015 0.16 -9999 0 -0.43 46 46
PIAS1 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.024 0.06 -9999 0 -10000 0 0
PTPN11 -0.025 0.16 -9999 0 -0.45 46 46
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.003 0.14 -10000 0 -0.73 8 8
BAG4 0.011 0.045 -10000 0 -0.86 1 1
PKC zeta/ceramide -0.017 0.04 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.038 0.19 -10000 0 -0.68 28 28
BAX -0.005 0.019 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.023 0.009 -10000 0 -10000 0 0
BAD -0.017 0.041 -10000 0 -10000 0 0
SMPD1 -0.006 0.097 -10000 0 -0.27 43 43
RB1 -0.017 0.041 -10000 0 -10000 0 0
FADD/Caspase 8 0.009 0.14 -10000 0 -0.69 8 8
MAP2K4 -0.009 0.038 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.01 0.049 -10000 0 -0.59 1 1
EGF -0.11 0.3 -10000 0 -0.86 51 51
mol:ceramide -0.028 0.043 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.022 0.035 -10000 0 -0.66 1 1
ASAH1 0.011 0.045 -10000 0 -0.86 1 1
negative regulation of cell cycle -0.017 0.04 -10000 0 -10000 0 0
cell proliferation -0.096 0.17 -10000 0 -0.41 81 81
BID -0.017 0.09 -10000 0 -0.39 9 9
MAP3K1 -0.017 0.041 -10000 0 -10000 0 0
EIF2A 0 0.037 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.003 0.046 -10000 0 -0.54 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.003 0.046 -10000 0 -0.54 1 1
Cathepsin D/ceramide -0.017 0.04 -10000 0 -10000 0 0
FADD -0.003 0.14 -10000 0 -0.73 8 8
KSR1 -0.018 0.051 -10000 0 -0.63 1 1
MAPK8 -0.005 0.046 -10000 0 -0.39 2 2
PRKRA -0.017 0.041 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.18 0.36 -10000 0 -0.82 86 86
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.043 -10000 0 -10000 0 0
CTSD 0.013 0 -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 -0.084 0.19 -10000 0 -0.44 81 81
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.022 0.035 -10000 0 -0.66 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.012 0.15 -10000 0 -0.64 11 11
TNFR1A/BAG4/TNF-alpha -0.069 0.18 -10000 0 -0.57 44 44
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.001 0.046 -10000 0 -0.56 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.001 0.05 0.18 18 -10000 0 18
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.034 -10000 0 -0.66 1 1
EIF2AK2 -0.009 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.067 0.18 -10000 0 -0.57 43 43
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.079 -10000 0 -0.34 8 8
MAP2K2 -0.001 0.046 -10000 0 -0.56 1 1
SMPD3 -0.012 0.12 -10000 0 -0.31 47 47
TNF -0.09 0.28 -10000 0 -0.8 48 48
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.022 0.11 0.28 51 -10000 0 51
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.001 0.05 0.18 18 -10000 0 18
BCL2 -0.038 0.2 -10000 0 -0.86 22 22
IL2 signaling events mediated by PI3K

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
BCL2L1 0.012 0.12 -10000 0 -0.6 8 8
UGCG -0.03 0.15 -10000 0 -0.83 12 12
AKT1/mTOR/p70S6K/Hsp90/TERT 0.027 0.12 -10000 0 -0.41 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.009 0.15 -10000 0 -0.81 12 12
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.051 0.12 -10000 0 -0.45 21 21
FRAP1 0.013 0.18 -10000 0 -0.48 32 32
FOXO3 0.027 0.15 -10000 0 -0.62 10 10
AKT1 0.019 0.16 -10000 0 -0.54 19 19
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 -0.005 0.021 -10000 0 -10000 0 0
SGMS1 -0.005 0.021 -10000 0 -10000 0 0
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 0.021 0.032 -10000 0 -0.59 1 1
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation 0.008 0.14 -10000 0 -0.44 21 21
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.022 0.036 -10000 0 -0.67 1 1
RPS6KB1 0.017 0.041 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 5 5
JAK3 -0.058 0.13 -10000 0 -0.3 89 89
PIK3R1 0.015 0.004 -10000 0 -10000 0 0
JAK1 0.015 0.004 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MYC 0.017 0.2 -10000 0 -0.92 12 12
MYB -0.016 0.2 -10000 0 -1.4 8 8
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.014 0.16 -10000 0 -0.6 15 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.037 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.014 0.15 -10000 0 -0.58 15 15
Rac1/GDP 0.026 0.03 -10000 0 -0.54 1 1
T cell proliferation 0.023 0.14 -10000 0 -0.56 13 13
SHC1 0.013 0.004 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.011 -10000 0 -0.053 12 12
PRKCZ 0.022 0.15 -10000 0 -0.58 13 13
NF kappa B1 p50/RelA -0.049 0.12 -10000 0 -0.53 11 11
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.002 0.13 -10000 0 -0.61 10 10
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.04 0.18 -10000 0 -0.86 16 16
IL2RB -0.015 0.14 -10000 0 -0.54 21 21
TERT 0 0.031 -10000 0 -10000 0 0
E2F1 -0.003 0.075 -10000 0 -0.45 8 8
SOS1 0.013 0.004 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.025 12 -10000 0 12
PTPN11 0.013 0.004 -10000 0 -10000 0 0
IL2RG -0.05 0.2 -10000 0 -0.51 47 47
actin cytoskeleton organization 0.023 0.14 -10000 0 -0.56 13 13
GRB2 0.013 0.004 -10000 0 -10000 0 0
IL2 0.007 0.007 -10000 0 -10000 0 0
PIK3CA 0.013 0.045 -10000 0 -0.86 1 1
Rac1/GTP 0.032 0.03 -10000 0 -0.51 1 1
LCK -0.01 0.11 -10000 0 -0.39 23 23
BCL2 -0.009 0.26 -10000 0 -0.84 29 29
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.011 0.045 -9999 0 -0.86 1 1
Caspase 8 (4 units) -0.022 0.061 -9999 0 -10000 0 0
NEF -0.012 0.053 -9999 0 -0.22 19 19
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 -0.005 0.2 -9999 0 -0.86 19 19
CYCS -0.008 0.099 -9999 0 -0.39 3 3
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.043 0.2 -9999 0 -0.73 24 24
MAP2K7 0.023 0.08 -9999 0 -10000 0 0
protein ubiquitination 0.039 0.087 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.013 0 -9999 0 -10000 0 0
BID -0.017 0.1 -9999 0 -0.31 21 21
NF-kappa-B/RelA/I kappa B alpha -0.021 0.078 -9999 0 -0.35 19 19
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.011 0.045 -9999 0 -0.86 1 1
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.021 0.078 -9999 0 -0.35 19 19
MAPK8 0.028 0.083 -9999 0 -0.42 2 2
APAF1 0.013 0 -9999 0 -10000 0 0
TRAF1 0.013 0 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.096 -9999 0 -0.31 26 26
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.024 0.1 -9999 0 -0.38 8 8
CHUK 0.039 0.092 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.025 -9999 0 -0.49 1 1
TCRz/NEF -0.063 0.18 -9999 0 -0.53 42 42
TNF -0.09 0.28 -9999 0 -0.8 48 48
FASLG -0.073 0.29 -9999 0 -0.83 42 42
NFKB1 0.009 0.029 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.069 0.18 -9999 0 -0.57 44 44
CASP6 -0.003 0.046 -9999 0 -10000 0 0
CASP7 0.028 0.17 -9999 0 -0.64 19 19
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.028 0.17 -9999 0 -0.64 19 19
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.034 -9999 0 -0.66 1 1
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.032 0.099 -9999 0 -0.35 5 5
APAF-1/Caspase 9 -0.045 0.12 -9999 0 -0.54 19 19
BCL2 0.007 0.13 -9999 0 -0.42 23 23
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.022 0.13 -9999 0 -0.71 12 12
PTK2 -0.034 0.14 -9999 0 -0.65 17 17
positive regulation of JNK cascade -0.016 0.073 -9999 0 -0.35 17 17
CDC42/GDP 0.036 0.11 -9999 0 -0.48 17 17
Rac1/GDP 0.038 0.11 -9999 0 -0.48 17 17
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.02 0.091 -9999 0 -0.44 17 17
nectin-3/I-afadin -0.03 0.14 -9999 0 -0.66 17 17
RAPGEF1 0.03 0.13 -9999 0 -0.55 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.02 0.15 -9999 0 -0.65 17 17
PDGFB-D/PDGFRB 0.013 0 -9999 0 -10000 0 0
TLN1 0.021 0.075 -9999 0 -0.97 1 1
Rap1/GTP -0.018 0.079 -9999 0 -0.38 17 17
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.03 0.14 -9999 0 -0.66 17 17
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.031 0.14 -9999 0 -0.61 17 17
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
PI3K -0.023 0.11 -9999 0 -0.52 17 17
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.004 0.027 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.017 0.077 -9999 0 -0.37 17 17
PVRL1 0.006 0.045 -9999 0 -0.3 8 8
PVRL3 -0.026 0.18 -9999 0 -0.86 17 17
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
CLDN1 -0.25 0.16 -9999 0 -0.86 10 10
JAM-A/CLDN1 -0.13 0.13 -9999 0 -0.58 27 27
SRC -0.035 0.16 -9999 0 -0.74 17 17
ITGB3 -0.015 0.15 -9999 0 -0.86 12 12
nectin-1(dimer)/I-afadin/I-afadin -0.004 0.027 -9999 0 -10000 0 0
FARP2 0.025 0.14 -9999 0 -0.6 17 17
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.026 0.12 -9999 0 -0.57 17 17
nectin-1/I-afadin -0.004 0.027 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
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 -0.029 0.12 -9999 0 -0.57 17 17
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.016 0.073 -9999 0 -0.35 17 17
alphaV/beta3 Integrin/Talin 0.018 0.14 -9999 0 -0.63 12 12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.014 0.08 -9999 0 -0.31 17 17
VAV2 0.024 0.14 -9999 0 -0.61 17 17
RAP1/GDP -0.02 0.092 -9999 0 -0.44 17 17
ITGAV 0.011 0.045 -9999 0 -0.86 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.026 0.12 -9999 0 -0.57 17 17
nectin-3(dimer)/I-afadin/I-afadin -0.03 0.14 -9999 0 -0.66 17 17
Rac1/GTP -0.021 0.095 -9999 0 -0.46 17 17
PTPRM -0.016 0.083 -9999 0 -0.35 17 17
E-cadherin/beta catenin/alpha catenin -0.002 0.013 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.009 0.076 -9999 0 -0.66 5 5
PDGFRB 0.013 0.005 -9999 0 -10000 0 0
SPHK1 -0.008 0.022 -9999 0 -10000 0 0
mol:S1P -0.01 0.027 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.009 0.15 -9999 0 -0.39 41 41
GNAO1 -0.013 0.14 -9999 0 -0.87 10 10
PDGFB-D/PDGFRB/PLCgamma1 0.02 0.14 -9999 0 -0.6 7 7
PLCG1 0.016 0.14 -9999 0 -0.62 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0.005 -9999 0 -10000 0 0
GNAI2 0.013 0.005 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GNAI1 0.011 0.045 -9999 0 -0.86 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.01 0.068 -9999 0 -0.58 5 5
S1P1/S1P -0.018 0.061 -9999 0 -0.44 5 5
negative regulation of cAMP metabolic process 0.01 0.15 -9999 0 -0.38 41 41
MAPK3 -0.001 0.21 -9999 0 -0.58 38 38
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.005 0.077 -9999 0 -0.86 3 3
PLCB2 0.027 0.07 -9999 0 -0.39 5 5
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.015 0.051 -9999 0 -0.37 5 5
receptor internalization -0.017 0.057 -9999 0 -0.41 5 5
PTGS2 -0.051 0.36 -9999 0 -1.1 38 38
Rac1/GTP -0.015 0.051 -9999 0 -0.37 5 5
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.008 0.063 -9999 0 -0.86 2 2
negative regulation of T cell proliferation 0.01 0.15 -9999 0 -0.38 41 41
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0.005 -9999 0 -10000 0 0
MAPK1 -0.001 0.21 -9999 0 -0.58 38 38
S1P1/S1P/PDGFB-D/PDGFRB 0.029 0.081 -9999 0 -0.44 5 5
ABCC1 0.013 0.002 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.012 0.016 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.033 0.059 -10000 0 -0.33 5 5
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.011 0.084 0.24 4 -0.42 10 14
RAR alpha/9cRA/Cyclin H -0.025 0.094 -10000 0 -0.4 22 22
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.029 0.066 -10000 0 -0.32 10 10
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.019 0.077 -10000 0 -0.48 4 4
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.01 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.022 0.17 -10000 0 -0.64 23 23
NCOA2 -0.04 0.21 -10000 0 -0.86 23 23
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.012 0.016 -10000 0 -10000 0 0
RARG 0.014 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.013 0.002 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.009 0.063 -10000 0 -0.86 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.041 0.16 -10000 0 -0.66 22 22
RARA 0.006 0.084 -10000 0 -0.32 24 24
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.009 0.12 -10000 0 -0.34 30 30
PRKCA -0.034 0.2 -10000 0 -0.86 22 22
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.033 0.17 -10000 0 -0.67 23 23
RXRG -0.11 0.12 -10000 0 -0.55 24 24
RXRA 0.011 0.093 -10000 0 -0.34 24 24
RXRB -0.002 0.11 -10000 0 -0.46 22 22
VDR/Vit D3/DNA -0.001 0.01 -10000 0 -10000 0 0
RBP1 -0.002 0.1 -10000 0 -0.61 9 9
CRBP1/9-cic-RA -0.011 0.079 -10000 0 -0.67 5 5
RARB -0.008 0.14 -10000 0 -0.86 10 10
PRKCG 0.008 0.023 -10000 0 -0.3 2 2
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.03 0.18 -10000 0 -0.7 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.011 0.15 -10000 0 -0.56 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.081 -10000 0 -0.43 5 5
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.033 0.17 -10000 0 -0.67 23 23
positive regulation of DNA binding -0.023 0.089 -10000 0 -0.37 22 22
NRIP1 -0.028 0.16 -10000 0 -0.61 22 22
RXRs/RARs -0.042 0.17 -10000 0 -0.66 23 23
RXRs/RXRs/DNA/9cRA -0.052 0.16 -10000 0 -0.69 22 22
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.012 0.046 -10000 0 -10000 0 0
CCNH 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.032 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.07 0.008 -9999 0 -10000 0 0
EGFR 0.001 0.099 -9999 0 -0.86 5 5
EPHA2 0.011 0.023 -9999 0 -0.3 2 2
MYO6 0.04 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -9999 0 -10000 0 0
AQP5 -0.04 0.14 -9999 0 -0.61 21 21
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.034 0.069 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.86 51 51
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.075 0.2 -9999 0 -0.61 46 46
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GDP 0 0.004 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.009 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.051 0.02 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.04 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.007 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.068 0.16 -9999 0 -0.45 56 56
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.047 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.013 0 -9999 0 -10000 0 0
IGF1 -0.18 0.36 -9999 0 -0.82 86 86
DIAPH1 0 0.002 -9999 0 -10000 0 0
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0.004 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.047 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.044 0.037 -9999 0 -0.45 2 2
Ephrin A1/EPHA2 0 0.006 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.034 0.07 -9999 0 -10000 0 0
HGF/MET -0.099 0.17 -9999 0 -0.51 51 51
HGF -0.1 0.3 -9999 0 -0.86 51 51
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.033 0 -9999 0 -10000 0 0
actin cable formation 0.086 0.014 -9999 0 -10000 0 0
KIAA1543 0.046 0.025 -9999 0 -0.44 1 1
KIFC3 0.04 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.04 0.007 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.04 0 -9999 0 -10000 0 0
PIP5K1C 0.04 0 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0 0.003 -9999 0 -10000 0 0
adherens junction assembly 0.063 0.023 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.098 0.18 -9999 0 -0.45 81 81
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.11 0.15 -9999 0 -0.3 154 154
PLEKHA7 0.039 0.026 -9999 0 -0.47 1 1
mol:GTP -0.001 0.009 -9999 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.066 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.032 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.047 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.033 0 -9999 0 -10000 0 0
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.024 0.09 -9999 0 -10000 0 0
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.31 0.48 -9999 0 -0.98 120 120
IFNAR2 0.014 0.003 -9999 0 -10000 0 0
AKT1 -0.001 0.07 -9999 0 -0.3 17 17
ER alpha/Oestrogen -0.045 0.14 -9999 0 -0.67 17 17
NFX1/SIN3/HDAC complex 0.048 0.019 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.86 51 51
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.005 0.01 -9999 0 -10000 0 0
TERT/c-Abl -0.037 0.065 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.029 0.1 -9999 0 -0.3 48 48
WRN 0.013 0 -9999 0 -10000 0 0
SP1 0.014 0.003 -9999 0 -10000 0 0
SP3 0.013 0.002 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.03 0.05 -9999 0 -10000 0 0
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.025 0.091 -9999 0 -10000 0 0
CCND1 -0.017 0.09 -9999 0 -10000 0 0
MAX 0.013 0.002 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
RBBP4 0.013 0 -9999 0 -10000 0 0
TERF2 0 0.005 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
Telomerase/911 0.034 0.021 -9999 0 -10000 0 0
CDKN1B -0.04 0.19 -9999 0 -0.55 46 46
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.011 0.045 -9999 0 -0.86 1 1
TRF2/PARP2 0 0.005 -9999 0 -10000 0 0
UBE3A 0.013 0.002 -9999 0 -10000 0 0
JUN -0.19 0.37 -9999 0 -0.86 88 88
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.003 0.005 -9999 0 -10000 0 0
FOS -0.22 0.39 -9999 0 -0.86 103 103
IFN-gamma/IRF1 -0.085 0.21 -9999 0 -0.64 47 47
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.012 0.016 -9999 0 -0.3 1 1
Telomerase 0.013 0.071 -9999 0 -0.48 4 4
IRF1 0.017 0.016 -9999 0 -0.29 1 1
ESR1 -0.049 0.19 -9999 0 -0.51 45 45
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.002 0.03 -9999 0 -0.59 1 1
ubiquitin-dependent protein catabolic process 0.053 0.018 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.053 0.018 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC2 0.014 0.003 -9999 0 -10000 0 0
ATM -0.002 0.03 -9999 0 -0.58 1 1
SMAD3 0.019 0.029 -9999 0 -10000 0 0
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0.002 -9999 0 -10000 0 0
MRE11A 0.013 0 -9999 0 -10000 0 0
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.031 0.058 -9999 0 -10000 0 0
NR2F2 0.011 0.003 -9999 0 -10000 0 0
MAPK3 0.016 0.006 -9999 0 -10000 0 0
MAPK1 0.016 0.006 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.007 0.042 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.002 0.03 -9999 0 -0.58 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.002 0.099 -9999 0 -0.86 5 5
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.1 0.23 -9999 0 -0.66 56 56
MYC -0.005 0.12 -9999 0 -0.86 8 8
IL2 0.005 0.007 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.007 0.042 -9999 0 -10000 0 0
TRF2/BLM 0 0.01 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.033 0.064 -9999 0 -10000 0 0
SP1/HDAC2 0.007 0.012 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.03 0.05 -9999 0 -10000 0 0
Smad3/Myc 0.006 0.091 -9999 0 -0.59 8 8
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.1 0.28 -9999 0 -0.84 46 46
Telomerase/PinX1 -0.03 0.05 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.02 0.036 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.03 0.05 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0.008 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.005 -9999 0 -10000 0 0
TRF2/WRN 0 0.005 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.03 0.05 -9999 0 -10000 0 0
E2F1 -0.084 0.14 -9999 0 -0.3 119 119
ZNFX1 0.013 0 -9999 0 -10000 0 0
PIF1 0.001 0.093 -9999 0 -0.62 7 7
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.019 0.086 -10000 0 -0.43 9 9
ACTA1 0.014 0.1 -10000 0 -0.52 9 9
NUMA1 0.019 0.086 -10000 0 -0.43 9 9
SPTAN1 0.016 0.1 -10000 0 -0.56 7 7
LIMK1 0.016 0.1 -10000 0 -0.56 7 7
BIRC3 -0.038 0.19 -10000 0 -0.68 28 28
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.013 0 -10000 0 -10000 0 0
CASP10 0 0.12 -10000 0 -0.63 9 9
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.019 0.086 -10000 0 -0.43 9 9
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.016 0.1 -10000 0 -0.55 7 7
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN 0.016 0.1 -10000 0 -0.57 7 7
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.056 0.22 -10000 0 -0.66 45 45
BID -0.012 0.066 -10000 0 -0.3 9 9
MAP3K1 0.014 0.04 -10000 0 -0.22 1 1
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.013 0.11 -10000 0 -0.54 8 8
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.016 0.05 -10000 0 -0.23 16 16
neuron apoptosis 0.023 0.015 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.022 0.098 -10000 0 -0.54 7 7
APAF1 0.013 0 -10000 0 -10000 0 0
CASP6 0.021 0.064 -10000 0 -0.4 4 4
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD 0.023 0.099 -10000 0 -0.54 7 7
CASP7 0.009 0.081 0.35 19 -10000 0 19
KRT18 0.016 0.018 -10000 0 -10000 0 0
apoptosis 0.029 0.091 -10000 0 -0.47 7 7
DFFA 0.016 0.1 -10000 0 -0.56 7 7
DFFB 0.016 0.1 -10000 0 -0.56 7 7
PARP1 0.016 0.05 0.23 16 -10000 0 16
actin filament polymerization -0.023 0.095 0.52 7 -10000 0 7
TNF -0.09 0.28 -10000 0 -0.8 48 48
CYCS 0.005 0.044 -10000 0 -0.22 9 9
SATB1 0.029 0.061 -10000 0 -0.38 4 4
SLK 0.016 0.1 -10000 0 -0.56 7 7
p15 BID/BAX -0.003 0.058 -10000 0 -0.34 2 2
CASP2 0.006 0.12 -10000 0 -0.47 8 8
JNK cascade -0.014 0.04 0.22 1 -10000 0 1
CASP3 0.008 0.11 -10000 0 -0.55 9 9
LMNB2 0.02 0.078 -10000 0 -0.32 4 4
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.013 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.029 0.12 -10000 0 -0.52 19 19
negative regulation of DNA binding -0.055 0.22 -10000 0 -0.65 45 45
stress fiber formation 0.016 0.1 -10000 0 -0.55 7 7
GZMB -0.013 0.13 -10000 0 -0.62 13 13
CASP1 0.014 0.037 -10000 0 -0.46 2 2
LMNB1 0.02 0.078 -10000 0 -0.32 4 4
APP 0.023 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM 0.023 0.09 -10000 0 -0.46 7 7
LMNA 0.02 0.078 -10000 0 -0.32 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.003 0.12 -10000 0 -0.31 43 43
LRDD 0.013 0 -10000 0 -10000 0 0
SREBF1 0.015 0.1 -10000 0 -0.56 7 7
APAF-1/Caspase 9 0.005 0.037 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.019 0.085 -10000 0 -0.43 9 9
CFL2 0.023 0.098 -10000 0 -0.53 7 7
GAS2 0.009 0.12 -10000 0 -0.55 12 12
positive regulation of apoptosis 0.022 0.08 -10000 0 -0.31 4 4
PRF1 0 0.094 -10000 0 -0.86 4 4
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 -0.005 0.12 -10000 0 -0.86 8 8
ANTXR2 0.011 0.045 -10000 0 -0.86 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.016 -10000 0 -0.1 9 9
monocyte activation -0.045 0.16 -10000 0 -0.48 45 45
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.002 0.014 -10000 0 -10000 0 0
MAP2K7 -0.002 0.014 -10000 0 -10000 0 0
MAP2K6 -0.011 0.068 -10000 0 -0.54 6 6
CYAA 0.004 0.08 -10000 0 -0.51 9 9
MAP2K4 -0.002 0.014 -10000 0 -10000 0 0
IL1B -0.023 0.13 -10000 0 -0.48 28 28
Channel -0.013 0.082 -10000 0 -0.54 9 9
NLRP1 -0.005 0.04 -10000 0 -0.52 2 2
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.016 0.1 9 -10000 0 9
MAPK3 -0.002 0.014 -10000 0 -10000 0 0
MAPK1 -0.002 0.014 -10000 0 -10000 0 0
PGR -0.024 0.087 -10000 0 -0.47 11 11
PA/Cellular Receptors -0.014 0.089 -10000 0 -0.58 9 9
apoptosis -0.003 0.016 -10000 0 -0.1 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.079 -10000 0 -0.5 9 9
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.09 0.28 -10000 0 -0.8 48 48
VCAM1 -0.045 0.17 -10000 0 -0.48 45 45
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.023 0.21 1 -10000 0 1
IL18 -0.008 0.083 -10000 0 -0.42 10 10
negative regulation of macrophage activation -0.003 0.016 -10000 0 -0.1 9 9
LEF -0.003 0.016 -10000 0 -0.11 9 9
CASP1 -0.004 0.022 -10000 0 -0.23 2 2
mol:cAMP -0.003 0.019 -10000 0 -10000 0 0
necrosis -0.003 0.016 -10000 0 -0.1 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.012 0.078 -10000 0 -0.51 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.046 0.056 -10000 0 -0.39 5 5
NFATC2 -0.009 0.082 -10000 0 -0.27 14 14
NFATC3 0.018 0.012 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.006 0.093 -10000 0 -0.3 24 24
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.002 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.027 0.091 -10000 0 -0.61 4 4
BCL2/BAX -0.038 0.16 -10000 0 -0.66 22 22
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.007 -10000 0 -10000 0 0
CaM/Ca2+ -0.002 0.007 -10000 0 -10000 0 0
BAX 0.013 0 -10000 0 -10000 0 0
MAPK14 0.009 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.01 0.088 -10000 0 -0.55 2 2
Calcineurin A alpha-beta B1/BCL2 -0.037 0.2 -10000 0 -0.85 22 22
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.01 0.087 0.54 2 -10000 0 2
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.012 0.001 -10000 0 -10000 0 0
SFN -0.21 0.17 -10000 0 -0.32 254 254
MAP3K8 0 0.089 -10000 0 -0.86 4 4
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.11 0.16 -10000 0 -0.48 13 13
CABIN1 0.006 0.094 -10000 0 -0.3 24 24
CALM1 0.009 0.006 -10000 0 -10000 0 0
RAN 0.012 0.001 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.004 0.1 -10000 0 -0.86 4 4
mol:Ca2+ -0.005 0.01 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 0.005 0.063 -10000 0 -0.86 2 2
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.008 0.045 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.003 0.005 -10000 0 -10000 0 0
CASP3 0.009 0.006 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.012 0.048 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.042 -10000 0 -10000 0 0
PRKCB -0.028 0.11 -10000 0 -0.31 48 48
PRKCE 0.006 0.077 -10000 0 -0.86 3 3
JNK2/NFAT4 0.021 0.014 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.012 0.001 -10000 0 -10000 0 0
PRKCZ 0.009 0.006 -10000 0 -10000 0 0
PRKCA -0.038 0.2 -10000 0 -0.86 22 22
PRKCG 0.005 0.023 -10000 0 -0.3 2 2
PRKCQ -0.001 0.11 -10000 0 -0.86 6 6
FKBP38/BCL2 -0.038 0.16 -10000 0 -0.66 22 22
EP300 0.009 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.038 0.068 -10000 0 -0.42 2 2
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.01 0.065 -10000 0 -0.59 4 4
NFATc/ERK1 0.052 0.053 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.026 0.089 -10000 0 -0.6 4 4
NR4A1 -0.19 0.38 -10000 0 -0.76 116 116
GSK3B 0.009 0.006 -10000 0 -10000 0 0
positive T cell selection 0.018 0.012 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.029 0.052 -10000 0 -0.49 1 1
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.009 0.006 -10000 0 -10000 0 0
AKAP5 0.013 0 -10000 0 -10000 0 0
MEF2D 0.009 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.04 0.059 -10000 0 -0.37 5 5
CREBBP 0.009 0.007 -10000 0 -10000 0 0
BCL2 -0.038 0.2 -10000 0 -0.86 22 22
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.001 0.032 0.31 1 -0.55 1 2
DAPP1 -0.057 0.14 -10000 0 -0.56 6 6
Src family/SYK family/BLNK-LAT/BTK-ITK -0.064 0.18 -10000 0 -0.58 14 14
mol:DAG -0.008 0.096 -10000 0 -0.28 10 10
HRAS 0.013 0.016 -10000 0 -0.29 1 1
RAP1A 0.014 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.025 0.035 -10000 0 -0.47 1 1
PLCG2 0.013 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.015 -10000 0 -10000 0 0
ARF1/GTP 0 0.022 0.29 1 -10000 0 1
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP 0 0.014 -10000 0 -10000 0 0
ADAP1 0 0.014 -10000 0 -10000 0 0
ARAP3 0 0.015 0.27 1 -10000 0 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.013 0 -10000 0 -10000 0 0
ARHGEF6 0.013 0 -10000 0 -10000 0 0
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.014 0.001 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.01 0.032 -10000 0 -10000 0 0
mol:Ca2+ 0.005 0.054 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.16 0.16 -10000 0 -0.3 210 210
ZAP70 -0.028 0.17 -10000 0 -0.66 23 23
mol:IP3 0.002 0.072 -10000 0 -10000 0 0
LYN 0.013 0 -10000 0 -10000 0 0
ARF1/GDP 0.025 0.035 -10000 0 -0.47 1 1
RhoA/GDP 0 0.021 0.29 1 -10000 0 1
PDK1/Src/Hsp90 -0.002 0.03 -10000 0 -0.57 1 1
BLNK 0.013 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.041 0.037 -10000 0 -10000 0 0
SRC 0.012 0.016 -10000 0 -10000 0 0
PLEKHA2 0.018 0.046 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.043 -10000 0 -0.83 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0.001 0.016 0.31 1 -10000 0 1
RhoA/GTP 0 0.014 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.056 0.16 -10000 0 -0.63 10 10
BLK -0.26 0.39 -10000 0 -0.86 113 113
PDPK1 0.011 0.045 -10000 0 -0.86 1 1
CYTH1 0 0.014 -10000 0 -10000 0 0
HCK -0.007 0.076 -10000 0 -0.3 24 24
CYTH3 -0.001 0.032 -10000 0 -0.57 1 1
CYTH2 0 0.014 -10000 0 -10000 0 0
KRAS 0.014 0.001 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.011 0.086 -10000 0 -0.62 7 7
SGK1 -0.012 0.097 -10000 0 -0.69 7 7
INPP5D -0.01 0.081 -10000 0 -0.3 28 28
mol:GDP 0.017 0.037 -10000 0 -0.5 1 1
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.013 0 -10000 0 -10000 0 0
ARF6/GDP 0 0.021 0.3 1 -10000 0 1
mol:PI-3-4-5-P3 0.001 0.02 0.37 1 -10000 0 1
ARAP3/RAP1A/GTP 0 0.014 -10000 0 -10000 0 0
VAV1 -0.013 0.1 -10000 0 -0.86 2 2
mol:PI-3-4-P2 0.008 0.056 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0 0.005 -10000 0 -10000 0 0
PLEKHA1 0.018 0.046 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.035 -10000 0 -0.47 1 1
LAT 0.003 0.09 -10000 0 -0.74 5 5
Rac1/GTP -0.002 0.053 -10000 0 -0.62 1 1
ITK -0.058 0.15 -10000 0 -0.46 45 45
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.019 0.13 -10000 0 -0.41 10 10
LCK -0.012 0.11 -10000 0 -0.4 23 23
BTK -0.011 0.05 -10000 0 -0.46 3 3
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.046 0.14 -9999 0 -0.46 38 38
TC10/GTP -0.003 0.033 -9999 0 -0.45 2 2
Insulin Receptor/Insulin/IRS1/Shp2 -0.051 0.16 -9999 0 -0.54 36 36
HRAS 0.012 0.016 -9999 0 -0.3 1 1
APS homodimer 0.012 0.016 -9999 0 -0.3 1 1
GRB14 -0.022 0.17 -9999 0 -0.86 15 15
FOXO3 -0.022 0.1 -9999 0 -0.72 7 7
AKT1 -0.009 0.16 -9999 0 -0.79 1 1
INSR 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 0.008 0.063 -9999 0 -0.86 2 2
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.037 0 -9999 0 -10000 0 0
CAV1 -0.038 0.18 -9999 0 -0.51 47 47
CBL/APS/CAP/Crk-II/C3G -0.003 0.036 -9999 0 -0.49 2 2
Insulin Receptor/Insulin/IRS1/NCK2 -0.051 0.16 -9999 0 -0.54 36 36
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.046 0.14 -9999 0 -0.47 37 37
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.009 0.098 -9999 0 -10000 0 0
RPS6KB1 0.001 0.15 -9999 0 -0.69 1 1
PARD6A 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.052 0.13 -9999 0 -0.68 1 1
HRAS/GTP -0.044 0.12 -9999 0 -0.52 1 1
Insulin Receptor 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.048 0.15 -9999 0 -0.5 36 36
PRKCI -0.014 0.034 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.061 0.15 -9999 0 -0.88 1 1
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K -0.047 0.14 -9999 0 -0.48 37 37
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.01 -9999 0 -10000 0 0
AKT2 -0.009 0.16 -9999 0 -0.79 1 1
PRKCZ -0.014 0.034 -9999 0 -10000 0 0
SH2B2 0.012 0.016 -9999 0 -0.3 1 1
SHC/SHIP -0.024 0.15 -9999 0 -0.48 36 36
F2RL2 -0.076 0.14 -9999 0 -0.86 1 1
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.003 0.038 -9999 0 -0.52 2 2
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D -0.033 0.16 -9999 0 -0.51 36 36
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.023 0.14 -9999 0 -1.1 7 7
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.07 0.26 -9999 0 -0.86 36 36
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.033 0.16 -9999 0 -0.5 36 36
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 0 0.15 -9999 0 -0.55 3 3
PTPRA 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.011 0.045 -9999 0 -0.86 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.001 0.11 -9999 0 -0.34 36 36
Insulin Receptor/Insulin/IRS1 -0.052 0.16 -9999 0 -0.55 36 36
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.033 0.056 -9999 0 -0.5 1 1
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.028 0.13 -10000 0 -0.66 16 16
ATM 0.011 0.045 -10000 0 -0.86 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.013 0 -10000 0 -10000 0 0
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.026 0.025 -10000 0 -0.45 1 1
protein ubiquitination -0.022 0.1 -10000 0 -0.48 17 17
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.013 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.011 -10000 0 -10000 0 0
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.013 0 -10000 0 -10000 0 0
CCNE1 0.013 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 0 0 -10000 0 -10000 0 0
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.028 0.13 -10000 0 -0.66 16 16
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA -0.003 0.068 -10000 0 -10000 0 0
DNA repair 0.055 0.096 -10000 0 -10000 0 0
BRCA1/BARD1/ubiquitin -0.028 0.13 -10000 0 -0.66 16 16
BARD1/DNA-PK -0.022 0.1 -10000 0 -0.52 16 16
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.028 0.13 0.66 16 -10000 0 16
BRCA1/BARD1/CTIP/M/R/N Complex 0.025 0.082 -10000 0 -0.35 17 17
BRCA1/BACH1/BARD1/TopBP1 -0.024 0.12 -10000 0 -0.57 16 16
BRCA1/BARD1/P53 -0.022 0.1 -10000 0 -0.52 16 16
BARD1/CSTF1/BRCA1 -0.024 0.12 -10000 0 -0.57 16 16
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 -0.024 0.18 -10000 0 -0.86 16 16
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.024 0.12 -10000 0 -0.57 16 16
BRCA1/BARD1/UbcH7 -0.024 0.12 -10000 0 -0.57 16 16
BRCA1/BARD1/RAD51/PCNA -0.023 0.11 -10000 0 -0.52 16 16
BARD1/DNA-PK/P53 -0.021 0.098 -10000 0 -0.49 16 16
BRCA1/BARD1/Ubiquitin -0.028 0.13 -10000 0 -0.66 16 16
BRCA1/BARD1/CTIP -0.023 0.11 -10000 0 -0.52 17 17
FA complex 0.038 0.02 -10000 0 -10000 0 0
BARD1/EWS -0.028 0.13 -10000 0 -0.66 16 16
RBBP8 0.022 0.035 -10000 0 -0.66 1 1
TP53 0.013 0 -10000 0 -10000 0 0
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.022 0.1 0.52 16 -10000 0 16
BRCA1/BARD1 -0.022 0.1 -10000 0 -0.49 17 17
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.028 0.14 -10000 0 -0.67 16 16
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.01 0.032 -10000 0 -0.3 4 4
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.028 0.13 -10000 0 -0.66 16 16
EWSR1 0.013 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.006 0.045 -9999 0 -0.3 8 8
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.015 -9999 0 -10000 0 0
GNAO1 -0.013 0.14 -9999 0 -0.86 10 10
mol:Sphinganine-1-P 0.019 0.031 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.007 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.013 0 -9999 0 -10000 0 0
S1PR2 0.012 0.016 -9999 0 -0.3 1 1
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.01 -9999 0 -10000 0 0
S1PR5 0.01 0.032 -9999 0 -0.3 4 4
S1PR4 0.009 0.035 -9999 0 -0.3 5 5
GNAI1 0.011 0.045 -9999 0 -0.86 1 1
S1P/S1P5/G12 -0.002 0.015 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.051 0.15 -9999 0 -0.38 17 17
S1P/S1P4/Gi 0.032 0.063 -9999 0 -0.33 10 10
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNA14 -0.2 0.37 -9999 0 -0.86 91 91
GNA15 -0.017 0.099 -9999 0 -0.31 35 35
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.006 0.077 -9999 0 -0.86 3 3
ABCC1 0.013 0 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.039 0.01 -10000 0 -10000 0 0
CDKN1A 0.034 0.027 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
FOXO3 0.039 0.01 -10000 0 -10000 0 0
AKT1 0 0.008 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
AKT3 0.017 0.025 -10000 0 -0.46 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.039 0.01 -10000 0 -10000 0 0
AKT1/ASK1 -0.002 0.024 -10000 0 -0.46 1 1
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.013 0 -10000 0 -10000 0 0
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.024 0.44 1 -10000 0 1
TSC1 0.039 0.01 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
AKT1/RAF1 0.038 0.01 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
mol:GDP 0 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.039 0.01 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.044 0.19 -10000 0 -0.58 44 44
MAP3K5 0.011 0.045 -10000 0 -0.86 1 1
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.012 0.032 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
AKT1S1 0.039 0.01 -10000 0 -10000 0 0
CASP9 0.039 0.01 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.009 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.002 0.03 -10000 0 -0.57 1 1
YWHAE 0.013 0 -10000 0 -10000 0 0
SRC 0.012 0.016 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.004 0.024 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.003 -10000 0 -10000 0 0
CHUK 0.039 0.01 -10000 0 -10000 0 0
BAD/BCL-XL 0.051 0.009 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.017 0.025 -10000 0 -0.46 1 1
FOXO1-3a-4/14-3-3 family 0.025 0.037 -10000 0 -10000 0 0
PDPK1 0.011 0.045 -10000 0 -0.86 1 1
MDM2 0.039 0.01 -10000 0 -10000 0 0
MAPKKK cascade -0.037 0.009 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0.006 -10000 0 -10000 0 0
TSC1/TSC2 0.046 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.006 -10000 0 -10000 0 0
glucose import -0.054 0.21 -10000 0 -0.56 55 55
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.033 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.055 0.22 -10000 0 -0.56 55 55
GSK3A 0.039 0.01 -10000 0 -10000 0 0
FOXO1 0.039 0.01 -10000 0 -10000 0 0
GSK3B 0.039 0.01 -10000 0 -10000 0 0
SFN -0.21 0.17 -10000 0 -0.32 254 254
G1/S transition of mitotic cell cycle 0.046 0.009 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0 0.047 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
KPNA1 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.027 0.055 -9999 0 -0.29 11 11
GNAO1 -0.011 0.14 -9999 0 -0.85 10 10
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.003 0.018 -9999 0 -10000 0 0
AKT3 0.049 0.041 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0 -9999 0 -10000 0 0
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
GNAI1 0.012 0.045 -9999 0 -0.86 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.015 0 -9999 0 -10000 0 0
S1PR2 0.012 0.016 -9999 0 -0.3 1 1
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.037 0.063 -9999 0 -0.33 10 10
MAPK3 0.043 0.06 -9999 0 -10000 0 0
MAPK1 0.043 0.06 -9999 0 -10000 0 0
JAK2 0.046 0.06 -9999 0 -10000 0 0
CXCR4 0.042 0.062 -9999 0 -10000 0 0
FLT1 0.016 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.043 0.06 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.037 0.063 -9999 0 -0.33 10 10
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.009 0.049 -9999 0 -0.29 10 10
VEGFA 0.012 0.063 -9999 0 -0.86 2 2
S1P/S1P2/Gi 0.032 0.064 -9999 0 -0.33 11 11
VEGFR1 homodimer/VEGFA homodimer 0.025 0.05 -9999 0 -0.66 2 2
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.069 0.17 -9999 0 -0.36 94 94
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.015 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.2 0.37 -9999 0 -0.86 91 91
GNA15 -0.017 0.099 -9999 0 -0.31 35 35
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.006 0.077 -9999 0 -0.86 3 3
Rac1/GTP -0.009 0.049 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.18 0.36 -9999 0 -0.86 84 84
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.013 0 -9999 0 -10000 0 0
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.022 -9999 0 -10000 0 0
HIF1A 0.022 0.023 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.035 -9999 0 -0.49 2 2
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.12 0.15 -9999 0 -10000 0 0
ARNT/IPAS -0.15 0.28 -9999 0 -0.66 84 84
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.022 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.022 -9999 0 -10000 0 0
PHD1-3/OS9 -0.016 0.079 -9999 0 -0.52 8 8
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.012 -9999 0 -10000 0 0
VHL 0.008 0.063 -9999 0 -0.86 2 2
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.022 -9999 0 -10000 0 0
EGLN3 -0.019 0.14 -9999 0 -0.48 25 25
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.046 -9999 0 -0.59 2 2
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.03 0.069 -9999 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.034 0.11 0.34 1 -0.36 37 38
FRAP1 0.009 0.023 -10000 0 -10000 0 0
AKT1 -0.028 0.091 0.25 1 -0.68 1 2
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.022 0.068 -10000 0 -0.54 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.02 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.018 0.058 -10000 0 -0.49 1 1
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.026 0.13 -10000 0 -0.43 36 36
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.007 0.024 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.013 0.054 -10000 0 -0.38 1 1
MAP3K5 0.01 0.024 -10000 0 -0.46 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.01 0.024 -10000 0 -0.46 1 1
mol:LY294002 0 0.001 0.001 1 -0.002 36 37
EIF4B 0.021 0.049 -10000 0 -0.32 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.011 0.034 -10000 0 -0.3 1 1
eIF4E/eIF4G1/eIF4A1 -0.001 0.006 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.016 0.12 -10000 0 -0.39 37 37
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.036 0.18 1 -0.27 1 2
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.018 0.057 -10000 0 -0.48 1 1
mol:Amino Acids 0 0.001 0.001 1 -0.002 36 37
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.032 0.1 0.26 1 -0.89 1 2
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.016 0.037 -10000 0 -0.63 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.023 0.073 -10000 0 -0.59 1 1
tumor necrosis factor receptor activity 0 0.001 0.002 36 -0.001 1 37
RPS6 0.013 0 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.036 0.14 -10000 0 -0.47 36 36
INS 0 0 -10000 0 -10000 0 0
PTEN 0.01 0.044 -10000 0 -0.85 1 1
PDK2 -0.031 0.097 0.26 1 -0.32 37 38
EIF4EBP1 0.012 0.009 -10000 0 -10000 0 0
PIK3CA 0.011 0.045 -10000 0 -0.86 1 1
PPP2R5D 0.017 0.022 -10000 0 -10000 0 0
peptide biosynthetic process 0.018 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -0.004 1 2
EEF2 0.018 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.018 0.008 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.01 0.047 -9999 0 -0.58 2 2
positive regulation of NF-kappaB transcription factor activity -0.002 0.035 -9999 0 -0.66 1 1
MAP2K4 0.048 0.021 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.011 0.045 -9999 0 -0.86 1 1
SMPD1 -0.001 0.016 -9999 0 -0.3 1 1
IKBKG 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.002 0.035 -9999 0 -0.66 1 1
TRAIL/TRAILR3 -0.059 0.093 -9999 0 -0.66 1 1
TRAIL/TRAILR1 -0.004 0.049 -9999 0 -0.66 2 2
TRAIL/TRAILR4 -0.002 0.035 -9999 0 -0.66 1 1
TRAIL/TRAILR1/DAP3/GTP -0.003 0.039 -9999 0 -0.53 2 2
IKK complex -0.001 0.012 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.037 -9999 0 -0.66 1 1
MAP3K1 -0.001 0.019 -9999 0 -0.33 1 1
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.011 0.044 -9999 0 -0.85 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.037 0.028 -9999 0 -0.34 2 2
CFLAR 0.013 0 -9999 0 -10000 0 0
MAPK1 0.022 0.037 -9999 0 -0.66 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP -0.003 0.036 -9999 0 -0.49 2 2
mol:ceramide -0.001 0.016 -9999 0 -0.3 1 1
FADD 0.013 0 -9999 0 -10000 0 0
MAPK8 0.052 0.042 -9999 0 -0.45 2 2
TRAF2 0.013 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.08 0.14 -9999 0 -0.3 114 114
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.003 0.042 -9999 0 -0.57 2 2
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.002 0.032 -9999 0 -0.55 1 1
JNK cascade -0.002 0.035 -9999 0 -0.66 1 1
TRAIL (trimer) 0.01 0.047 -9999 0 -0.58 2 2
TNFRSF10C -0.081 0.14 -9999 0 -0.3 114 114
TRAIL/TRAILR1/DAP3/GTP/FADD -0.003 0.036 -9999 0 -0.5 2 2
TRAIL/TRAILR2/FADD -0.002 0.03 -9999 0 -0.57 1 1
cell death -0.001 0.016 -9999 0 -0.3 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.038 0.02 -9999 0 -0.34 1 1
TRAILR2 (trimer) 0.013 0 -9999 0 -10000 0 0
CASP8 0 0.009 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.002 0.026 -9999 0 -0.49 1 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.004 0.13 -10000 0 -0.5 11 11
BAG4 0.011 0.045 -10000 0 -0.86 1 1
BAD 0.018 0.046 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.038 0.19 -10000 0 -0.68 28 28
BAX 0.018 0.046 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.004 0.034 -10000 0 -0.12 8 8
IKBKB 0.013 0.12 -10000 0 -0.53 8 8
MAP2K2 0.028 0.055 -10000 0 -0.39 1 1
MAP2K1 0.028 0.055 -10000 0 -0.39 1 1
SMPD1 0.01 0.034 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.013 0.13 -10000 0 -0.55 8 8
MAP2K4 0.024 0.047 -10000 0 -10000 0 0
protein ubiquitination 0.014 0.13 -10000 0 -0.54 8 8
EnzymeConsortium:2.7.1.37 0.031 0.06 -10000 0 -0.39 1 1
response to UV 0 0.001 -10000 0 -0.003 1 1
RAF1 0.022 0.055 -10000 0 -0.42 1 1
CRADD 0.013 0 -10000 0 -10000 0 0
mol:ceramide 0.01 0.048 -10000 0 -0.17 8 8
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.017 0.047 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.03 0.054 -10000 0 -0.38 1 1
MAPK1 0.03 0.054 -10000 0 -0.38 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.004 0.13 -10000 0 -0.57 8 8
KSR1 0.016 0.054 -10000 0 -0.45 1 1
MAPK8 0.028 0.056 -10000 0 -0.45 2 2
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.013 0.12 -10000 0 -0.53 8 8
TNF R/SODD -0.002 0.034 -10000 0 -0.66 1 1
TNF -0.09 0.28 -10000 0 -0.8 48 48
CYCS 0.026 0.054 0.16 18 -10000 0 18
IKBKG 0.013 0.12 -10000 0 -0.53 8 8
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.004 0.14 -10000 0 -0.45 19 19
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.026 0.054 0.16 18 -10000 0 18
TNF/TNF R/SODD -0.068 0.18 -10000 0 -0.57 44 44
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.033 -10000 0 -10000 0 0
NSMAF 0.005 0.13 -10000 0 -0.56 8 8
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 1 1
BCL2 -0.038 0.2 -10000 0 -0.86 22 22
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.069 0.057 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.026 0.072 -9999 0 -0.66 1 1
NFKBIA 0.049 0 -9999 0 -10000 0 0
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG -0.004 0.017 -9999 0 -10000 0 0
IKK complex/A20 -0.049 0.13 -9999 0 -0.42 43 43
NEMO/A20/RIP2 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.042 0.038 -9999 0 -0.45 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.012 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.002 0.029 -9999 0 -0.57 1 1
NOD2 -0.03 0.11 -9999 0 -0.86 1 1
NFKB1 0.017 0 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.013 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.011 0.045 -9999 0 -0.86 1 1
TNF/TNFR1A -0.078 0.21 -9999 0 -0.66 43 43
TRAF6 0.011 0.045 -9999 0 -0.86 1 1
PRKCA -0.038 0.2 -9999 0 -0.86 22 22
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.09 0.28 -9999 0 -0.8 48 48
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.049 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex -0.002 0.013 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.024 0.097 -9999 0 -0.41 22 22
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.057 0.12 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.029 -10000 0 -10000 0 0
myoblast fusion 0.03 0.045 -10000 0 -10000 0 0
mol:GTP -0.026 0.038 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.086 0.1 0.55 1 -10000 0 1
ARF1/GTP -0.015 0.021 -10000 0 -10000 0 0
mol:GM1 -0.011 0.032 -10000 0 -10000 0 0
mol:Choline 0.012 0.028 -10000 0 -10000 0 0
lamellipodium assembly -0.003 0.061 -10000 0 -10000 0 0
MAPK3 -0.016 0.062 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.086 0.1 -10000 0 -0.55 1 1
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.03 0.045 -10000 0 -10000 0 0
ARF1/GDP 0.004 0.056 -10000 0 -10000 0 0
ARF6 -0.002 0.021 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.16 0.16 -10000 0 -0.3 210 210
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.016 0.062 -10000 0 -10000 0 0
actin filament bundle formation 0.024 0.036 -10000 0 -10000 0 0
KALRN -0.006 0.049 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.024 0.036 -10000 0 -10000 0 0
NME1 0.01 0.007 -10000 0 -10000 0 0
Rac1/GDP -0.024 0.036 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.026 0.037 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.003 0.061 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.026 0.037 -10000 0 -10000 0 0
ARF6/GTP -0.026 0.038 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.021 -10000 0 -10000 0 0
mol:GDP -0.011 0.062 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.009 0.013 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0.001 0.032 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.003 0.061 -10000 0 -10000 0 0
ruffle organization 0.012 0.029 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.026 0.037 -10000 0 -10000 0 0
PLD2 0.001 0.032 -10000 0 -10000 0 0
PIP5K1A 0.012 0.029 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.012 0.028 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.062 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.061 0.17 -9999 0 -0.53 43 43
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.05 0.14 -9999 0 -0.43 43 43
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones -0.025 0.068 -9999 0 -10000 0 0
YY1/LSF 0.027 0.052 -9999 0 -0.56 3 3
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.044 0.12 -9999 0 -0.38 43 43
I kappa B alpha/HDAC1 -0.028 0.082 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA -0.003 0.12 -9999 0 -0.33 43 43
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.028 0.082 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.05 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.003 0.11 -9999 0 -0.3 43 43
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.012 0.016 -9999 0 -0.3 1 1
GATA1 0.009 0.006 -9999 0 -10000 0 0
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.06 0.002 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.013 0 -9999 0 -10000 0 0
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA -0.008 0.1 -9999 0 -0.29 43 43
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.045 0.016 -9999 0 -10000 0 0
SIN3 complex -0.001 0.027 -9999 0 -0.52 1 1
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.011 0.045 -9999 0 -0.86 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.024 0.072 -9999 0 -10000 0 0
YY1/HDAC2 0.032 0 -9999 0 -10000 0 0
YY1/HDAC1 0.032 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.05 0 -9999 0 -10000 0 0
PPARG -0.06 0.16 -9999 0 -0.47 47 47
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.028 0.082 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 -0.008 0.1 -9999 0 -10000 0 0
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.032 0 -9999 0 -10000 0 0
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0 -9999 0 -10000 0 0
STAT3 0.027 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.004 0.045 -9999 0 -0.51 3 3
YY1/SAP30/HDAC1 -0.001 0.026 -9999 0 -0.51 1 1
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.027 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.1 -9999 0 -0.29 43 43
histone deacetylation 0.05 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.025 0.073 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.029 0.082 -9999 0 -10000 0 0
GATA1/HDAC1 0 0 -9999 0 -10000 0 0
GATA1/HDAC3 -0.03 0.083 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.078 0.21 -9999 0 -0.66 43 43
SIN3/HDAC complex/Mad/Max 0.049 0.013 -9999 0 -10000 0 0
NuRD Complex 0.059 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.024 0.067 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 0 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.09 0.28 -9999 0 -0.8 48 48
negative regulation of cell growth 0.049 0.013 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.05 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.052 0.14 -9999 0 -0.46 43 43
SIN3/HDAC complex/NCoR1 0.047 0.013 -9999 0 -10000 0 0
TFCP2 0.006 0.077 -9999 0 -0.86 3 3
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.013 0 -9999 0 -10000 0 0
MBD2 0.013 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.039 0.016 -9999 0 -10000 0 0
PLK1 0.11 0.094 -9999 0 -10000 0 0
CDKN1B 0.15 0.033 -9999 0 -10000 0 0
FOXO3 0.11 0.094 -9999 0 -10000 0 0
KAT2B 0.025 0.009 -9999 0 -10000 0 0
FOXO1/SIRT1 0.011 0.026 -9999 0 -10000 0 0
CAT 0.11 0.087 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.028 0.01 -9999 0 -10000 0 0
FOXO1 0.042 0.011 -9999 0 -10000 0 0
MAPK10 0.044 0.006 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.038 -9999 0 -0.47 1 1
response to oxidative stress 0.015 0.012 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.015 0.058 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.015 0.001 -9999 0 -10000 0 0
BCL2L11 0.041 0.026 -9999 0 -10000 0 0
FOXO1/SKP2 0.042 0.029 -9999 0 -0.49 1 1
mol:GDP 0.015 0.012 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.13 0.034 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.037 -9999 0 -10000 0 0
MST1 0.022 0.048 -9999 0 -0.84 1 1
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.013 0.058 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.042 0.041 -9999 0 -0.52 2 2
MAPK9 0.044 0.006 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.007 0.02 -9999 0 -10000 0 0
SOD2 0.16 0.046 -9999 0 -10000 0 0
RBL2 0.12 0.098 -9999 0 -1.2 1 1
RAL/GDP 0.033 0.012 -9999 0 -10000 0 0
CHUK 0.025 0.009 -9999 0 -10000 0 0
Ran/GTP 0.015 0.001 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.042 0.009 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.069 0.4 -9999 0 -1.5 25 25
SKP2 0.011 0.045 -9999 0 -0.86 1 1
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.025 0.009 -9999 0 -10000 0 0
CCNB1 0.11 0.087 -9999 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.004 0.033 -9999 0 -0.41 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.029 -9999 0 -0.49 1 1
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.009 0.12 -9999 0 -0.84 7 7
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.025 0.002 -9999 0 -10000 0 0
ZFAND5 0.11 0.033 -9999 0 -10000 0 0
SFN -0.21 0.17 -9999 0 -0.32 254 254
CDK2 0.013 0.002 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.016 0.059 -9999 0 -10000 0 0
CREBBP 0.013 0.002 -9999 0 -10000 0 0
FBXO32 0.11 0.089 -9999 0 -10000 0 0
BCL6 0.12 0.097 -9999 0 -1.2 1 1
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.006 0.021 -10000 0 -10000 0 0
AES 0.005 0.018 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.031 0.18 -10000 0 -0.66 25 25
TLE1 0 0.063 -10000 0 -0.83 2 2
MACF1 0.013 0 -10000 0 -10000 0 0
CTNNB1 0.047 0.042 -10000 0 -10000 0 0
WIF1 -0.033 0.1 -10000 0 -0.3 47 47
beta catenin/RanBP3 0.02 0.089 0.37 19 -10000 0 19
KREMEN2 -0.01 0.081 -10000 0 -10000 0 0
DKK1 -0.034 0.12 -10000 0 -0.32 54 54
beta catenin/beta TrCP1 0.052 0.04 -10000 0 -10000 0 0
FZD1 0.013 0.001 -10000 0 -10000 0 0
AXIN2 -0.047 0.31 -10000 0 -1.6 14 14
AXIN1 0.013 0 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.018 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.063 0.038 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.007 0.033 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.058 0.018 -10000 0 -10000 0 0
HNF1A 0.005 0.019 -10000 0 -10000 0 0
CTBP1 0.005 0.02 -10000 0 -10000 0 0
MYC -0.024 0.24 -10000 0 -1.6 8 8
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.038 0.13 -10000 0 -0.6 16 16
NKD1 -0.02 0.16 -10000 0 -0.75 16 16
TCF4 0.005 0.019 -10000 0 -10000 0 0
TCF3 0.005 0.019 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.001 0.011 -10000 0 -10000 0 0
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.028 0.11 0.46 21 -10000 0 21
LEF1 0 0.045 -10000 0 -0.3 7 7
DVL1 0.014 0.026 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.069 0.065 -10000 0 -0.53 2 2
DKK1/LRP6/Kremen 2 -0.034 0.079 -10000 0 -0.65 2 2
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.006 0.021 -10000 0 -10000 0 0
NLK 0.013 0.004 -10000 0 -10000 0 0
CCND1 0 0.069 -10000 0 -0.46 2 2
WNT1 0.008 0.028 -10000 0 -0.3 3 3
GSK3A 0.013 0 -10000 0 -10000 0 0
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.032 0.066 0.37 13 -10000 0 13
APC 0.038 0.015 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.034 0.035 -10000 0 -10000 0 0
CREBBP 0.005 0.019 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0.081 -9999 0 -0.44 10 10
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.011 0.045 -9999 0 -0.86 1 1
ITGA4 0.006 0.047 -9999 0 -0.3 9 9
alpha4/beta7 Integrin/MAdCAM1 -0.032 0.094 -9999 0 -0.52 10 10
EPO 0.006 0.017 -9999 0 -0.3 1 1
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.64 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.005 0.029 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.003 0.022 -9999 0 -10000 0 0
lamellipodium assembly 0 0.028 -9999 0 -0.52 1 1
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
PI3K -0.002 0.034 -9999 0 -0.66 1 1
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 -0.003 0.014 -9999 0 -10000 0 0
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.014 0.082 -9999 0 -0.3 29 29
cell adhesion -0.032 0.093 -9999 0 -0.52 10 10
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.024 0.06 -9999 0 -0.52 3 3
ITGB7 -0.024 0.15 -9999 0 -0.5 27 27
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.01 0.06 -9999 0 -0.57 3 3
p130Cas/Crk/Dock1 -0.008 0.049 -9999 0 -0.44 4 4
VCAM1 0.001 0.086 -9999 0 -0.48 9 9
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.003 0.018 -9999 0 -10000 0 0
BCAR1 0.033 0.057 -9999 0 -0.48 3 3
EPOR 0.01 0.032 -9999 0 -0.3 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.029 -9999 0 -0.54 1 1
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.009 0.05 0.3 10 -10000 0 10
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.002 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.013 0.14 -10000 0 -0.86 10 10
RhoA/GTP -0.01 0.05 -10000 0 -0.3 10 10
negative regulation of cAMP metabolic process 0.024 0.063 -10000 0 -0.33 11 11
GNAZ 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 0.01 0.032 -10000 0 -0.3 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.024 0.064 -10000 0 -0.34 11 11
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.011 0.045 -10000 0 -0.86 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.022 0.13 -9999 0 -0.71 12 12
AKT1 0.083 0.084 -9999 0 -0.61 4 4
PTK2B 0.034 0.14 -9999 0 -0.92 5 5
VEGFR2 homodimer/Frs2 -0.009 0.089 -9999 0 -0.85 4 4
CAV1 -0.012 0.15 -9999 0 -0.86 11 11
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.011 0.09 -9999 0 -0.69 6 6
endothelial cell proliferation 0.071 0.1 -9999 0 -0.63 3 3
mol:Ca2+ 0.05 0.088 -9999 0 -0.79 3 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.01 0.085 -9999 0 -0.84 3 3
RP11-342D11.1 0.041 0.088 -9999 0 -0.63 6 6
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer -0.005 0.053 -9999 0 -0.52 4 4
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.008 0.063 -9999 0 -0.86 2 2
HRAS/GDP -0.008 0.068 -9999 0 -0.68 3 3
SH2D2A -0.039 0.19 -9999 0 -0.86 19 19
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.008 0.064 -9999 0 -0.62 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.039 0.15 -9999 0 -0.58 24 24
VEGFR1 homodimer 0.013 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.009 0.077 -9999 0 -0.76 3 3
GRB10 0.05 0.088 -9999 0 -0.79 3 3
PTPN11 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.01 0.081 -9999 0 -0.81 3 3
HRAS 0.012 0.016 -9999 0 -0.3 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.039 0.082 -9999 0 -0.51 5 5
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.01 0.084 -9999 0 -0.82 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.004 0.089 -9999 0 -0.86 4 4
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.011 0.09 -9999 0 -0.69 6 6
mol:GDP -0.009 0.074 -9999 0 -0.73 3 3
mol:NADP 0.075 0.064 -9999 0 -0.51 3 3
eNOS/Hsp90 0.078 0.061 -9999 0 -0.48 3 3
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.05 0.089 -9999 0 -0.81 3 3
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.063 -9999 0 -0.85 2 2
VEGFC 0.011 0.045 -9999 0 -0.86 1 1
FAK1/Vinculin 0.056 0.12 -9999 0 -0.78 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.027 0.14 -9999 0 -0.98 5 5
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.018 0.057 -9999 0 -0.5 4 4
mol:L-citrulline 0.075 0.064 -9999 0 -0.51 3 3
ITGAV 0.011 0.045 -9999 0 -0.86 1 1
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.01 0.085 -9999 0 -0.69 5 5
VEGFR2 homodimer/VEGFA homodimer -0.011 0.089 -9999 0 -0.69 6 6
VEGFR2/3 heterodimer -0.015 0.12 -9999 0 -0.8 7 7
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.053 0.092 -9999 0 -0.68 5 5
VEGFR2 homodimer 0.028 0.1 -9999 0 -0.95 4 4
FLT1 0.013 0 -9999 0 -10000 0 0
NEDD4 0.015 0 -9999 0 -10000 0 0
MAPK3 0.04 0.096 -9999 0 -0.7 4 4
MAPK1 0.04 0.096 -9999 0 -0.7 4 4
VEGFA145/NRP2 -0.022 0.072 -9999 0 -0.66 2 2
VEGFR1/2 heterodimer -0.009 0.089 -9999 0 -0.85 4 4
KDR 0.028 0.1 -9999 0 -0.95 4 4
VEGFA165/NRP1/VEGFR2 homodimer -0.018 0.087 -9999 0 -0.85 3 3
SRC 0.012 0.016 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.043 0.097 -9999 0 -0.72 4 4
PI3K -0.011 0.081 -9999 0 -0.77 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.011 0.09 -9999 0 -0.69 6 6
FES 0.05 0.091 -9999 0 -0.82 3 3
GAB1 -0.01 0.082 -9999 0 -0.79 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.011 0.09 -9999 0 -0.69 6 6
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.066 0.097 -9999 0 -0.57 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.011 0.09 -9999 0 -0.69 6 6
PI3K/GAB1 0.084 0.082 -9999 0 -0.64 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.01 0.081 -9999 0 -0.81 3 3
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.015 0.12 -9999 0 -0.81 7 7
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.05 0.091 -9999 0 -0.82 3 3
actin cytoskeleton reorganization -0.039 0.14 -9999 0 -0.57 24 24
PTK2 0.05 0.13 -9999 0 -0.76 7 7
EDG1 0.041 0.088 -9999 0 -0.63 6 6
mol:DAG 0.05 0.089 -9999 0 -0.81 3 3
CaM/Ca2+ -0.009 0.075 -9999 0 -0.74 3 3
MAP2K3 0.052 0.1 -9999 0 -0.78 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.01 0.084 -9999 0 -0.84 3 3
PLCG1 0.05 0.091 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.011 0.085 -9999 0 -0.84 3 3
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.011 0.09 -9999 0 -0.69 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.011 0.09 -9999 0 -0.69 6 6
cell migration 0.08 0.1 -9999 0 -0.67 4 4
mol:PI-3-4-5-P3 -0.01 0.074 -9999 0 -0.69 3 3
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.009 0.077 -9999 0 -0.75 3 3
mol:NO 0.075 0.064 -9999 0 -0.51 3 3
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.008 0.068 -9999 0 -0.68 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.01 0.085 -9999 0 -0.84 3 3
VHL 0.008 0.063 -9999 0 -0.86 2 2
ITGB3 -0.015 0.15 -9999 0 -0.86 12 12
NOS3 0.077 0.072 -9999 0 -0.59 3 3
VEGFR2 homodimer/VEGFA homodimer/Sck -0.014 0.097 -9999 0 -0.65 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.027 0.15 -9999 0 -0.9 3 3
PRKCB 0.038 0.1 -9999 0 -0.73 4 4
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.04 0.088 -9999 0 -0.64 6 6
VEGFR1/2 heterodimer/VEGFA homodimer -0.011 0.09 -9999 0 -0.69 6 6
VEGFA165/NRP2 -0.022 0.072 -9999 0 -0.66 2 2
MAPKKK cascade -0.008 0.068 -9999 0 -0.68 3 3
NRP2 -0.017 0.092 -9999 0 -10000 0 0
VEGFC homodimer 0.011 0.044 -9999 0 -0.85 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.056 0.12 -9999 0 -0.78 5 5
MAP3K13 0.044 0.1 -9999 0 -0.82 3 3
PDPK1 0.075 0.084 -9999 0 -0.63 4 4
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.044 0.007 -9999 0 -10000 0 0
KLHL20 -0.008 0.022 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.072 0.009 -9999 0 -10000 0 0
ENAH 0.044 0.007 -9999 0 -10000 0 0
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.002 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.003 0.015 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.019 0.087 -9999 0 -0.52 10 10
RAPGEF1 0.057 0.006 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.051 0.007 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.026 0.11 -9999 0 -0.66 10 10
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.044 0.007 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.011 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.073 0.069 -9999 0 -0.53 1 1
PI3K -0.001 0.014 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0 0 -9999 0 -10000 0 0
TIAM1 -0.16 0.16 -9999 0 -0.3 210 210
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0.008 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.072 0.009 -9999 0 -10000 0 0
actin cytoskeleton organization -0.006 0.016 -9999 0 -10000 0 0
CDC42/GDP 0.072 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.026 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.5 27 27
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.071 0.01 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.002 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.032 -9999 0 -0.14 10 10
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.044 0.007 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0.002 -9999 0 -10000 0 0
WASF2 0.002 0.009 -9999 0 -10000 0 0
Rap1/GTP 0 0.003 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.081 -9999 0 -0.49 10 10
CCND1 0.017 0.038 -9999 0 -0.17 10 10
VAV2 0.055 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.002 -9999 0 -10000 0 0
adherens junction assembly 0.044 0.001 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.016 0.076 -9999 0 -0.46 10 10
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.043 0.01 -9999 0 -10000 0 0
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
Rac1/GTP 0.004 0.038 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.013 0.14 -9999 0 -0.86 10 10
CDC42/GTP -0.01 0.05 -9999 0 -0.3 10 10
PLCG1 0.031 0.06 -9999 0 -0.32 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.009 0.05 -9999 0 -0.3 10 10
S1PR5 0.01 0.032 -9999 0 -0.3 4 4
S1PR4 0.009 0.035 -9999 0 -0.3 5 5
MAPK3 0.031 0.06 -9999 0 -0.32 10 10
MAPK1 0.031 0.06 -9999 0 -0.32 10 10
S1P/S1P5/Gi 0.024 0.064 -9999 0 -0.34 11 11
GNAI1 0.011 0.045 -9999 0 -0.86 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.002 0.016 -9999 0 -10000 0 0
RHOA 0.032 0.017 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.024 0.064 -9999 0 -0.34 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.002 0.015 -9999 0 -10000 0 0
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.021 0.035 -9999 0 -10000 0 0
CLOCK -0.014 0.15 -9999 0 -0.86 11 11
TIMELESS/CRY2 -0.001 0.06 -9999 0 -10000 0 0
DEC1/BMAL1 -0.027 0.068 -9999 0 -10000 0 0
ATR 0.013 0 -9999 0 -10000 0 0
NR1D1 -0.05 0.12 -9999 0 -10000 0 0
ARNTL -0.029 0.1 -9999 0 -0.32 15 15
TIMELESS -0.008 0.068 -9999 0 -10000 0 0
NPAS2 0.007 0.05 -9999 0 -0.48 3 3
CRY2 0.013 0 -9999 0 -10000 0 0
mol:CO 0.006 0.029 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME -0.006 0.029 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.018 0.13 -9999 0 -0.61 12 12
BMAL1/CLOCK -0.039 0.13 -9999 0 -0.64 6 6
S phase of mitotic cell cycle -0.021 0.035 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.021 0.036 -9999 0 -10000 0 0
mol:NADPH -0.006 0.029 -9999 0 -10000 0 0
PER1/TIMELESS -0.001 0.06 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0.016 -9999 0 -0.3 1 1
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.007 0.015 -9999 0 -10000 0 0
BIRC5 -0.021 0.1 -9999 0 -0.31 39 39
NFKBIA 0.032 0.009 -9999 0 -10000 0 0
CPEB1 -0.051 0.23 -9999 0 -0.86 28 28
AKT1 0.032 0.009 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.003 0.012 -9999 0 -10000 0 0
NDEL1/TACC3 0.003 0.014 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GSK3B 0.012 0.005 -9999 0 -10000 0 0
PAK1/Aurora A 0.007 0.015 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
JUB 0.008 0.063 -9999 0 -0.86 2 2
TPX2 -0.003 0.071 -9999 0 -10000 0 0
TP53 0.008 0.015 -9999 0 -10000 0 0
DLG7 0.021 0.009 -9999 0 -10000 0 0
AURKAIP1 0.013 0 -9999 0 -10000 0 0
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.003 0.015 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.012 -9999 0 -10000 0 0
AURKA 0.026 0.012 -9999 0 -10000 0 0
AURKB -0.013 0.026 -9999 0 -10000 0 0
CDC25B 0.006 0.021 -9999 0 -10000 0 0
G2/M transition checkpoint 0 0.04 -9999 0 -0.53 2 2
mRNA polyadenylation -0.036 0.14 -9999 0 -0.53 28 28
Aurora A/CPEB -0.037 0.14 -9999 0 -0.53 28 28
Aurora A/TACC1/TRAP/chTOG 0.004 0.015 -9999 0 -10000 0 0
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication 0.007 0.015 -9999 0 -10000 0 0
regulation of centrosome cycle 0 0.006 -9999 0 -10000 0 0
spindle assembly 0 0 -9999 0 -10000 0 0
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.011 0.038 -9999 0 -0.47 1 1
CENPA -0.009 0.027 -9999 0 -0.26 3 3
Aurora A/PP2A 0.007 0.015 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.038 0.008 -9999 0 -10000 0 0
negative regulation of DNA binding 0.031 0.007 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0 0.04 -9999 0 -0.53 2 2
mitotic prometaphase 0.005 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.012 -9999 0 -10000 0 0
TACC1 0.013 0 -9999 0 -10000 0 0
TACC3 0.012 0.016 -9999 0 -0.3 1 1
Aurora A/Antizyme1 0.004 0.014 -9999 0 -10000 0 0
Aurora A/RasGAP 0.007 0.015 -9999 0 -10000 0 0
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0.005 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.003 0.071 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.016 0.053 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.059 0.092 -9999 0 -10000 0 0
CRKL 0.043 0.03 -9999 0 -10000 0 0
mol:DAG 0.046 0.039 -9999 0 -10000 0 0
HRAS 0.066 0.028 -9999 0 -10000 0 0
MAPK8 0.031 0.047 -9999 0 -0.55 2 2
RAP1A 0.043 0.03 -9999 0 -10000 0 0
GAB1 0.043 0.03 -9999 0 -10000 0 0
MAPK14 0.034 0.019 -9999 0 -10000 0 0
EPO 0.009 0.017 -9999 0 -10000 0 0
PLCG1 0.023 0.044 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.012 0.032 -9999 0 -0.3 4 4
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.045 0.15 -9999 0 -0.6 27 27
GAB1/SHC/GRB2/SOS1 -0.003 0.011 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.018 0.025 -9999 0 -10000 0 0
IRS2 0.043 0.03 -9999 0 -10000 0 0
STAT1 0.048 0.066 -9999 0 -10000 0 0
STAT5B 0.048 0.054 -9999 0 -10000 0 0
cell proliferation 0.038 0.044 -9999 0 -0.51 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.006 0.016 -9999 0 -10000 0 0
TEC 0.043 0.03 -9999 0 -10000 0 0
SOCS3 -0.05 0.22 -9999 0 -0.84 28 28
STAT1 (dimer) 0.047 0.066 -9999 0 -10000 0 0
JAK2 0.014 0.004 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.047 0.035 -9999 0 -10000 0 0
EPO/EPOR 0.018 0.025 -9999 0 -10000 0 0
LYN 0.014 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.051 0.029 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.012 0.032 -9999 0 -0.3 4 4
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.032 0.023 -9999 0 -10000 0 0
mol:IP3 0.046 0.039 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.008 0.021 -9999 0 -10000 0 0
SH2B3 0.014 0.004 -9999 0 -10000 0 0
NFKB1 0.034 0.019 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.021 0.075 -9999 0 -0.29 27 27
PTPN6 0.036 0.031 -9999 0 -10000 0 0
TEC/VAV2/GRB2 0.025 0.035 -9999 0 -10000 0 0
EPOR 0.012 0.032 -9999 0 -0.3 4 4
INPP5D -0.01 0.081 -9999 0 -0.3 28 28
mol:GDP -0.003 0.011 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.025 0.035 -9999 0 -10000 0 0
VAV2 0.043 0.03 -9999 0 -10000 0 0
CBL 0.043 0.03 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.003 0.013 -9999 0 -10000 0 0
STAT5A 0.048 0.054 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.06 0.085 -9999 0 -10000 0 0
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
BTK 0.028 0.065 -9999 0 -0.46 3 3
BCL2 0.019 0.25 -9999 0 -0.99 22 22
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.032 0 -9999 0 -10000 0 0
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.031 0.009 -9999 0 -10000 0 0
MAPK12 0.022 0.07 -9999 0 -0.52 6 6
CCND1 0.018 0.03 -9999 0 -0.2 6 6
p38 gamma/SNTA1 0.028 0.066 -9999 0 -0.48 6 6
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.022 0.07 -9999 0 -0.52 6 6
MAP2K6 0.016 0.075 -9999 0 -0.57 6 6
MAPT 0.025 0.042 -9999 0 -0.41 2 2
MAPK13 0.024 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.018 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.001 0.005 -9999 0 -10000 0 0
DOCK1 0.011 0.045 -9999 0 -0.86 1 1
ITGA4 0.006 0.047 -9999 0 -0.3 9 9
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.64 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.003 0.022 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.022 0.089 -9999 0 -0.52 10 10
lamellipodium assembly -0.001 0.039 -9999 0 -0.75 1 1
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
PI3K -0.002 0.034 -9999 0 -0.66 1 1
ARF6 0.013 0 -9999 0 -10000 0 0
TLN1 0.013 0 -9999 0 -10000 0 0
PXN 0.024 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.013 -9999 0 -10000 0 0
cell adhesion -0.002 0.016 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.003 0.018 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.5 27 27
ARF6/GDP 0.001 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.008 0.05 -9999 0 -0.49 3 3
p130Cas/Crk/Dock1 -0.002 0.029 -9999 0 -0.57 1 1
VCAM1 0.001 0.086 -9999 0 -0.48 9 9
alpha4/beta1 Integrin/Paxillin/Talin -0.002 0.016 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.016 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.002 0.016 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.002 0.016 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.047 -9999 0 -0.9 1 1
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.001 0.01 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.002 0.12 -9999 0 -0.57 16 16
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.032 -9999 0 -10000 0 0
NFKBIA 0.024 0.036 -9999 0 -0.28 4 4
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0 -9999 0 -10000 0 0
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.024 0.18 -9999 0 -0.86 16 16
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.009 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
NF kappa B1 p50 dimer 0.021 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.024 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.036 -9999 0 -0.28 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.047 0.031 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -10000 0 0
PI3K -0.002 0.034 -9999 0 -0.66 1 1
NF kappa B1 p50/RelA 0.031 0.036 -9999 0 -0.28 4 4
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.029 0.034 -9999 0 -10000 0 0
cell death -0.003 0.022 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.002 0.12 -9999 0 -0.57 16 16
LCK -0.012 0.11 -9999 0 -0.4 23 23
BCL3 0.012 0.016 -9999 0 -0.3 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.001 0.019 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SLAP -0.001 0.01 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0 0.008 -9999 0 -10000 0 0
AKT1 0.06 0.033 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.025 0.033 -9999 0 -10000 0 0
PIK3CA 0.011 0.045 -9999 0 -0.86 1 1
FGR 0.004 0.012 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.029 -9999 0 -10000 0 0
MYC 0.023 0.14 -9999 0 -0.87 8 8
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.018 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB -0.002 0.03 -9999 0 -0.58 1 1
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
GO:0007205 0.021 0.029 -9999 0 -10000 0 0
PTEN 0.011 0.045 -9999 0 -0.86 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 -0.033 0.11 -9999 0 -0.3 56 56
PDGFB-D/PDGFRB/SHP2 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.001 0.01 -9999 0 -10000 0 0
HRAS 0.012 0.016 -9999 0 -0.3 1 1
HIF1A 0.066 0.03 -9999 0 -10000 0 0
GAB1 0.014 0.048 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.02 0.045 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.016 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0 0 -9999 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.004 0.028 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.021 0.029 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.012 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.028 0.068 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.19 0.28 -9999 0 -0.62 113 113
PTPN2 0.013 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.018 0.054 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0 0 -9999 0 -10000 0 0
LCK -0.006 0.066 -9999 0 -0.62 4 4
PDGFRB 0.014 0.002 -9999 0 -10000 0 0
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0.007 0.023 -9999 0 -10000 0 0
ABL1 0.01 0.047 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/CBL 0.01 0.05 -9999 0 -10000 0 0
PTPN1 0.013 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.005 0.05 -9999 0 -0.3 10 10
cell proliferation 0.024 0.12 -9999 0 -0.75 8 8
SLA 0.012 0.016 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.021 0.026 -9999 0 -10000 0 0
SRC 0.007 0.012 -9999 0 -10000 0 0
PI3K -0.003 0.031 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.022 0.052 -9999 0 -10000 0 0
SH2B2 0.012 0.016 -9999 0 -0.3 1 1
PLCgamma1/SPHK1 0.025 0.033 -9999 0 -10000 0 0
LYN 0.007 0.013 -9999 0 -10000 0 0
LRP1 0.011 0.045 -9999 0 -0.86 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0.001 0.006 -9999 0 -10000 0 0
SPHK1 0.007 0.045 -9999 0 -0.3 8 8
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.021 0.029 -9999 0 -10000 0 0
PLCG1 0.021 0.029 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.011 -9999 0 -10000 0 0
YES1 0.005 0.01 -9999 0 -10000 0 0
cell migration -0.001 0.011 -9999 0 -10000 0 0
SHC/Grb2/SOS1 0.001 0.006 -9999 0 -10000 0 0
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
SLC9A3R1 0.011 0.023 -9999 0 -0.3 2 2
NHERF1-2/PDGFRB/PTEN -0.002 0.028 -9999 0 -0.53 1 1
FYN 0.007 0.012 -9999 0 -10000 0 0
DOK1 0.034 0.005 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.01 -9999 0 -10000 0 0
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.031 0.073 -9999 0 -10000 0 0
PRKCD 0.035 0.006 -9999 0 -10000 0 0
FER 0.032 0.041 -9999 0 -0.53 2 2
MAPKKK cascade 0 0.005 -9999 0 -10000 0 0
RASA1 0.035 0.006 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.016 0.02 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0 0 -9999 0 -10000 0 0
chemotaxis 0.01 0.046 -9999 0 -10000 0 0
STAT1-3-5/STAT1-3-5 -0.002 0.013 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.003 0.004 -9999 0 -10000 0 0
PTPRJ 0.013 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.002 0.032 -9999 0 -0.43 2 2
TRAF2/ASK1 -0.002 0.03 -9999 0 -0.58 1 1
ATM 0.011 0.045 -9999 0 -0.86 1 1
MAP2K3 0.028 0.058 -9999 0 -0.54 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.028 0.076 -9999 0 -0.43 5 5
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0 0.1 -9999 0 -0.7 7 7
TXN 0.009 0.006 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GADD45B -0.021 0.17 -9999 0 -0.86 15 15
MAP3K1 0.013 0 -9999 0 -10000 0 0
MAP3K6 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
MAP3K4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.002 0.034 -9999 0 -0.66 1 1
TAK1/TAB family -0.001 0.011 -9999 0 -0.22 1 1
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.007 0.034 -9999 0 -0.48 1 1
TRAF6 0.008 0.025 -9999 0 -0.47 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.001 0.099 -9999 0 -0.86 5 5
CCM2 0.013 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.008 0.066 -9999 0 -0.58 5 5
MAPK11 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.008 0.076 -9999 0 -0.63 5 5
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 -0.027 0.15 -9999 0 -0.48 34 34
TAOK2 0.017 0.025 -9999 0 -0.46 1 1
TAOK3 0.017 0.025 -9999 0 -0.46 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.011 0.045 -9999 0 -0.86 1 1
MAP3K10 0.013 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
TRX/ASK1 0.014 0.031 -9999 0 -0.57 1 1
GADD45/MTK1/MTK1 -0.027 0.12 -9999 0 -0.52 19 19
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.044 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.049 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.021 0 -9999 0 -10000 0 0
MAP3K1 0.013 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.028 0.13 -9999 0 -0.66 16 16
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 -0.024 0.18 -9999 0 -0.86 16 16
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.013 0 -9999 0 -10000 0 0
KPNA2 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0 0 -9999 0 -10000 0 0
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC5 0 0 -9999 0 -10000 0 0
GATA2/HDAC5 -0.001 0.01 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.002 0.029 -9999 0 -0.57 1 1
HDAC9 -0.022 0.098 -9999 0 -0.3 42 42
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.012 0.016 -9999 0 -0.3 1 1
HDAC4/RFXANK 0 0 -9999 0 -10000 0 0
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.013 0 -9999 0 -10000 0 0
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 0 0 -9999 0 -10000 0 0
Histones 0.034 0.024 -9999 0 -10000 0 0
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 -0.004 0.1 -9999 0 -0.86 4 4
Tubulin/HDAC6 -0.006 0.059 -9999 0 -0.57 4 4
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.009 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.007 0.068 -9999 0 -0.66 4 4
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
BCL6/BCoR -0.002 0.034 -9999 0 -0.66 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.01 0.062 -9999 0 -0.57 4 4
HDAC4/ER alpha -0.044 0.14 -9999 0 -0.66 17 17
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.034 0.023 -9999 0 -10000 0 0
cell motility -0.006 0.058 -9999 0 -0.57 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.011 0.045 -9999 0 -0.86 1 1
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.049 0.19 -9999 0 -0.51 45 45
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0 0 -9999 0 -10000 0 0
GNG2 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A 0.004 0.089 -9999 0 -0.86 4 4
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.013 0 -9999 0 -10000 0 0
nuclear import 0 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.009 0.035 -9999 0 -0.3 5 5
PLK4 0.013 0 -9999 0 -10000 0 0
regulation of centriole replication 0.021 0.024 -9999 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.009 0.019 -9999 0 -10000 0 0
BUB1B 0.016 0.028 -9999 0 -10000 0 0
PLK1 0.017 0.01 -9999 0 -0.1 1 1
PLK1S1 0.015 0.006 -9999 0 -10000 0 0
KIF2A 0.024 0.009 -9999 0 -10000 0 0
regulation of mitotic centrosome separation 0.017 0.01 -9999 0 -0.1 1 1
GOLGA2 0.013 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.007 0.078 -9999 0 -10000 0 0
WEE1 0.022 0.01 -9999 0 -10000 0 0
cytokinesis 0.005 0.06 -9999 0 -0.32 1 1
PP2A-alpha B56 -0.014 0.018 -9999 0 -10000 0 0
AURKA 0.016 0.007 -9999 0 -10000 0 0
PICH/PLK1 0.007 0.016 -9999 0 -10000 0 0
CENPE 0.02 0.038 -9999 0 -0.52 1 1
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.009 -9999 0 -10000 0 0
PPP2CA 0.013 0 -9999 0 -10000 0 0
FZR1 0.013 0 -9999 0 -10000 0 0
TPX2 0.008 0.022 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
SPC24 -0.009 0.078 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
CLSPN 0.005 0.027 -9999 0 -10000 0 0
GORASP1 0.013 0 -9999 0 -10000 0 0
metaphase 0.001 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP 0.009 0.006 -9999 0 -0.069 1 1
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
STAG2 0.013 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.003 -9999 0 -10000 0 0
spindle elongation 0.017 0.01 -9999 0 -0.1 1 1
ODF2 0.013 0.001 -9999 0 -10000 0 0
BUB1 -0.022 0.028 -9999 0 -10000 0 0
TPT1 0.015 0.006 -9999 0 -10000 0 0
CDC25C 0.01 0.024 -9999 0 -10000 0 0
CDC25B 0.011 0.027 -9999 0 -0.3 3 3
SGOL1 0.009 0.019 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.006 0.014 -9999 0 -10000 0 0
CDC14B 0.005 0.071 -9999 0 -0.68 4 4
CDC20 0.009 0.035 -9999 0 -10000 0 0
PLK1/PBIP1 0.003 0.022 -9999 0 -10000 0 0
mitosis 0 0.001 -9999 0 -0.023 1 1
FBXO5 0.021 0.008 -9999 0 -10000 0 0
CDC2 0.001 0.001 -9999 0 -10000 0 0
NDC80 -0.044 0.12 -9999 0 -10000 0 0
metaphase plate congression 0.015 0.006 -9999 0 -10000 0 0
ERCC6L 0.008 0.016 -9999 0 -10000 0 0
NLP/gamma Tubulin 0.013 0.007 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.015 0.006 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -9999 0 -0.011 1 1
PPP1R12A 0.013 0 -9999 0 -10000 0 0
interphase 0 0.001 -9999 0 -0.011 1 1
PLK1/PRC1-2 0.002 0.06 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0 0.003 -9999 0 -10000 0 0
RAB1A 0.013 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.02 0.027 -9999 0 -0.5 1 1
mitotic prometaphase 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.036 -9999 0 -0.33 2 2
microtubule-based process -0.007 0.064 -9999 0 -10000 0 0
Golgi organization 0.017 0.01 -9999 0 -0.1 1 1
Cohesin/SA2 0 0.004 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.048 0.12 -9999 0 -0.3 74 74
APC/C/CDC20 0.021 0.022 -9999 0 -10000 0 0
PPP2R1A 0.013 0 -9999 0 -10000 0 0
chromosome segregation 0.003 0.021 -9999 0 -10000 0 0
PRC1 0.013 0 -9999 0 -10000 0 0
ECT2 0.024 0.009 -9999 0 -10000 0 0
C13orf34 0.02 0.028 -9999 0 -0.51 1 1
NUDC 0.015 0.006 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.016 0.028 -9999 0 -10000 0 0
spindle assembly 0.017 0.009 -9999 0 -0.096 1 1
spindle stabilization 0.015 0.006 -9999 0 -10000 0 0
APC/C/HCDH1 0.012 0.062 -9999 0 -0.59 4 4
MKLP2/PLK1 -0.007 0.064 -9999 0 -10000 0 0
CCNB1 0.013 0.001 -9999 0 -10000 0 0
PPP1CB 0.013 0 -9999 0 -10000 0 0
BTRC 0.013 0 -9999 0 -10000 0 0
ROCK2 0.012 0.08 -9999 0 -0.53 8 8
TUBG1 0.015 0.006 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.009 -9999 0 -10000 0 0
MLF1IP 0.008 0.031 -9999 0 -10000 0 0
INCENP 0.012 0.001 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.001 0.022 -9999 0 -10000 0 0
oxygen homeostasis 0.016 0.011 -9999 0 -10000 0 0
TCEB2 0.013 0 -9999 0 -10000 0 0
TCEB1 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.009 0.045 -9999 0 -0.52 1 1
EPO 0.19 0.12 -9999 0 -10000 0 0
FIH (dimer) 0.028 0.011 -9999 0 -10000 0 0
APEX1 0.026 0.011 -9999 0 -10000 0 0
SERPINE1 0.18 0.15 -9999 0 -0.66 1 1
FLT1 0.001 0.017 -9999 0 -10000 0 0
ADORA2A 0.19 0.13 -9999 0 -10000 0 0
germ cell development 0.19 0.13 -9999 0 -10000 0 0
SLC11A2 0.19 0.13 -9999 0 -10000 0 0
BHLHE40 0.18 0.15 -9999 0 -10000 0 0
HIF1AN 0.028 0.011 -9999 0 -10000 0 0
HIF2A/ARNT/SIRT1 0 0.046 -9999 0 -10000 0 0
ETS1 0.029 0.003 -9999 0 -10000 0 0
CITED2 -0.081 0.3 -9999 0 -1.2 26 26
KDR -0.009 0.12 -9999 0 -1.4 3 3
PGK1 0.19 0.13 -9999 0 -10000 0 0
SIRT1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0.001 -9999 0 -10000 0 0
HIF2A/ARNT 0.21 0.14 -9999 0 -10000 0 0
EPAS1 0.11 0.089 -9999 0 -10000 0 0
SP1 0.021 0.002 -9999 0 -10000 0 0
ABCG2 0.19 0.15 -9999 0 -0.82 3 3
EFNA1 0.19 0.13 -9999 0 -10000 0 0
FXN 0.19 0.13 -9999 0 -10000 0 0
POU5F1 0.19 0.13 -9999 0 -10000 0 0
neuron apoptosis -0.2 0.14 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
EGLN3 -0.004 0.14 -9999 0 -0.53 19 19
EGLN2 0.028 0.011 -9999 0 -10000 0 0
EGLN1 0.028 0.011 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C -0.003 0.042 -9999 0 -0.57 2 2
VHL 0.008 0.063 -9999 0 -0.86 2 2
ARNT 0.026 0.011 -9999 0 -10000 0 0
SLC2A1 0.19 0.13 -9999 0 -10000 0 0
TWIST1 0.18 0.16 -9999 0 -0.63 5 5
ELK1 0.015 0.025 -9999 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.001 0.045 -9999 0 -10000 0 0
VEGFA 0.19 0.14 -9999 0 -0.69 2 2
CREBBP 0.013 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.052 0.026 -10000 0 -0.46 1 1
adherens junction organization 0.043 0.032 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.051 0.057 -10000 0 -10000 0 0
FMN1 0.03 0.091 -10000 0 -0.47 12 12
mol:IP3 -0.001 0.022 -10000 0 -0.43 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.008 -10000 0 -10000 0 0
CTNNB1 0.012 0 -10000 0 -10000 0 0
AKT1 0.05 0.024 -10000 0 -0.42 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.045 0.006 -10000 0 -10000 0 0
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.046 0.008 -10000 0 -10000 0 0
VASP 0.046 0.008 -10000 0 -10000 0 0
ZYX 0.046 0.008 -10000 0 -10000 0 0
JUB 0.044 0.038 -10000 0 -0.46 2 2
EGFR(dimer) 0.038 0.058 -10000 0 -0.46 5 5
E-cadherin/beta catenin-gamma catenin 0 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.023 -10000 0 -0.45 1 1
PIK3CA 0.012 0.045 -10000 0 -0.86 1 1
PI3K -0.001 0.024 -10000 0 -0.46 1 1
FYN 0.051 0.026 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.022 -10000 0 -0.42 1 1
JUP 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG -0.001 0.022 -10000 0 -0.43 1 1
CDH1 0.012 0 -10000 0 -10000 0 0
RhoA/GDP 0.051 0.057 -10000 0 -0.4 6 6
establishment of polarity of embryonic epithelium 0.046 0.008 -10000 0 -10000 0 0
SRC 0.012 0.016 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR 0.001 0.099 -10000 0 -0.86 5 5
CASR 0.043 0.029 -10000 0 -0.4 1 1
RhoA/GTP -0.001 0.02 -10000 0 -0.38 1 1
AKT2 0.05 0.024 -10000 0 -0.42 1 1
actin cable formation 0.038 0.089 -10000 0 -0.45 12 12
apoptosis 0.001 0.022 0.44 1 -10000 0 1
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.045 0.061 -10000 0 -0.43 6 6
PIP5K1A 0.046 0.008 -10000 0 -10000 0 0
PLCG1 -0.001 0.023 -10000 0 -0.44 1 1
Rac1/GTP -0.006 0.048 -10000 0 -0.42 5 5
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.081 0.11 -9999 0 -9999 0 0
TP53 -0.027 0.031 -9999 0 -9999 0 0
Senescence -0.027 0.031 -9999 0 -9999 0 0
Apoptosis -0.027 0.031 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.052 0.059 -9999 0 -9999 0 0
MDM4 0.013 0 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0 0 -9999 0 -9999 0 0
HDAC4 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.013 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.03 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.013 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.013 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0 0 -9999 0 -9999 0 0
RANGAP1 0.013 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.013 0 -9999 0 -9999 0 0
UBE2I 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.013 0 -9999 0 -9999 0 0
PIAS1 0.013 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.024 0.17 -10000 0 -0.76 18 18
CLTC 0.034 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.028 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0 0 -10000 0 -10000 0 0
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.031 0 -10000 0 -10000 0 0
CPE 0.008 0.081 -10000 0 -0.58 7 7
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0 0 -10000 0 -10000 0 0
CTNND1 0.034 0 -10000 0 -10000 0 0
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0 -10000 0 -10000 0 0
TSHR 0.016 0.044 -10000 0 -0.58 2 2
INS 0.013 0 -10000 0 -10000 0 0
BIN1 0.013 0 -10000 0 -10000 0 0
mol:Choline 0 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.031 0 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.027 -10000 0 -0.53 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.031 0 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.045 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.026 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.001 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.003 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.045 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.034 0 -10000 0 -10000 0 0
NME1 0.02 0 -10000 0 -10000 0 0
clathrin coat assembly 0.034 0 -10000 0 -10000 0 0
IL2RA 0.013 0.064 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.018 0.084 -10000 0 -0.43 15 15
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0 -10000 0 -10000 0 0
SDC1 0.03 0.007 -10000 0 -10000 0 0
ARF6/GDP 0.019 0 -10000 0 -10000 0 0
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
endocytosis 0.001 0.027 0.53 1 -10000 0 1
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.027 0.081 -10000 0 -0.46 10 10
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.011 0.045 -10000 0 -0.86 1 1
Dynamin 2/GDP 0.026 0 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.029 0.073 -10000 0 -0.46 8 8
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0.013 0 -9999 0 -9999 0 0
JUP 0.013 0 -9999 0 -9999 0 0
CDH1 0.013 0 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0 -9999 0 -10000 0 0
CD4 0.003 0.054 -9999 0 -0.3 12 12
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.013 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.027 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.035 0.013 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.026 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -9999 0 0
FBXW11 0.013 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -9999 0 0
CHUK 0.013 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -9999 0 0
NFKB1 0.013 0 -9999 0 -9999 0 0
MAP3K14 0.013 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0 0 -9999 0 -9999 0 0
RELB 0.013 0 -9999 0 -9999 0 0
NFKB2 0.013 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -9999 0 0
regulation of B cell activation 0 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 379 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.J8.A3YH TCGA.J8.A3YG TCGA.J8.A3YE TCGA.J8.A3YD
109_MAP3K5 -0.013 -0.013 -0.22 0.057
47_PPARGC1A -0.86 -0.86 0.013 0.013
105_BMP4 0.013 0.013 -0.86 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 0.013 0.013 0.013
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR -0.52 -0.52 -0.52 0
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.013
84_STAT5B 0.0047 0.0023 -0.068 0.11
84_STAT5A 0.0047 0.0023 -0.068 0.11
Methods & Data
Input

  • Expression Data Normalization = Expression data was not used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/2398258/0.mRNAseq_preprocessor.Finished/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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