Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNA 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 50 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Signaling events mediated by Stem cell factor receptor (c-Kit) 246
Signaling mediated by p38-alpha and p38-beta 238
EGFR-dependent Endothelin signaling events 180
Endothelins 165
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 163
Class IB PI3K non-lipid kinase events 137
IGF1 pathway 135
Arf6 signaling events 133
Nongenotropic Androgen signaling 99
FOXM1 transcription factor network 99
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events mediated by Stem cell factor receptor (c-Kit) 246 19242 78 -1.1 0.35 1000 -1000 -0.05 -1000
Signaling mediated by p38-alpha and p38-beta 238 10505 44 -0.73 0.016 1000 -1000 -0.043 -1000
EGFR-dependent Endothelin signaling events 180 3794 21 -0.45 0.016 1000 -1000 -0.045 -1000
Endothelins 165 15863 96 -0.83 0.03 1000 -1000 -0.048 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 163 11118 68 -1 0.47 1000 -1000 -0.066 -1000
Class IB PI3K non-lipid kinase events 137 411 3 -0.18 -1000 1000 -1000 -0.001 -1000
IGF1 pathway 135 7706 57 -0.37 0.15 1000 -1000 -0.06 -1000
Arf6 signaling events 133 8299 62 -0.45 0.018 1000 -1000 -0.034 -1000
Nongenotropic Androgen signaling 99 5188 52 -0.59 0.28 1000 -1000 -0.043 -1000
FOXM1 transcription factor network 99 5077 51 -0.84 0.017 1000 -1000 -0.084 -1000
Signaling events mediated by PTP1B 98 7499 76 -0.48 0.21 1000 -1000 -0.058 -1000
Calcium signaling in the CD4+ TCR pathway 96 2997 31 -0.54 0.026 1000 -1000 -0.061 -1000
S1P1 pathway 95 3429 36 -0.67 0.016 1000 -1000 -0.049 -1000
HIF-1-alpha transcription factor network 91 6983 76 -0.51 0.054 1000 -1000 -0.043 -1000
Glucocorticoid receptor regulatory network 88 10101 114 -1.2 0.3 1000 -1000 -0.053 -1000
IL23-mediated signaling events 86 5194 60 -0.93 0.019 1000 -1000 -0.086 -1000
Ras signaling in the CD4+ TCR pathway 76 1308 17 -0.23 0.013 1000 -1000 -0.03 -1000
PDGFR-alpha signaling pathway 75 3315 44 -0.84 0.046 1000 -1000 -0.057 -1000
IL6-mediated signaling events 74 5581 75 -0.52 0.052 1000 -1000 -0.047 -1000
BMP receptor signaling 72 5869 81 -0.6 0.04 1000 -1000 -0.074 -1000
Ephrin B reverse signaling 72 3456 48 -0.26 0.14 1000 -1000 -0.044 -1000
FAS signaling pathway (CD95) 69 3284 47 -0.97 0.072 1000 -1000 -0.028 -1000
Fc-epsilon receptor I signaling in mast cells 61 6010 97 -0.51 0.039 1000 -1000 -0.07 -1000
Plasma membrane estrogen receptor signaling 60 5187 86 -0.35 0.16 1000 -1000 -0.063 -1000
IL4-mediated signaling events 59 5376 91 -0.63 0.23 1000 -1000 -0.17 -1000
Integrins in angiogenesis 58 4893 84 -0.57 0.053 1000 -1000 -0.062 -1000
Glypican 1 network 48 2348 48 -0.55 0.061 1000 -1000 -0.035 -1000
p75(NTR)-mediated signaling 47 5917 125 -0.25 0.016 1000 -1000 -0.068 -1000
Nectin adhesion pathway 44 2775 63 -0.1 0.016 1000 -1000 -0.047 -1000
TCGA08_rtk_signaling 44 1164 26 -0.38 0.028 1000 -1000 -0.016 -1000
E-cadherin signaling in keratinocytes 42 1838 43 -0.38 0.044 1000 -1000 -0.053 -1000
ErbB2/ErbB3 signaling events 41 2708 65 -0.48 0.03 1000 -1000 -0.047 -1000
Stabilization and expansion of the E-cadherin adherens junction 41 3105 74 -0.38 0.08 1000 -1000 -0.068 -1000
Insulin Pathway 41 3049 74 -0.39 0.046 1000 -1000 -0.066 -1000
ErbB4 signaling events 40 2792 69 -0.5 0.12 1000 -1000 -0.063 -1000
Syndecan-3-mediated signaling events 40 1423 35 -0.51 0.016 1000 -1000 -0.048 -1000
Visual signal transduction: Rods 40 2094 52 -0.58 0.029 1000 -1000 -0.063 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 38 3261 85 -0.54 0.035 1000 -1000 -0.056 -1000
Presenilin action in Notch and Wnt signaling 36 2208 61 -0.53 0.04 1000 -1000 -0.058 -1000
Signaling events regulated by Ret tyrosine kinase 36 2992 82 -0.18 0.018 1000 -1000 -0.072 -1000
EPHB forward signaling 36 3103 85 -0.26 0.12 1000 -1000 -0.067 -1000
Signaling events mediated by the Hedgehog family 35 1840 52 -0.22 0.14 1000 -1000 -0.061 -1000
S1P5 pathway 34 585 17 -0.25 0.078 1000 -1000 -0.038 -1000
TCGA08_retinoblastoma 34 277 8 -0.043 0.021 1000 -1000 -0.01 -1000
Ceramide signaling pathway 31 2386 76 -0.35 0.098 1000 -1000 -0.038 -1000
RXR and RAR heterodimerization with other nuclear receptor 31 1656 52 -0.53 0.089 1000 -1000 -0.043 -1000
Neurotrophic factor-mediated Trk receptor signaling 31 3779 120 -0.42 0.18 1000 -1000 -0.059 -1000
Syndecan-2-mediated signaling events 29 2002 69 -0.46 0.046 1000 -1000 -0.036 -1000
Regulation of nuclear SMAD2/3 signaling 28 3856 136 -0.52 0.065 1000 -1000 -0.036 -1000
LPA receptor mediated events 27 2796 102 -0.51 0.045 1000 -1000 -0.058 -1000
IL27-mediated signaling events 26 1365 51 -0.52 0.04 1000 -1000 -0.062 -1000
Reelin signaling pathway 25 1439 56 -0.1 0.044 1000 -1000 -0.047 -1000
IL1-mediated signaling events 25 1604 62 -0.12 0.082 1000 -1000 -0.053 -1000
amb2 Integrin signaling 24 2036 82 -0.62 0.049 1000 -1000 -0.062 -1000
Angiopoietin receptor Tie2-mediated signaling 24 2146 88 -0.55 0.068 1000 -1000 -0.099 -1000
Wnt signaling 23 164 7 -0.029 0.012 1000 -1000 -0.01 -1000
S1P4 pathway 23 593 25 -0.25 0.03 1000 -1000 -0.036 -1000
mTOR signaling pathway 22 1202 53 -0.072 0.042 1000 -1000 -0.049 -1000
Signaling events mediated by VEGFR1 and VEGFR2 22 2859 125 -0.52 0.059 1000 -1000 -0.078 -1000
Regulation of Telomerase 22 2249 102 -0.51 0.067 1000 -1000 -0.068 -1000
E-cadherin signaling events 22 113 5 -0.039 0.014 1000 -1000 -0.028 -1000
FOXA2 and FOXA3 transcription factor networks 21 990 46 -0.84 0.075 1000 -1000 -0.02 -1000
Canonical Wnt signaling pathway 21 1072 51 -0.53 0.2 1000 -1000 -0.049 -1000
Regulation of Androgen receptor activity 21 1490 70 -0.6 0.061 1000 -1000 -0.054 -1000
Aurora B signaling 21 1443 67 -0.52 0.077 1000 -1000 -0.045 -1000
IL12-mediated signaling events 20 1810 87 -0.88 0.027 1000 -1000 -0.07 -1000
Osteopontin-mediated events 20 787 38 -0.51 0.062 1000 -1000 -0.068 -1000
Thromboxane A2 receptor signaling 20 2136 105 -0.38 0.098 1000 -1000 -0.049 -1000
Coregulation of Androgen receptor activity 19 1516 76 -0.25 0.026 1000 -1000 -0.039 -1000
Regulation of p38-alpha and p38-beta 19 1063 54 -0.43 0.051 1000 -1000 -0.046 -1000
S1P3 pathway 19 805 42 -0.25 0.041 1000 -1000 -0.04 -1000
Sphingosine 1-phosphate (S1P) pathway 18 529 28 -0.25 0.03 1000 -1000 -0.033 -1000
Insulin-mediated glucose transport 18 602 32 -0.11 0.049 1000 -1000 -0.044 -1000
Syndecan-4-mediated signaling events 17 1146 67 -0.55 0.05 1000 -1000 -0.071 -1000
Syndecan-1-mediated signaling events 15 539 34 -0.1 0.016 1000 -1000 -0.04 -1000
PLK2 and PLK4 events 15 46 3 -0.019 -0.009 1000 -1000 -0.007 -1000
Noncanonical Wnt signaling pathway 15 412 26 -0.042 0.032 1000 -1000 -0.059 -1000
IL2 signaling events mediated by PI3K 15 891 58 -0.11 0.04 1000 -1000 -0.062 -1000
E-cadherin signaling in the nascent adherens junction 15 1141 76 -0.055 0.046 1000 -1000 -0.058 -1000
Arf6 trafficking events 15 1073 71 -0.41 0.054 1000 -1000 -0.05 -1000
Caspase cascade in apoptosis 14 1094 74 -0.22 0.074 1000 -1000 -0.031 -1000
Hedgehog signaling events mediated by Gli proteins 14 920 65 -0.25 0.08 1000 -1000 -0.044 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 14 642 45 -0.049 0.07 1000 -1000 -0.065 -1000
BCR signaling pathway 14 1395 99 -0.24 0.076 1000 -1000 -0.069 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 13 713 54 -0.1 0.044 1000 -1000 -0.059 -1000
FoxO family signaling 13 836 64 -0.027 0.11 1000 -1000 -0.035 -1000
Signaling events mediated by PRL 13 469 34 -0.44 0.025 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 12 848 68 -0.24 0.069 1000 -1000 -0.04 -1000
TRAIL signaling pathway 11 545 48 -0.024 0.047 1000 -1000 -0.046 -1000
JNK signaling in the CD4+ TCR pathway 10 177 17 -0.083 0.057 1000 -1000 -0.038 -1000
Signaling mediated by p38-gamma and p38-delta 10 154 15 0 0.03 1000 -1000 -0.01 -1000
Cellular roles of Anthrax toxin 9 375 39 -0.14 0.023 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class III 9 381 40 -0.1 0.029 1000 -1000 -0.029 -1000
VEGFR1 specific signals 9 543 56 -0.52 0.071 1000 -1000 -0.064 -1000
Signaling events mediated by HDAC Class II 8 602 75 -0.18 0.043 1000 -1000 -0.038 -1000
EPO signaling pathway 8 483 55 -0.13 0.064 1000 -1000 -0.064 -1000
IFN-gamma pathway 8 553 68 -0.055 0.086 1000 -1000 -0.063 -1000
ceramide signaling pathway 8 417 49 -0.13 0.06 1000 -1000 -0.03 -1000
Paxillin-independent events mediated by a4b1 and a4b7 7 259 37 -0.055 0.051 1000 -1000 -0.036 -1000
PDGFR-beta signaling pathway 7 695 97 -0.19 0.045 1000 -1000 -0.064 -1000
Visual signal transduction: Cones 6 231 38 -0.03 0.026 1000 -1000 -0.042 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 556 83 -0.13 0.066 1000 -1000 -0.056 -1000
Retinoic acid receptors-mediated signaling 6 404 58 -0.1 0.042 1000 -1000 -0.058 -1000
Paxillin-dependent events mediated by a4b1 6 236 36 -0.055 0.029 1000 -1000 -0.049 -1000
TCR signaling in naïve CD8+ T cells 6 639 93 -0.083 0.089 1000 -1000 -0.055 -1000
p38 MAPK signaling pathway 6 305 44 -0.036 0.039 1000 -1000 -0.052 -1000
HIF-2-alpha transcription factor network 5 235 43 -0.21 0.22 1000 -1000 -0.11 -1000
Atypical NF-kappaB pathway 4 154 31 -0.055 0.063 1000 -1000 -0.036 -1000
IL2 signaling events mediated by STAT5 4 92 22 -0.054 0.087 1000 -1000 -0.02 -1000
Class I PI3K signaling events 4 348 73 -0.027 0.089 1000 -1000 -0.033 -1000
Aurora A signaling 3 208 60 -0.087 0.047 1000 -1000 -0.043 -1000
Arf6 downstream pathway 3 132 43 -0.039 0.04 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class I 3 413 104 -0.24 0.074 1000 -1000 -0.046 -1000
LPA4-mediated signaling events 1 13 12 0 0.042 1000 -1000 -0.012 -1000
Nephrin/Neph1 signaling in the kidney podocyte 1 37 34 -0.004 0.057 1000 -1000 -0.041 -1000
Ephrin A reverse signaling 1 7 7 0 0.03 1000 -1000 -0.024 -1000
Effects of Botulinum toxin 1 29 26 -0.046 0.024 1000 -1000 -0.043 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 18 23 -0.029 0.063 1000 -1000 -0.049 -1000
Canonical NF-kappaB pathway 0 4 39 -0.018 0.11 1000 -1000 -0.059 -1000
BARD1 signaling events 0 12 57 -0.078 0.052 1000 -1000 -0.048 -1000
Circadian rhythm pathway 0 14 22 -0.053 0.065 1000 -1000 -0.056 -1000
a4b1 and a4b7 Integrin signaling 0 0 5 -0.003 0.016 1000 -1000 -0.031 -1000
Aurora C signaling 0 1 7 -0.014 0.021 1000 -1000 -0.022 -1000
PLK1 signaling events 0 41 85 -0.09 0.067 1000 -1000 -0.036 -1000
TCGA08_p53 0 0 7 -0.004 0.015 1000 -1000 -0.009 -1000
Glypican 2 network 0 0 4 -0.007 -1000 1000 -1000 -0.012 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 0 0.039 1000 -1000 -0.04 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0 4 33 -0.017 0.05 1000 -1000 -0.05 -1000
Rapid glucocorticoid signaling 0 16 20 -0.003 0.016 1000 -1000 -0.024 -1000
Arf1 pathway 0 6 54 -0.001 0.045 1000 -1000 -0.028 -1000
Alternative NF-kappaB pathway 0 3 13 -0.002 0.016 1000 -1000 -0.041 -1000
Total 4598 279159 7203 -41 -2000 131000 -131000 -6.3 -131000
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.3 0.16 -10000 0 -0.39 414 414
CRKL -0.33 0.18 -10000 0 -0.42 414 414
HRAS -0.25 0.15 -10000 0 -0.35 129 129
mol:PIP3 -0.33 0.18 -10000 0 -0.42 412 412
SPRED1 0.013 0.045 -10000 0 -0.72 2 2
SPRED2 0.016 0 -10000 0 -10000 0 0
GAB1 -0.36 0.18 -10000 0 -0.45 415 415
FOXO3 -0.3 0.16 -10000 0 -0.38 413 413
AKT1 -0.33 0.18 -10000 0 -0.41 414 414
BAD -0.3 0.16 -10000 0 -0.38 413 413
megakaryocyte differentiation -0.35 0.18 -10000 0 -0.44 414 414
GSK3B -0.3 0.16 -10000 0 -0.38 413 413
RAF1 -0.2 0.13 -10000 0 -0.31 17 17
SHC1 0.016 0 -10000 0 -10000 0 0
STAT3 -0.36 0.18 -10000 0 -0.44 414 414
STAT1 -0.87 0.45 -10000 0 -1 442 442
HRAS/SPRED1 -0.21 0.11 -10000 0 -0.33 21 21
cell proliferation -0.35 0.18 -10000 0 -0.44 414 414
PIK3CA 0.015 0.007 -10000 0 -10000 0 0
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 -0.35 0.18 -10000 0 -0.44 414 414
HRAS/SPRED2 -0.21 0.1 -10000 0 -0.31 20 20
LYN/TEC/p62DOK -0.33 0.16 -10000 0 -0.41 413 413
MAPK3 -0.14 0.098 -10000 0 -0.29 2 2
STAP1 -0.36 0.18 -10000 0 -0.45 419 419
GRAP2 0.014 0.019 -10000 0 -10000 0 0
JAK2 -0.72 0.34 -10000 0 -0.88 416 416
STAT1 (dimer) -0.85 0.43 -10000 0 -1 442 442
mol:Gleevec 0.013 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.33 0.16 -10000 0 -0.41 413 413
actin filament polymerization -0.36 0.18 -10000 0 -0.43 440 440
LYN 0.016 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.49 0.25 -10000 0 -0.61 420 420
PIK3R1 -0.056 0.22 -10000 0 -0.72 51 51
CBL/CRKL/GRB2 -0.3 0.15 -10000 0 -0.37 414 414
PI3K -0.36 0.21 -10000 0 -0.45 416 416
PTEN -0.002 0.12 -10000 0 -0.72 13 13
SCF/KIT/EPO/EPOR -1 0.55 -10000 0 -1.3 413 413
MAPK8 -0.36 0.18 -10000 0 -0.45 414 414
STAT3 (dimer) -0.35 0.18 -10000 0 -0.44 414 414
positive regulation of transcription -0.11 0.084 -10000 0 -0.23 2 2
mol:GDP -0.28 0.13 -10000 0 -0.34 376 376
PIK3C2B -0.36 0.18 -10000 0 -0.45 414 414
CBL/CRKL -0.3 0.17 -10000 0 -0.38 414 414
FER -0.36 0.18 -10000 0 -0.44 414 414
SH2B3 -0.36 0.18 -10000 0 -0.44 414 414
PDPK1 -0.3 0.16 -10000 0 -0.38 411 411
SNAI2 -0.41 0.23 -10000 0 -0.5 427 427
positive regulation of cell proliferation -0.61 0.31 -10000 0 -0.74 442 442
KITLG -0.019 0.077 -10000 0 -0.75 3 3
cell motility -0.61 0.31 -10000 0 -0.74 442 442
PTPN6 0.032 0.018 -10000 0 -10000 0 0
EPOR -0.22 0.14 -10000 0 -0.62 1 1
STAT5A (dimer) -0.5 0.26 -10000 0 -0.6 443 443
SOCS1 0.015 0.012 -10000 0 -10000 0 0
cell migration 0.35 0.18 0.44 416 -10000 0 416
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.02 0.058 -10000 0 -10000 0 0
VAV1 0.012 0.027 -10000 0 -10000 0 0
GRB10 -0.36 0.19 -10000 0 -0.45 414 414
PTPN11 0.029 0.007 -10000 0 -10000 0 0
SCF/KIT -0.38 0.19 -10000 0 -0.46 437 437
GO:0007205 0.018 0.01 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.32 2 2
CBL 0.016 0 -10000 0 -10000 0 0
KIT -1.1 0.58 -10000 0 -1.4 414 414
MAP2K2 -0.15 0.11 -10000 0 -0.32 2 2
SHC/Grb2/SOS1 -0.33 0.16 -10000 0 -0.41 413 413
STAT5A -0.51 0.26 -10000 0 -0.62 443 443
GRB2 0.013 0.022 -10000 0 -10000 0 0
response to radiation -0.4 0.22 -10000 0 -0.49 427 427
SHC/GRAP2 -0.001 0.009 -10000 0 -10000 0 0
PTPRO -0.36 0.18 -10000 0 -0.45 414 414
SH2B2 -0.36 0.18 -10000 0 -0.44 440 440
DOK1 0.014 0.019 -10000 0 -10000 0 0
MATK -0.36 0.18 -10000 0 -0.45 416 416
CREBBP 0.006 0.037 -10000 0 -0.72 1 1
BCL2 -0.44 0.55 -10000 0 -1.5 105 105
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.73 0.63 -9999 0 -1.2 317 317
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 -0.18 0.16 -9999 0 -0.31 317 317
ATF2/c-Jun -0.26 0.38 -9999 0 -1 97 97
MAPK11 -0.18 0.16 -9999 0 -0.31 317 317
MITF -0.21 0.21 -9999 0 -0.37 319 319
MAPKAPK5 -0.2 0.2 -9999 0 -0.37 317 317
KRT8 -0.21 0.21 -9999 0 -0.37 317 317
MAPKAPK3 0.015 0.012 -9999 0 -10000 0 0
MAPKAPK2 0.016 0.01 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.27 0.25 -9999 0 -0.47 317 317
CEBPB -0.21 0.21 -9999 0 -0.37 317 317
SLC9A1 -0.2 0.2 -9999 0 -0.37 317 317
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.22 0.23 -9999 0 -0.38 317 317
p38alpha-beta/MNK1 -0.22 0.18 -9999 0 -0.46 78 78
JUN -0.26 0.38 -9999 0 -1 97 97
PPARGC1A -0.27 0.3 -9999 0 -0.45 328 328
USF1 -0.21 0.2 -9999 0 -0.37 317 317
RAB5/GDP/GDI1 -0.16 0.13 -9999 0 -0.33 78 78
NOS2 -0.22 0.2 -9999 0 -0.38 317 317
DDIT3 -0.21 0.2 -9999 0 -0.37 317 317
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 -0.17 0.18 -9999 0 -0.36 125 125
p38alpha-beta/HBP1 -0.22 0.18 -9999 0 -0.37 317 317
CREB1 -0.22 0.21 -9999 0 -0.38 319 319
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.17 0.18 -9999 0 -0.4 78 78
RPS6KA4 -0.2 0.2 -9999 0 -0.37 317 317
PLA2G4A -0.43 0.34 -9999 0 -0.66 328 328
GDI1 -0.21 0.2 -9999 0 -0.37 317 317
TP53 -0.26 0.25 -9999 0 -0.46 317 317
RPS6KA5 -0.22 0.22 -9999 0 -0.38 330 330
ESR1 -0.32 0.27 -9999 0 -0.45 390 390
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C -0.24 0.26 -9999 0 -0.41 325 325
MEF2A -0.2 0.2 -9999 0 -0.37 317 317
EIF4EBP1 -0.22 0.21 -9999 0 -0.38 318 318
KRT19 -0.22 0.22 -9999 0 -0.39 319 319
ELK4 -0.2 0.2 -9999 0 -0.37 317 317
ATF6 -0.2 0.2 -9999 0 -0.37 317 317
ATF1 -0.22 0.21 -9999 0 -0.38 319 319
p38alpha-beta/MAPKAPK2 -0.22 0.18 -9999 0 -0.37 317 317
p38alpha-beta/MAPKAPK3 -0.22 0.18 -9999 0 -0.37 317 317
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.015 0.012 -9999 0 -10000 0 0
EGFR -0.38 0.37 -9999 0 -0.72 277 277
EGF/EGFR -0.45 0.34 -9999 0 -0.6 393 393
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.33 0.26 -9999 0 -0.47 372 372
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.013 0.046 -9999 0 -0.72 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.24 0.35 -9999 0 -0.72 178 178
EGF/EGFR dimer/SHC -0.39 0.29 -9999 0 -0.55 372 372
mol:GDP -0.33 0.25 -9999 0 -0.46 372 372
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.22 0.34 -9999 0 -0.72 169 169
GRB2/SOS1 -0.001 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.3 0.23 -9999 0 -0.43 372 372
SHC1 0.016 0 -9999 0 -10000 0 0
HRAS/GDP -0.3 0.24 -9999 0 -0.43 372 372
FRAP1 -0.29 0.26 -9999 0 -0.44 372 372
EGF/EGFR dimer -0.45 0.33 -9999 0 -0.64 372 372
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.18 0.25 -9999 0 -0.54 171 171
Endothelins

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.11 0.24 -9999 0 -0.46 172 172
PTK2B 0.016 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.14 0.3 -9999 0 -0.75 76 76
EDN1 -0.21 0.35 -9999 0 -0.72 169 169
EDN3 -0.6 0.28 -9999 0 -0.72 437 437
EDN2 -0.061 0.09 -9999 0 -0.72 2 2
HRAS/GDP -0.24 0.25 -9999 0 -0.5 206 206
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.11 0.19 -9999 0 -0.35 168 168
ADCY4 -0.096 0.21 -9999 0 -0.38 174 174
ADCY5 -0.094 0.2 -9999 0 -0.38 173 173
ADCY6 -0.092 0.2 -9999 0 -0.38 172 172
ADCY7 -0.092 0.2 -9999 0 -0.38 172 172
ADCY1 -0.093 0.2 -9999 0 -0.38 172 172
ADCY2 -0.098 0.21 -9999 0 -0.39 176 176
ADCY3 -0.092 0.2 -9999 0 -0.38 172 172
ADCY8 -0.092 0.2 -9999 0 -0.38 172 172
ADCY9 -0.092 0.2 -9999 0 -0.38 172 172
arachidonic acid secretion -0.53 0.37 -9999 0 -0.7 400 400
ETB receptor/Endothelin-1/Gq/GTP -0.26 0.25 -9999 0 -0.43 318 318
GNAO1 0.016 0 -9999 0 -10000 0 0
HRAS 0.009 0.014 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.095 0.24 -9999 0 -0.42 171 171
ETA receptor/Endothelin-1/Gs/GTP -0.093 0.23 -9999 0 -0.41 172 172
mol:GTP -0.007 0.009 -9999 0 -10000 0 0
COL3A1 -0.11 0.24 -9999 0 -0.45 171 171
EDNRB -0.35 0.37 -9999 0 -0.72 260 260
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.11 0.24 -9999 0 -0.45 171 171
CYSLTR1 -0.11 0.25 -9999 0 -0.46 173 173
SLC9A1 -0.063 0.14 -9999 0 -0.26 151 151
mol:GDP -0.27 0.27 -9999 0 -0.53 219 219
SLC9A3 -0.4 0.41 -9999 0 -0.66 331 331
RAF1 -0.36 0.29 -9999 0 -0.56 313 313
JUN -0.24 0.47 -9999 0 -1.1 109 109
JAK2 -0.11 0.25 -9999 0 -0.46 171 171
mol:IP3 -0.23 0.24 -9999 0 -0.46 221 221
ETA receptor/Endothelin-1 -0.12 0.29 -9999 0 -0.54 173 173
PLCB1 -0.1 0.25 -9999 0 -0.73 74 74
PLCB2 0.005 0.008 -9999 0 -10000 0 0
ETA receptor/Endothelin-3 -0.44 0.21 -9999 0 -0.54 437 437
FOS -0.71 0.47 -9999 0 -1 374 374
Gai/GDP -0.1 0.16 -9999 0 -0.79 2 2
CRK 0.014 0.032 -9999 0 -0.72 1 1
mol:Ca ++ -0.3 0.33 -9999 0 -0.65 213 213
BCAR1 0.017 0.001 -9999 0 -10000 0 0
PRKCB1 -0.22 0.24 -9999 0 -0.47 193 193
GNAQ -0.008 0.01 -9999 0 -10000 0 0
GNAZ 0.008 0.078 -9999 0 -0.72 6 6
GNAL 0.012 0.056 -9999 0 -0.72 3 3
Gs family/GDP -0.25 0.22 -9999 0 -0.48 208 208
ETA receptor/Endothelin-1/Gq/GTP -0.085 0.17 -9999 0 -0.31 162 162
MAPK14 -0.24 0.25 -9999 0 -0.44 267 267
TRPC6 -0.15 0.32 -9999 0 -0.8 76 76
GNAI2 0.016 0.007 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.27 0.27 -9999 0 -0.45 301 301
ETB receptor/Endothelin-2 -0.29 0.29 -9999 0 -0.58 262 262
ETB receptor/Endothelin-3 -0.67 0.34 -9999 0 -0.78 455 455
ETB receptor/Endothelin-1 -0.41 0.38 -9999 0 -0.68 329 329
MAPK3 -0.62 0.42 -9999 0 -0.86 380 380
MAPK1 -0.62 0.42 -9999 0 -0.86 380 380
Rac1/GDP -0.24 0.25 -9999 0 -0.5 203 203
cAMP biosynthetic process -0.039 0.19 -9999 0 -0.36 61 61
MAPK8 -0.16 0.29 -9999 0 -0.62 118 118
SRC 0.016 0.007 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.3 0.32 -9999 0 -0.64 209 209
p130Cas/CRK/Src/PYK2 -0.24 0.29 -9999 0 -0.56 189 189
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.24 0.25 -9999 0 -0.5 206 206
COL1A2 -0.32 0.35 -9999 0 -0.69 193 193
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 0.03 0.077 -9999 0 -0.53 4 4
mol:DAG -0.23 0.24 -9999 0 -0.46 221 221
MAP2K2 -0.47 0.34 -9999 0 -0.66 381 381
MAP2K1 -0.47 0.34 -9999 0 -0.66 382 382
EDNRA 0.024 0.053 -9999 0 -0.71 2 2
positive regulation of muscle contraction -0.089 0.21 -9999 0 -0.39 172 172
Gq family/GDP -0.22 0.21 -9999 0 -0.47 168 168
HRAS/GTP -0.28 0.26 -9999 0 -0.44 311 311
PRKCH -0.22 0.24 -9999 0 -0.46 210 210
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.22 0.24 -9999 0 -0.47 193 193
PRKCB -0.23 0.24 -9999 0 -0.44 243 243
PRKCE -0.22 0.24 -9999 0 -0.47 192 192
PRKCD -0.22 0.24 -9999 0 -0.46 211 211
PRKCG -0.22 0.24 -9999 0 -0.46 209 209
regulation of vascular smooth muscle contraction -0.83 0.55 -9999 0 -1.2 374 374
PRKCQ -0.23 0.24 -9999 0 -0.46 213 213
PLA2G4A -0.6 0.44 -9999 0 -0.8 400 400
GNA14 -0.018 0.09 -9999 0 -0.73 6 6
GNA15 0.006 0.021 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA11 0.009 0.008 -9999 0 -10000 0 0
Rac1/GTP -0.094 0.24 -9999 0 -0.42 171 171
MMP1 0.026 0.14 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.022 0.012 -10000 0 -10000 0 0
NFATC2 -0.065 0.22 -10000 0 -0.54 80 80
NFATC3 -0.17 0.14 -10000 0 -0.31 157 157
CD40LG -0.79 0.56 -10000 0 -1.1 362 362
ITCH -0.056 0.15 -10000 0 -0.59 1 1
CBLB -0.057 0.15 -10000 0 -1.1 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.33 0.24 -10000 0 -0.72 65 65
JUNB 0.012 0.056 -10000 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.12 0.15 -10000 0 -0.31 197 197
T cell anergy -0.13 0.24 -10000 0 -0.43 197 197
TLE4 -0.048 0.23 -10000 0 -0.85 28 28
Jun/NFAT1-c-4/p21SNFT -0.7 0.54 -10000 0 -1 362 362
AP-1/NFAT1-c-4 -1 0.74 -10000 0 -1.4 366 366
IKZF1 -0.029 0.16 -10000 0 -0.63 11 11
T-helper 2 cell differentiation -0.15 0.29 -10000 0 -0.85 46 46
AP-1/NFAT1 -0.47 0.35 -10000 0 -0.66 360 360
CALM1 -0.039 0.095 -10000 0 -0.3 1 1
EGR2 -0.89 0.85 -10000 0 -1.4 359 359
EGR3 -0.98 0.85 -10000 0 -1.6 327 327
NFAT1/FOXP3 -0.035 0.16 -10000 0 -0.51 21 21
EGR1 -0.6 0.28 -10000 0 -0.72 436 436
JUN -0.12 0.29 -10000 0 -0.72 97 97
EGR4 0.001 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.062 0.1 -10000 0 -0.19 197 197
GBP3 -0.073 0.28 -10000 0 -0.88 45 45
FOSL1 0.016 0.01 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.64 0.51 -10000 0 -0.94 362 362
DGKA -0.028 0.16 -10000 0 -0.51 22 22
CREM 0.016 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.92 0.57 -10000 0 -1.3 364 364
CTLA4 -0.02 0.14 -10000 0 -0.54 10 10
NFAT1-c-4 (dimer)/EGR1 -0.95 0.58 -10000 0 -1.3 364 364
NFAT1-c-4 (dimer)/EGR4 -0.64 0.52 -10000 0 -0.96 362 362
FOS -0.51 0.34 -10000 0 -0.72 374 374
IFNG -0.19 0.26 -10000 0 -0.91 41 41
T cell activation -0.48 0.39 -10000 0 -0.76 314 314
MAF -0.051 0.21 -10000 0 -0.72 48 48
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.47 0.43 0.74 362 -10000 0 362
TNF -0.76 0.52 -10000 0 -1.1 363 363
FASLG -0.95 0.82 -10000 0 -1.4 362 362
TBX21 -0.034 0.19 -10000 0 -0.72 35 35
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.01 0.047 -10000 0 -0.72 1 1
PTPN1 -0.03 0.16 -10000 0 -0.56 19 19
NFAT1-c-4/ICER1 -0.64 0.51 -10000 0 -0.95 362 362
GATA3 -0.076 0.19 -10000 0 -0.72 38 38
T-helper 1 cell differentiation -0.19 0.25 -10000 0 -0.89 41 41
IL2RA -0.34 0.24 -10000 0 -0.61 128 128
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.027 0.16 -10000 0 -0.63 11 11
E2F1 0.004 0.055 -10000 0 -10000 0 0
PPARG -0.53 0.32 -10000 0 -0.72 388 388
SLC3A2 -0.028 0.16 -10000 0 -0.62 12 12
IRF4 0.011 0.03 -10000 0 -10000 0 0
PTGS2 -0.96 0.64 -10000 0 -1.3 390 390
CSF2 -0.79 0.56 -10000 0 -1.1 363 363
JunB/Fra1/NFAT1-c-4 -0.61 0.49 -10000 0 -0.91 362 362
IL4 -0.16 0.31 -10000 0 -0.9 45 45
IL5 -0.79 0.56 -10000 0 -1.1 363 363
IL2 -0.48 0.4 -10000 0 -0.78 310 310
IL3 -0.085 0.051 -10000 0 -10000 0 0
RNF128 -0.26 0.4 -10000 0 -0.78 197 197
NFATC1 -0.47 0.43 -10000 0 -0.74 362 362
CDK4 0.28 0.26 0.52 204 -10000 0 204
PTPRK -0.081 0.3 -10000 0 -0.9 54 54
IL8 -0.8 0.57 -10000 0 -1.1 366 366
POU2F1 0.026 0 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.18 0.32 0.72 137 -10000 0 137
PI3K Class IB/PDE3B -0.18 0.32 -10000 0 -0.72 137 137
PDE3B -0.18 0.32 -10000 0 -0.72 137 137
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.016 0.01 -10000 0 -10000 0 0
PTK2 0.015 0.014 -10000 0 -10000 0 0
CRKL -0.23 0.29 -10000 0 -0.46 280 280
GRB2/SOS1/SHC 0.002 0.011 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
IRS1/Crk -0.23 0.29 -10000 0 -0.47 280 280
IGF-1R heterotetramer/IGF1/PTP1B -0.25 0.26 -10000 0 -0.49 265 265
AKT1 -0.21 0.28 -10000 0 -0.62 118 118
BAD -0.18 0.26 -10000 0 -0.62 99 99
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.23 0.29 -10000 0 -0.46 280 280
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.23 0.29 -10000 0 -0.47 280 280
RAF1 -0.17 0.24 -10000 0 -0.58 95 95
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.23 0.26 -10000 0 -0.45 266 266
YWHAZ 0.014 0.017 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.26 0.31 -10000 0 -0.51 280 280
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.21 0.28 -10000 0 -0.62 119 119
GNB2L1 0.016 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.14 0.21 -10000 0 -0.48 95 95
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.2 0.23 -10000 0 -0.62 78 78
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.19 0.21 -10000 0 -0.38 265 265
IGF-1R heterotetramer -0.074 0.18 -10000 0 -0.84 23 23
IGF-1R heterotetramer/IGF1/IRS/Nck -0.25 0.28 -10000 0 -0.47 280 280
Crk/p130 Cas/Paxillin -0.22 0.25 -10000 0 -0.42 265 265
IGF1R -0.074 0.18 -10000 0 -0.84 23 23
IGF1 -0.37 0.38 -10000 0 -0.75 262 262
IRS2/Crk -0.31 0.37 -10000 0 -0.57 301 301
PI3K -0.27 0.3 -10000 0 -0.5 276 276
apoptosis 0.15 0.22 0.52 95 -10000 0 95
HRAS/GDP -0.001 0.007 -10000 0 -10000 0 0
PRKCD -0.23 0.3 -10000 0 -0.51 265 265
RAF1/14-3-3 E -0.14 0.21 -10000 0 -0.48 95 95
BAD/14-3-3 -0.16 0.24 -10000 0 -0.56 95 95
PRKCZ -0.22 0.28 -10000 0 -0.44 276 276
Crk/p130 Cas/Paxillin/FAK1 -0.19 0.21 -10000 0 -0.57 95 95
PTPN1 0.008 0.036 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.26 0.31 -10000 0 -0.54 265 265
BCAR1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.22 0.24 -10000 0 -0.43 265 265
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.23 0.29 -10000 0 -0.46 280 280
GRB10 0.011 0.064 -10000 0 -0.72 4 4
PTPN11 -0.23 0.29 -10000 0 -0.46 280 280
IRS1 -0.26 0.31 -10000 0 -0.51 280 280
IRS2 -0.34 0.38 -10000 0 -0.6 307 307
IGF-1R heterotetramer/IGF1 -0.31 0.32 -10000 0 -0.62 265 265
GRB2 0.013 0.022 -10000 0 -10000 0 0
PDPK1 -0.23 0.3 -10000 0 -0.46 276 276
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
PRKD1 -0.3 0.36 -10000 0 -0.6 281 281
SHC1 0.016 0 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.001 0.021 -10000 0 -0.48 1 1
ARNO/beta Arrestin1-2 -0.19 0.18 -10000 0 -0.35 285 285
EGFR -0.38 0.37 -10000 0 -0.72 277 277
EPHA2 0.005 0.09 -10000 0 -0.72 8 8
USP6 0.015 0.016 -10000 0 -10000 0 0
IQSEC1 0.016 0 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.45 0.33 -10000 0 -0.64 372 372
ARRB2 0.018 0.037 -10000 0 -0.41 4 4
mol:GTP 0.008 0.005 0.081 1 -10000 0 1
ARRB1 0.014 0.035 -10000 0 -0.72 1 1
FBXO8 0.016 0 -10000 0 -10000 0 0
TSHR 0.01 0.064 -10000 0 -0.72 4 4
EGF -0.24 0.35 -10000 0 -0.72 178 178
somatostatin receptor activity 0 0 -10000 0 -0.001 316 316
ARAP2 0 0 -10000 0 0 314 314
mol:GDP -0.16 0.14 -10000 0 -0.29 234 234
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 317 317
ITGA2B 0.016 0.01 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.053 -10000 0 -0.41 8 8
ADAP1 0 0 -10000 0 0 312 312
KIF13B 0.015 0.032 -10000 0 -0.72 1 1
HGF/MET -0.054 0.16 -10000 0 -0.54 52 52
PXN 0.016 0 -10000 0 -10000 0 0
ARF6/GTP -0.18 0.13 -10000 0 -0.27 315 315
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.39 0.29 -10000 0 -0.55 372 372
ADRB2 -0.38 0.37 -10000 0 -0.72 284 284
receptor agonist activity 0 0 -10000 0 0 315 315
actin filament binding 0 0 -10000 0 -0.001 316 316
SRC 0.016 0.007 -10000 0 -10000 0 0
ITGB3 0.014 0.02 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -0.001 313 313
EFA6/PI-4-5-P2 -0.001 0 -10000 0 -0.001 314 314
ARF6/GDP -0.029 0.057 -10000 0 -0.24 5 5
ARF6/GDP/GULP/ACAP1 -0.2 0.2 -10000 0 -0.4 216 216
alphaIIb/beta3 Integrin/paxillin/GIT1 0.002 0.015 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 0 35 35
ACAP2 0 0 -10000 0 0 315 315
LHCGR/beta Arrestin2 0.015 0.054 -10000 0 -0.6 4 4
EFNA1 0.013 0.022 -10000 0 -10000 0 0
HGF 0.015 0.01 -10000 0 -10000 0 0
CYTH3 0 0 -10000 0 -0.001 317 317
CYTH2 -0.003 0.002 -10000 0 -0.004 317 317
NCK1 0.016 0 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 278 278
endosomal lumen acidification 0 0 -10000 0 0 193 193
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.12 0.29 -10000 0 -0.72 97 97
GNAQ/ARNO -0.004 0.003 -10000 0 -0.006 313 313
mol:Phosphatidic acid 0 0 -10000 0 0 315 315
PIP3-E 0.011 0.049 -10000 0 -0.72 2 2
MET -0.057 0.22 -10000 0 -0.72 52 52
GNA14 -0.008 0.09 -10000 0 -0.72 6 6
GNA15 0.014 0.02 -10000 0 -10000 0 0
GIT1 0.015 0.016 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -0.001 315 315
GNA11 0.016 0 -10000 0 -10000 0 0
LHCGR 0.009 0.066 -10000 0 -0.72 4 4
AGTR1 -0.32 0.35 -10000 0 -0.72 224 224
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.053 -10000 0 -0.59 4 4
IPCEF1/ARNO -0.31 0.24 -10000 0 -0.44 373 373
alphaIIb/beta3 Integrin -0.001 0.011 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.013 0.009 -10000 0 -10000 0 0
GNB1/GNG2 -0.049 0.15 -10000 0 -0.43 70 70
regulation of S phase of mitotic cell cycle -0.044 0.15 -10000 0 -0.33 112 112
GNAO1 0.016 0 -10000 0 -10000 0 0
HRAS 0.013 0.012 -10000 0 -10000 0 0
SHBG/T-DHT 0.006 0.005 -10000 0 -10000 0 0
PELP1 0.014 0.002 -10000 0 -10000 0 0
AKT1 0.014 0.013 -10000 0 -10000 0 0
MAP2K1 -0.08 0.15 -10000 0 -0.43 69 69
T-DHT/AR -0.07 0.19 -10000 0 -0.56 69 69
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.005 0.004 -10000 0 -0.007 374 374
GNAI2 0.016 0.007 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.25 0.35 -10000 0 -0.72 189 189
mol:GDP -0.098 0.21 -10000 0 -0.6 69 69
cell proliferation -0.26 0.23 -10000 0 -0.45 205 205
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
FOS -0.59 0.42 -10000 0 -0.85 374 374
mol:Ca2+ -0.036 0.039 -10000 0 -0.076 244 244
MAPK3 -0.18 0.19 -10000 0 -0.56 61 61
MAPK1 -0.13 0.12 -10000 0 -0.29 61 61
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
mol:IP3 -0.003 0.002 -10000 0 -0.005 374 374
cAMP biosynthetic process 0.03 0.032 -10000 0 -10000 0 0
GNG2 0.015 0.032 -10000 0 -0.72 1 1
potassium channel inhibitor activity -0.003 0.002 -10000 0 -0.005 374 374
HRAS/GTP -0.067 0.14 -10000 0 -0.42 69 69
actin cytoskeleton reorganization -0.036 0.11 -10000 0 -0.37 51 51
SRC 0.014 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.003 0.002 -10000 0 -0.005 374 374
PI3K -0.045 0.14 -10000 0 -0.47 51 51
apoptosis 0.28 0.22 0.41 374 -10000 0 374
T-DHT/AR/PELP1 -0.056 0.17 -10000 0 -0.48 69 69
HRAS/GDP -0.082 0.2 -10000 0 -0.57 69 69
CREB1 -0.3 0.24 -10000 0 -0.44 374 374
RAC1-CDC42/GTP -0.036 0.11 -10000 0 -0.38 51 51
AR -0.085 0.25 -10000 0 -0.73 69 69
GNB1 0.016 0.01 -10000 0 -10000 0 0
RAF1 -0.067 0.15 -10000 0 -0.43 69 69
RAC1-CDC42/GDP -0.086 0.19 -10000 0 -0.53 69 69
T-DHT/AR/PELP1/Src -0.051 0.15 -10000 0 -0.44 69 69
MAP2K2 -0.08 0.15 -10000 0 -0.43 69 69
T-DHT/AR/PELP1/Src/PI3K -0.044 0.15 -10000 0 -0.33 112 112
GNAZ 0.007 0.078 -10000 0 -0.72 6 6
SHBG 0.016 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.061 0.13 -10000 0 -0.38 14 14
mol:T-DHT -0.002 0.002 -10000 0 -0.003 313 313
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.014 0.12 -10000 0 -0.55 26 26
Gi family/GTP -0.11 0.13 -10000 0 -0.26 193 193
CDC42 0.016 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.29 0.46 -10000 0 -0.86 132 132
PLK1 0.01 0.055 -10000 0 -10000 0 0
BIRC5 -0.025 0.071 -10000 0 -10000 0 0
HSPA1B -0.3 0.46 -10000 0 -0.79 194 194
MAP2K1 0.011 0.036 -10000 0 -10000 0 0
BRCA2 -0.3 0.47 -10000 0 -0.85 152 152
FOXM1 -0.36 0.55 -10000 0 -0.98 175 175
XRCC1 -0.29 0.46 -10000 0 -0.9 110 110
FOXM1B/p19 -0.41 0.42 0.5 1 -0.88 195 196
Cyclin D1/CDK4 -0.29 0.45 -10000 0 -0.83 143 143
CDC2 -0.32 0.49 -10000 0 -0.91 145 145
TGFA -0.32 0.5 -10000 0 -0.97 131 131
SKP2 -0.29 0.46 -10000 0 -0.87 131 131
CCNE1 -0.023 0.071 -10000 0 -10000 0 0
CKS1B -0.29 0.46 -10000 0 -0.9 111 111
RB1 -0.13 0.14 -10000 0 -0.56 9 9
FOXM1C/SP1 -0.33 0.51 -10000 0 -0.91 177 177
AURKB 0.003 0.062 -10000 0 -10000 0 0
CENPF -0.31 0.47 -10000 0 -0.87 147 147
CDK4 0.009 0.024 -10000 0 -10000 0 0
MYC -0.28 0.45 -10000 0 -0.83 140 140
CHEK2 0.009 0.044 -10000 0 -10000 0 0
ONECUT1 -0.3 0.47 -10000 0 -0.83 165 165
CDKN2A -0.015 0.06 -10000 0 -10000 0 0
LAMA4 -0.3 0.47 -10000 0 -0.88 134 134
FOXM1B/HNF6 -0.35 0.55 -10000 0 -0.98 165 165
FOS -0.84 0.7 -10000 0 -1.3 378 378
SP1 0.017 0.003 -10000 0 -10000 0 0
CDC25B -0.3 0.46 -10000 0 -0.89 121 121
response to radiation -0.01 0.036 -10000 0 -10000 0 0
CENPB -0.29 0.46 -10000 0 -0.9 110 110
CENPA -0.31 0.47 -10000 0 -0.86 152 152
NEK2 -0.32 0.47 -10000 0 -0.86 157 157
HIST1H2BA -0.29 0.46 -10000 0 -0.91 107 107
CCNA2 -0.045 0.082 -10000 0 -10000 0 0
EP300 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.34 0.52 -10000 0 -1.1 94 94
CCNB2 -0.31 0.47 -10000 0 -0.92 114 114
CCNB1 -0.32 0.49 -10000 0 -0.89 154 154
ETV5 -0.31 0.49 -10000 0 -0.92 137 137
ESR1 -0.44 0.63 -10000 0 -1.2 193 193
CCND1 -0.29 0.47 -10000 0 -0.85 146 146
GSK3A 0.015 0.029 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.023 0.088 -10000 0 -10000 0 0
CDK2 0.007 0.027 -10000 0 -0.16 12 12
G2/M transition of mitotic cell cycle -0.013 0.042 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.38 0.39 -10000 0 -0.83 192 192
GAS1 -0.5 0.67 -10000 0 -1.2 201 201
MMP2 -0.3 0.47 -10000 0 -0.96 92 92
RB1/FOXM1C -0.29 0.47 -10000 0 -0.84 159 159
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.34 0.22 -10000 0 -0.5 340 340
PTP1B/AKT1 -0.17 0.13 -10000 0 -0.28 296 296
FYN 0.013 0.045 -10000 0 -0.72 2 2
p210 bcr-abl/PTP1B -0.21 0.15 -10000 0 -0.32 298 298
EGFR -0.39 0.37 -10000 0 -0.74 277 277
EGF/EGFR -0.48 0.32 -10000 0 -0.66 372 372
CSF1 0.016 0.007 -10000 0 -10000 0 0
AKT1 0.013 0.02 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.2 0.15 -10000 0 -0.31 297 297
Insulin Receptor/Insulin -0.12 0.084 -10000 0 -10000 0 0
HCK 0.013 0.024 -10000 0 -10000 0 0
CRK 0.015 0.032 -10000 0 -0.72 1 1
TYK2 -0.19 0.14 -10000 0 -0.3 297 297
EGF -0.25 0.35 -10000 0 -0.74 178 178
YES1 0.015 0.032 -10000 0 -0.72 1 1
CAV1 -0.43 0.26 -10000 0 -0.57 388 388
TXN 0.004 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.22 0.19 -10000 0 -0.35 299 299
cell migration 0.21 0.15 0.32 298 -10000 0 298
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.021 0.07 -10000 0 -10000 0 0
ITGA2B 0.013 0.01 -10000 0 -10000 0 0
CSF1R 0.016 0 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.05 0.024 -10000 0 -10000 0 0
FGR 0.016 0 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.19 0.14 -10000 0 -0.3 297 297
Crk/p130 Cas -0.17 0.14 -10000 0 -0.28 297 297
DOK1 -0.15 0.12 -10000 0 -0.26 208 208
JAK2 -0.094 0.088 -10000 0 -0.78 1 1
Jak2/Leptin Receptor/Leptin -0.36 0.23 -10000 0 -0.5 343 343
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
PTPN1 -0.21 0.15 -10000 0 -0.33 298 298
LYN 0.016 0.01 -10000 0 -10000 0 0
CDH2 -0.013 0.062 -10000 0 -10000 0 0
SRC -0.057 0.055 -10000 0 -10000 0 0
ITGB3 0.011 0.02 -10000 0 -10000 0 0
CAT1/PTP1B -0.15 0.14 -10000 0 -0.47 17 17
CAPN1 0.003 0.016 -10000 0 -10000 0 0
CSK 0.016 0.01 -10000 0 -10000 0 0
PI3K -0.14 0.14 -10000 0 -0.5 51 51
mol:H2O2 -0.007 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.32 0.21 -10000 0 -0.46 298 298
negative regulation of transcription -0.093 0.088 -10000 0 -0.76 1 1
FCGR2A 0.013 0.023 -10000 0 -10000 0 0
FER 0.004 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.002 0.011 -10000 0 -10000 0 0
BLK 0.002 0.045 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.005 0.007 -10000 0 -10000 0 0
LEPR -0.47 0.35 -10000 0 -0.72 344 344
BCAR1 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0.022 -10000 0 -10000 0 0
mol:NADPH -0.007 0.004 -10000 0 -10000 0 0
TRPV6 0.026 0.059 -10000 0 -0.54 1 1
PRL 0.021 0.003 -10000 0 -10000 0 0
SOCS3 0.003 0.25 -10000 0 -1.4 15 15
SPRY2 -0.48 0.35 -10000 0 -0.73 350 350
Insulin Receptor/Insulin/IRS1 -0.061 0.16 -10000 0 -0.46 69 69
CSF1/CSF1R -0.17 0.14 -10000 0 -0.28 297 297
Ras protein signal transduction 0.076 0.044 -10000 0 -10000 0 0
IRS1 -0.081 0.25 -10000 0 -0.72 69 69
INS 0.016 0.001 -10000 0 -10000 0 0
LEP -0.35 0.37 -10000 0 -0.72 258 258
STAT5B -0.16 0.12 -10000 0 -0.25 296 296
STAT5A -0.16 0.12 -10000 0 -0.26 296 296
GRB2 0.013 0.022 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.19 0.14 -10000 0 -0.3 297 297
CSN2 0.071 0.031 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
LAT -0.056 0.056 -10000 0 -10000 0 0
YBX1 0.018 0.017 -10000 0 -10000 0 0
LCK 0 0.049 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
NOX4 -0.019 0.069 -10000 0 -0.74 1 1
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.016 0.036 -9999 0 -0.47 2 2
NFATC2 0.018 0.029 -9999 0 -0.47 1 1
NFATC3 0.018 0.02 -9999 0 -10000 0 0
CD40LG -0.34 0.32 -9999 0 -0.58 297 297
PTGS2 -0.54 0.44 -9999 0 -0.82 342 342
JUNB 0.012 0.056 -9999 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.006 -9999 0 -10000 0 0
CaM/Ca2+ 0.002 0.006 -9999 0 -10000 0 0
CALM1 0.015 0.005 -9999 0 -10000 0 0
JUN -0.12 0.29 -9999 0 -0.73 97 97
mol:Ca2+ -0.006 0.006 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.005 -9999 0 -10000 0 0
FOSL1 0.016 0.01 -9999 0 -10000 0 0
CREM 0.016 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.084 0.16 -9999 0 -0.41 90 90
FOS -0.51 0.34 -9999 0 -0.73 374 374
IFNG -0.35 0.33 -9999 0 -0.59 297 297
AP-1/NFAT1-c-4 -0.41 0.39 -9999 0 -0.7 297 297
FASLG -0.34 0.32 -9999 0 -0.58 297 297
NFAT1-c-4/ICER1 0.001 0.035 -9999 0 -0.37 3 3
IL2RA -0.34 0.32 -9999 0 -0.58 297 297
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.34 0.32 -9999 0 -0.58 297 297
JunB/Fra1/NFAT1-c-4 0.01 0.046 -9999 0 -0.36 5 5
IL4 -0.34 0.32 -9999 0 -0.57 297 297
IL2 -0.011 0.067 -9999 0 -1.5 1 1
IL3 -0.009 0.019 -9999 0 -10000 0 0
FKBP1A 0.016 0.01 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.026 0 -9999 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.097 0.17 -9999 0 -0.36 147 147
PDGFRB 0.007 0.008 -9999 0 -10000 0 0
SPHK1 -0.049 0.098 -9999 0 -1.1 4 4
mol:S1P -0.059 0.095 -9999 0 -1 4 4
S1P1/S1P/Gi -0.34 0.34 -9999 0 -0.69 215 215
GNAO1 0.007 0.009 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.28 0.29 -9999 0 -0.59 206 206
PLCG1 -0.31 0.31 -9999 0 -0.64 206 206
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.007 0.008 -9999 0 -10000 0 0
GNAI2 0.007 0.012 -9999 0 -10000 0 0
GNAI3 0.007 0.009 -9999 0 -10000 0 0
GNAI1 -0.26 0.36 -9999 0 -0.73 189 189
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.22 0.38 -9999 0 -0.83 147 147
S1P1/S1P -0.24 0.31 -9999 0 -0.73 147 147
negative regulation of cAMP metabolic process -0.33 0.33 -9999 0 -0.66 215 215
MAPK3 -0.43 0.4 -9999 0 -0.71 323 323
calcium-dependent phospholipase C activity -0.005 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.037 0.09 -9999 0 -10000 0 0
PLCB2 -0.19 0.28 -9999 0 -0.62 147 147
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.19 0.25 -9999 0 -0.58 147 147
receptor internalization -0.22 0.28 -9999 0 -0.66 147 147
PTGS2 -0.67 0.57 -9999 0 -1.1 317 317
Rac1/GTP -0.19 0.25 -9999 0 -0.58 147 147
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.06 0.12 -9999 0 -0.36 30 30
negative regulation of T cell proliferation -0.33 0.33 -9999 0 -0.66 215 215
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.001 0.079 -9999 0 -0.73 6 6
MAPK1 -0.43 0.4 -9999 0 -0.71 323 323
S1P1/S1P/PDGFB-D/PDGFRB -0.24 0.34 -9999 0 -0.77 147 147
ABCC1 0.008 0.027 -9999 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.1 0.47 -10000 0 -0.78 118 118
HDAC7 0.002 0.005 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.14 0.3 0.56 1 -0.67 67 68
SMAD4 0.015 0.045 -10000 0 -0.72 2 2
ID2 -0.1 0.47 -10000 0 -0.78 117 117
AP1 -0.47 0.35 -10000 0 -0.67 375 375
ABCG2 -0.12 0.5 -10000 0 -0.84 121 121
HIF1A 0.001 0.12 -10000 0 -0.69 5 5
TFF3 -0.18 0.54 -10000 0 -0.88 146 146
GATA2 0.003 0.043 -10000 0 -10000 0 0
AKT1 0.006 0.1 -10000 0 -0.29 4 4
response to hypoxia -0.014 0.11 -10000 0 -0.17 14 14
MCL1 -0.1 0.47 -10000 0 -0.78 118 118
NDRG1 -0.11 0.48 -10000 0 -0.78 118 118
SERPINE1 -0.1 0.48 -10000 0 -0.78 117 117
FECH -0.1 0.47 -10000 0 -0.78 119 119
FURIN -0.1 0.47 -10000 0 -0.78 118 118
NCOA2 0.017 0.014 -10000 0 -10000 0 0
EP300 0.032 0.15 -10000 0 -10000 0 0
HMOX1 -0.1 0.48 -10000 0 -0.78 117 117
BHLHE40 -0.12 0.47 -10000 0 -0.77 122 122
BHLHE41 -0.12 0.47 -10000 0 -0.77 122 122
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.029 0.083 0.29 1 -0.5 7 8
ENG 0.052 0.14 -10000 0 -0.45 7 7
JUN -0.12 0.29 -10000 0 -0.73 97 97
RORA -0.11 0.49 -10000 0 -0.81 118 118
ABCB1 -0.41 0.57 -10000 0 -1.2 169 169
TFRC -0.11 0.48 -10000 0 -0.79 119 119
CXCR4 -0.11 0.48 -10000 0 -0.77 122 122
TF -0.12 0.49 -10000 0 -0.81 123 123
CITED2 -0.11 0.48 -10000 0 -0.8 117 117
HIF1A/ARNT -0.23 0.44 0.64 22 -0.88 117 139
LDHA -0.022 0.038 -10000 0 -10000 0 0
ETS1 -0.1 0.47 -10000 0 -0.78 119 119
PGK1 -0.1 0.47 -10000 0 -0.78 117 117
NOS2 -0.12 0.47 -10000 0 -0.77 122 122
ITGB2 -0.1 0.48 -10000 0 -0.78 117 117
ALDOA -0.1 0.47 -10000 0 -0.78 118 118
Cbp/p300/CITED2 -0.12 0.47 -10000 0 -0.86 88 88
FOS -0.51 0.34 -10000 0 -0.73 374 374
HK2 -0.1 0.47 -10000 0 -0.78 118 118
SP1 0.004 0.049 -10000 0 -10000 0 0
GCK 0.054 0.2 -10000 0 -10000 0 0
HK1 -0.1 0.47 -10000 0 -0.78 117 117
NPM1 -0.1 0.47 -10000 0 -0.78 117 117
EGLN1 -0.1 0.47 -10000 0 -0.78 117 117
CREB1 0.026 0.002 -10000 0 -10000 0 0
PGM1 -0.11 0.48 -10000 0 -0.78 120 120
SMAD3 0.017 0.033 -10000 0 -0.72 1 1
EDN1 -0.46 0.64 -10000 0 -1.4 169 169
IGFBP1 -0.1 0.47 -10000 0 -0.78 117 117
VEGFA -0.033 0.37 -10000 0 -0.61 71 71
HIF1A/JAB1 -0.013 0.061 -10000 0 -0.6 4 4
CP -0.22 0.56 -10000 0 -0.89 162 162
CXCL12 -0.22 0.6 -10000 0 -0.96 170 170
COPS5 0.018 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.003 0.04 -10000 0 -0.54 3 3
BNIP3 -0.11 0.48 -10000 0 -0.78 120 120
EGLN3 -0.11 0.48 -10000 0 -0.79 118 118
CA9 -0.11 0.48 -10000 0 -0.79 119 119
TERT -0.1 0.47 -10000 0 -0.78 119 119
ENO1 -0.1 0.47 -10000 0 -0.78 118 118
PFKL -0.1 0.47 -10000 0 -0.78 117 117
NCOA1 0.015 0.032 -10000 0 -0.72 1 1
ADM -0.25 0.55 -10000 0 -0.86 182 182
ARNT 0.008 0.09 -10000 0 -10000 0 0
HNF4A 0.022 0 -10000 0 -10000 0 0
ADFP -0.12 0.5 -10000 0 -0.82 127 127
SLC2A1 -0.03 0.36 -10000 0 -0.61 68 68
LEP -0.3 0.6 -10000 0 -0.9 216 216
HIF1A/ARNT/Cbp/p300 -0.13 0.34 -10000 0 -0.7 68 68
EPO 0.004 0.32 -10000 0 -0.59 13 13
CREBBP 0.032 0.15 -10000 0 -0.5 1 1
HIF1A/ARNT/Cbp/p300/HDAC7 -0.15 0.3 0.56 1 -0.66 78 79
PFKFB3 -0.11 0.48 -10000 0 -0.79 117 117
NT5E -0.11 0.49 -10000 0 -0.8 119 119
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.016 0.071 0.39 1 -10000 0 1
SMARCC2 0.016 0 -10000 0 -10000 0 0
SMARCC1 0.014 0.02 -10000 0 -10000 0 0
TBX21 -0.091 0.27 -10000 0 -1 36 36
SUMO2 0.003 0.009 -10000 0 -10000 0 0
STAT1 (dimer) -0.001 0.064 -10000 0 -10000 0 0
FKBP4 0.01 0.031 -10000 0 -10000 0 0
FKBP5 -0.002 0.11 -10000 0 -0.72 11 11
GR alpha/HSP90/FKBP51/HSP90 0.09 0.15 0.33 30 -0.36 15 45
PRL -0.037 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.26 0.25 0.48 273 -10000 0 273
RELA -0.1 0.081 -10000 0 -0.3 9 9
FGG 0.26 0.21 0.45 229 -10000 0 229
GR beta/TIF2 0.11 0.15 0.35 32 -0.44 7 39
IFNG -0.51 0.32 -10000 0 -0.76 290 290
apoptosis -0.25 0.15 0.56 1 -0.54 17 18
CREB1 0.026 0.004 -10000 0 -10000 0 0
histone acetylation 0.05 0.15 0.45 45 -0.29 19 64
BGLAP -0.05 0.13 -10000 0 -0.56 1 1
GR/PKAc 0.11 0.14 0.32 23 -0.39 8 31
NF kappa B1 p50/RelA -0.18 0.15 -10000 0 -0.45 35 35
SMARCD1 0.016 0 -10000 0 -10000 0 0
MDM2 0.13 0.091 0.22 213 -10000 0 213
GATA3 -0.063 0.19 -10000 0 -0.71 38 38
AKT1 -0.002 0.02 -10000 0 -10000 0 0
CSF2 0.001 0.11 -10000 0 -0.46 1 1
GSK3B 0.002 0.012 -10000 0 -10000 0 0
NR1I3 -0.2 0.16 0.54 1 -0.54 3 4
CSN2 0.22 0.18 0.39 215 -10000 0 215
BRG1/BAF155/BAF170/BAF60A 0.002 0.013 -10000 0 -10000 0 0
NFATC1 0.024 0.046 -10000 0 -0.71 2 2
POU2F1 0.026 0 -10000 0 -10000 0 0
CDKN1A 0.058 0.099 -10000 0 -1.5 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.012 0.006 -10000 0 -10000 0 0
SFN 0.012 0.048 -10000 0 -0.72 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.33 27 -0.38 6 33
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.7 0.37 0.52 1 -0.87 436 437
JUN -0.24 0.27 -10000 0 -0.56 185 185
IL4 -0.052 0.13 -10000 0 -0.5 6 6
CDK5R1 0.001 0.019 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.64 0.36 -10000 0 -0.77 422 422
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.14 0.33 29 -0.37 8 37
cortisol/GR alpha (monomer) 0.3 0.3 0.56 274 -0.47 2 276
NCOA2 0.015 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.59 0.34 -10000 0 -0.8 374 374
AP-1/NFAT1-c-4 -0.86 0.48 -10000 0 -1.1 410 410
AFP -0.18 0.22 -10000 0 -0.58 75 75
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.19 0.16 0.49 26 -10000 0 26
TP53 0.043 0.032 -10000 0 -0.47 2 2
PPP5C 0.014 0.02 -10000 0 -10000 0 0
KRT17 -1.1 0.75 -10000 0 -1.7 339 339
KRT14 -0.94 0.72 -10000 0 -1.5 334 334
TBP 0.028 0.001 -10000 0 -10000 0 0
CREBBP 0.17 0.14 0.28 311 -0.46 1 312
HDAC1 0.003 0.005 -10000 0 -10000 0 0
HDAC2 0.011 0.017 -10000 0 -10000 0 0
AP-1 -0.87 0.5 -10000 0 -1.1 410 410
MAPK14 0.003 0.007 -10000 0 -10000 0 0
MAPK10 -0.016 0.11 -10000 0 -0.73 12 12
MAPK11 0.003 0.007 -10000 0 -10000 0 0
KRT5 -1.2 0.73 -10000 0 -1.7 365 365
interleukin-1 receptor activity -0.003 0.002 -10000 0 -10000 0 0
NCOA1 0.019 0.032 -10000 0 -0.71 1 1
STAT1 -0.001 0.064 -10000 0 -10000 0 0
CGA -0.068 0.14 -10000 0 -0.52 5 5
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.17 0.18 0.32 277 -0.37 4 281
MAPK3 0.003 0.007 -10000 0 -10000 0 0
MAPK1 0.003 0.007 -10000 0 -10000 0 0
ICAM1 -0.28 0.23 -10000 0 -0.71 48 48
NFKB1 -0.1 0.081 -10000 0 -0.3 9 9
MAPK8 -0.13 0.18 -10000 0 -0.39 107 107
MAPK9 0.003 0.01 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.26 0.15 0.56 1 -0.56 17 18
BAX 0.063 0.035 -10000 0 -10000 0 0
POMC -0.14 0.2 -10000 0 -0.76 15 15
EP300 0.17 0.14 0.28 309 -10000 0 309
cortisol/GR alpha (dimer)/p53 0.28 0.26 0.5 274 -10000 0 274
proteasomal ubiquitin-dependent protein catabolic process 0.086 0.078 0.23 25 -10000 0 25
SGK1 0.25 0.16 0.37 333 -10000 0 333
IL13 -0.36 0.24 -10000 0 -0.7 90 90
IL6 -0.88 0.53 -10000 0 -1.2 392 392
PRKACG 0.015 0.032 -10000 0 -0.72 1 1
IL5 -0.31 0.2 -10000 0 -0.63 53 53
IL2 -0.5 0.32 -10000 0 -0.72 315 315
CDK5 -0.001 0.027 -10000 0 -10000 0 0
PRKACB -0.007 0.099 -10000 0 -0.72 8 8
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
IL8 -0.28 0.23 -10000 0 -0.66 66 66
CDK5R1/CDK5 -0.003 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.1 0.13 -10000 0 -0.52 17 17
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.26 0.24 0.47 270 -10000 0 270
SMARCA4 0.015 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.16 0.34 229 -10000 0 229
NF kappa B1 p50/RelA/Cbp -0.014 0.16 0.37 12 -0.43 2 14
JUN (dimer) -0.24 0.27 -10000 0 -0.56 185 185
YWHAH 0.015 0.012 -10000 0 -10000 0 0
VIPR1 -0.053 0.17 -10000 0 -0.6 30 30
NR3C1 0.18 0.2 0.36 203 -0.52 11 214
NR4A1 -0.01 0.16 -10000 0 -0.72 26 26
TIF2/SUV420H1 -0.001 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.25 0.15 0.56 1 -0.54 17 18
cortisol/GR alpha (dimer)/Src-1 0.27 0.26 0.49 269 -10000 0 269
PBX1 0.008 0.065 -10000 0 -0.72 2 2
POU1F1 0.025 0.032 -10000 0 -0.72 1 1
SELE -0.35 0.38 -10000 0 -1 85 85
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.34 228 -10000 0 228
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.26 0.24 0.47 270 -10000 0 270
mol:cortisol 0.19 0.17 0.32 279 -10000 0 279
MMP1 -0.17 0.08 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.35 0.46 -10000 0 -1.2 60 60
IL23A -0.31 0.38 -10000 0 -1 43 43
NF kappa B1 p50/RelA/I kappa B alpha -0.35 0.3 -10000 0 -0.7 147 147
positive regulation of T cell mediated cytotoxicity -0.35 0.41 -10000 0 -0.69 274 274
ITGA3 -0.31 0.38 -10000 0 -0.98 45 45
IL17F -0.22 0.3 -10000 0 -0.64 73 73
IL12B 0.012 0.035 -10000 0 -10000 0 0
STAT1 (dimer) -0.34 0.4 -10000 0 -0.68 252 252
CD4 -0.31 0.37 -10000 0 -0.9 52 52
IL23 -0.3 0.37 -10000 0 -0.97 42 42
IL23R -0.04 0.13 -10000 0 -1.6 2 2
IL1B -0.32 0.39 -10000 0 -0.87 76 76
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.31 0.37 -10000 0 -0.96 44 44
TYK2 0.009 0.019 -10000 0 -10000 0 0
STAT4 0.005 0.086 -10000 0 -0.72 7 7
STAT3 0.017 0 -10000 0 -10000 0 0
IL18RAP -0.046 0.21 -10000 0 -0.72 45 45
IL12RB1 0.009 0.019 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.006 0.026 -10000 0 -10000 0 0
IL23R/JAK2 -0.048 0.14 -10000 0 -1.2 3 3
positive regulation of chronic inflammatory response -0.35 0.41 -10000 0 -0.69 274 274
natural killer cell activation 0.003 0.009 0.079 2 -10000 0 2
JAK2 0.011 0.043 -10000 0 -0.76 1 1
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
NFKB1 0.014 0.004 -10000 0 -10000 0 0
RELA 0.014 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.29 0.36 -10000 0 -0.92 43 43
ALOX12B -0.31 0.37 -10000 0 -0.95 45 45
CXCL1 -0.77 0.7 -10000 0 -1.3 304 304
T cell proliferation -0.35 0.41 -10000 0 -0.69 274 274
NFKBIA 0.013 0.033 -10000 0 -0.73 1 1
IL17A -0.15 0.25 -10000 0 -0.48 71 71
PI3K -0.39 0.34 -10000 0 -0.75 173 173
IFNG -0.012 0.03 0.15 2 -0.094 17 19
STAT3 (dimer) -0.36 0.32 -10000 0 -0.79 117 117
IL18R1 0.015 0.035 -10000 0 -0.72 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.25 -10000 0 -0.55 50 50
IL18/IL18R -0.01 0.15 -10000 0 -0.47 45 45
macrophage activation -0.021 0.016 -10000 0 -0.042 42 42
TNF -0.32 0.38 -10000 0 -1 44 44
STAT3/STAT4 -0.36 0.32 0.36 1 -0.64 255 256
STAT4 (dimer) -0.34 0.4 -10000 0 -0.67 255 255
IL18 0.003 0.055 -10000 0 -0.72 1 1
IL19 -0.32 0.37 -10000 0 -0.95 45 45
STAT5A (dimer) -0.34 0.39 -10000 0 -0.66 273 273
STAT1 -0.011 0.061 -10000 0 -10000 0 0
SOCS3 -0.005 0.12 -10000 0 -0.72 15 15
CXCL9 -0.33 0.39 -10000 0 -1 47 47
MPO -0.31 0.37 -10000 0 -0.95 44 44
positive regulation of humoral immune response -0.35 0.41 -10000 0 -0.69 274 274
IL23/IL23R/JAK2/TYK2 -0.36 0.43 -10000 0 -0.7 273 273
IL6 -0.93 0.66 -10000 0 -1.3 391 391
STAT5A 0.013 0.045 -10000 0 -0.72 2 2
IL2 0.019 0.034 -10000 0 -0.72 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.009 0.079 2 -10000 0 2
CD3E -0.31 0.37 -10000 0 -0.95 45 45
keratinocyte proliferation -0.35 0.41 -10000 0 -0.69 274 274
NOS2 -0.32 0.37 -10000 0 -0.63 274 274
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.23 0.2 -9999 0 -0.36 374 374
MAP3K8 -0.093 0.25 -9999 0 -0.73 70 70
FOS -0.12 0.12 -9999 0 -0.3 58 58
PRKCA 0.005 0.013 -9999 0 -10000 0 0
PTPN7 -0.003 0.038 -9999 0 -10000 0 0
HRAS 0.013 0.012 -9999 0 -10000 0 0
PRKCB -0.013 0.01 -9999 0 -0.019 374 374
NRAS 0.012 0.019 -9999 0 -10000 0 0
RAS family/GTP -0.002 0.015 -9999 0 -10000 0 0
MAPK3 -0.052 0.065 -9999 0 -10000 0 0
MAP2K1 -0.055 0.091 -9999 0 -0.27 58 58
ELK1 0 0.018 -9999 0 -10000 0 0
BRAF -0.018 0.015 -9999 0 -10000 0 0
mol:GTP -0.004 0.003 -9999 0 -0.006 374 374
MAPK1 -0.052 0.065 -9999 0 -10000 0 0
RAF1 -0.018 0.015 -9999 0 -10000 0 0
KRAS 0.01 0.026 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.099 0.25 -9999 0 -0.76 64 64
PDGF/PDGFRA/CRKL -0.068 0.18 -9999 0 -0.56 64 64
positive regulation of JUN kinase activity -0.05 0.14 -9999 0 -0.42 64 64
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.071 0.19 -9999 0 -0.57 65 65
AP1 -0.84 0.54 -9999 0 -1.2 375 375
mol:IP3 -0.084 0.19 -9999 0 -0.6 64 64
PLCG1 -0.084 0.19 -9999 0 -0.6 64 64
PDGF/PDGFRA/alphaV Integrin -0.07 0.18 -9999 0 -0.56 65 65
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
mol:Ca2+ -0.084 0.19 -9999 0 -0.59 64 64
CAV3 0.013 0.046 -9999 0 -0.72 2 2
CAV1 -0.52 0.33 -9999 0 -0.72 385 385
SHC/Grb2/SOS1 -0.05 0.14 -9999 0 -0.42 64 64
PDGF/PDGFRA/Shf -0.068 0.18 -9999 0 -0.56 64 64
FOS -0.8 0.55 -9999 0 -1.1 375 375
JUN -0.15 0.23 -9999 0 -0.62 97 97
oligodendrocyte development -0.07 0.18 -9999 0 -0.56 65 65
GRB2 0.013 0.022 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
mol:DAG -0.084 0.19 -9999 0 -0.6 64 64
PDGF/PDGFRA -0.099 0.25 -9999 0 -0.76 64 64
actin cytoskeleton reorganization -0.07 0.18 -9999 0 -0.56 65 65
SRF 0.046 0.012 -9999 0 -10000 0 0
SHC1 0.016 0 -9999 0 -10000 0 0
PI3K -0.1 0.23 -9999 0 -0.56 95 95
PDGF/PDGFRA/Crk/C3G -0.058 0.16 -9999 0 -0.48 64 64
JAK1 -0.058 0.19 -9999 0 -0.56 66 66
ELK1/SRF -0.024 0.16 -9999 0 -0.45 64 64
SHB 0.013 0.037 -9999 0 -0.72 1 1
SHF 0.015 0.012 -9999 0 -10000 0 0
CSNK2A1 0.046 0.028 -9999 0 -10000 0 0
GO:0007205 -0.091 0.2 -9999 0 -0.62 64 64
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.05 0.14 -9999 0 -0.42 64 64
PDGF/PDGFRA/SHB -0.07 0.18 -9999 0 -0.56 65 65
PDGF/PDGFRA/Caveolin-1 -0.47 0.31 -9999 0 -0.64 387 387
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
ELK1 -0.099 0.18 -9999 0 -0.57 64 64
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.069 0.19 -9999 0 -0.57 64 64
JAK-STAT cascade -0.058 0.19 -9999 0 -0.56 66 66
cell proliferation -0.068 0.18 -9999 0 -0.56 64 64
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.082 0.26 -10000 0 -0.68 38 38
CRP -0.082 0.26 -10000 0 -0.77 27 27
cell cycle arrest -0.099 0.3 -10000 0 -0.62 105 105
TIMP1 -0.099 0.23 -10000 0 -0.51 87 87
IL6ST -0.01 0.15 -10000 0 -0.72 21 21
Rac1/GDP -0.16 0.22 -10000 0 -0.47 117 117
AP1 -0.29 0.26 -10000 0 -0.48 292 292
GAB2 0.019 0.018 -10000 0 -10000 0 0
TNFSF11 -0.089 0.26 -10000 0 -0.72 34 34
HSP90B1 0.02 0.065 -10000 0 -0.96 1 1
GAB1 0.017 0.034 -10000 0 -0.72 1 1
MAPK14 -0.2 0.24 -10000 0 -0.76 56 56
AKT1 0.044 0.079 -10000 0 -10000 0 0
FOXO1 -0.004 0.17 -10000 0 -0.38 71 71
MAP2K6 -0.21 0.24 -10000 0 -0.52 125 125
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.12 0.23 -10000 0 -0.48 114 114
MITF -0.19 0.24 -10000 0 -0.51 117 117
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.016 0 -10000 0 -10000 0 0
A2M -0.16 0.5 -10000 0 -1.5 65 65
CEBPB 0.025 0.033 -10000 0 -0.72 1 1
GRB2/SOS1/GAB family/SHP2 -0.025 0.093 0.3 1 -10000 0 1
STAT3 -0.11 0.32 -10000 0 -0.66 106 106
STAT1 -0.001 0.034 -10000 0 -10000 0 0
CEBPD -0.16 0.42 -10000 0 -1.1 71 71
PIK3CA 0.018 0.007 -10000 0 -10000 0 0
PI3K -0.028 0.17 -10000 0 -0.54 51 51
JUN -0.12 0.29 -10000 0 -0.72 97 97
PIAS3/MITF -0.18 0.23 -10000 0 -0.49 111 111
MAPK11 -0.2 0.24 -10000 0 -0.74 59 59
STAT3 (dimer)/FOXO1 -0.12 0.32 -10000 0 -0.66 98 98
GRB2/SOS1/GAB family -0.17 0.17 -10000 0 -0.64 42 42
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.22 0.23 -10000 0 -0.44 160 160
GRB2 0.016 0.023 -10000 0 -10000 0 0
JAK2 0.015 0.033 -10000 0 -0.72 1 1
LBP -0.088 0.22 -10000 0 -0.62 31 31
PIK3R1 -0.054 0.22 -10000 0 -0.72 51 51
JAK1 0.017 0.046 -10000 0 -0.73 2 2
MYC -0.11 0.34 -10000 0 -1.1 38 38
FGG -0.083 0.26 -10000 0 -0.7 36 36
macrophage differentiation -0.099 0.3 -10000 0 -0.62 105 105
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.3 0.22 -10000 0 -0.4 396 396
JUNB -0.092 0.26 -10000 0 -0.64 49 49
FOS -0.51 0.34 -10000 0 -0.72 374 374
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.21 0.24 -10000 0 -0.51 130 130
STAT1/PIAS1 -0.17 0.23 -10000 0 -0.5 109 109
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.082 -10000 0 -10000 0 0
STAT3 (dimer) -0.1 0.31 -10000 0 -0.65 105 105
PRKCD -0.092 0.24 -10000 0 -0.48 112 112
IL6R 0.018 0.033 -10000 0 -0.72 1 1
SOCS3 -0.2 0.27 -10000 0 -0.85 56 56
gp130 (dimer)/JAK1/JAK1/LMO4 0.017 0.15 -10000 0 -0.47 44 44
Rac1/GTP -0.15 0.23 -10000 0 -0.48 116 116
HCK 0.013 0.024 -10000 0 -10000 0 0
MAPKKK cascade 0.005 0.083 -10000 0 -10000 0 0
bone resorption -0.093 0.25 -10000 0 -0.68 34 34
IRF1 -0.084 0.26 -10000 0 -0.7 36 36
mol:GDP -0.18 0.23 -10000 0 -0.49 119 119
SOS1 0.02 0.008 -10000 0 -10000 0 0
VAV1 -0.19 0.24 -10000 0 -0.5 119 119
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.22 0.24 -10000 0 -0.78 56 56
PTPN11 -0.009 0.02 -10000 0 -10000 0 0
IL6/IL6RA -0.38 0.25 -10000 0 -0.53 391 391
gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.14 -10000 0 -0.47 43 43
gp130 (dimer)/JAK2/JAK2/LMO4 0.01 0.15 -10000 0 -0.48 43 43
IL6 -0.52 0.32 -10000 0 -0.72 391 391
PIAS3 0.016 0 -10000 0 -10000 0 0
PTPRE 0.002 0.045 -10000 0 -0.72 2 2
PIAS1 0.016 0.007 -10000 0 -10000 0 0
RAC1 0.017 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.23 0.21 -10000 0 -0.33 395 395
LMO4 -0.017 0.15 -10000 0 -0.72 22 22
STAT3 (dimer)/PIAS3 -0.17 0.26 0.36 1 -0.64 105 106
MCL1 0.052 0.073 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.036 0.077 -9999 0 -0.42 9 9
SMAD6-7/SMURF1 0 0.004 -9999 0 -10000 0 0
NOG 0.014 0.035 -9999 0 -0.72 1 1
SMAD9 -0.084 0.18 -9999 0 -0.91 20 20
SMAD4 0.013 0.045 -9999 0 -0.72 2 2
SMAD5 -0.15 0.21 -9999 0 -0.41 169 169
BMP7/USAG1 -0.4 0.24 -9999 0 -0.55 377 377
SMAD5/SKI -0.13 0.2 -9999 0 -0.52 70 70
SMAD1 0.025 0.045 -9999 0 -10000 0 0
BMP2 -0.34 0.37 -9999 0 -0.72 252 252
SMAD1/SMAD1/SMAD4 -0.002 0.021 -9999 0 -10000 0 0
BMPR1A 0.009 0.072 -9999 0 -0.72 5 5
BMPR1B -0.046 0.079 -9999 0 -10000 0 0
BMPR1A-1B/BAMBI -0.012 0.16 -9999 0 -0.51 41 41
AHSG 0.016 0 -9999 0 -10000 0 0
CER1 0.016 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.28 0.28 -9999 0 -0.51 289 289
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.21 -9999 0 -0.5 97 97
BMP2-4 (homodimer) -0.33 0.32 -9999 0 -0.6 289 289
RGMB 0.016 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.14 0.23 -9999 0 -0.45 182 182
RGMA -0.097 0.27 -9999 0 -0.72 81 81
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.16 0.22 -9999 0 -0.53 97 97
BMP2-4/USAG1 -0.6 0.34 -9999 0 -0.7 444 444
SMAD6/SMURF1/SMAD5 -0.13 0.2 -9999 0 -0.52 70 70
SOSTDC1 -0.51 0.33 -9999 0 -0.72 377 377
BMP7/BMPR2/BMPR1A-1B 0.038 0.065 -9999 0 -0.44 5 5
SKI 0.016 0.007 -9999 0 -10000 0 0
BMP6 (homodimer) -0.24 0.35 -9999 0 -0.72 180 180
HFE2 0.011 0.056 -9999 0 -0.72 3 3
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0.01 -9999 0 -10000 0 0
BMP2-4/CHRD -0.28 0.28 -9999 0 -0.51 289 289
SMAD5/SMAD5/SMAD4 -0.14 0.2 -9999 0 -0.53 71 71
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.13 0.16 -9999 0 -0.44 95 95
BMP7 (homodimer) -0.002 0.051 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.18 0.26 -9999 0 -0.54 180 180
SMAD1/SKI 0.033 0.043 -9999 0 -10000 0 0
SMAD6 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.28 0.28 -9999 0 -0.51 289 289
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
GREM1 -0.002 0.051 -9999 0 -10000 0 0
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.001 0.032 -9999 0 -0.46 2 2
BMPR1A-1B (homodimer) -0.035 0.065 -9999 0 -0.57 5 5
CHRDL1 -0.42 0.36 -9999 0 -0.72 309 309
ENDOFIN/SMAD1 0.033 0.043 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0 0.014 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI -0.064 0.19 -9999 0 -0.72 37 37
SMURF2 0.015 0.012 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.53 0.4 -9999 0 -0.74 378 378
BMP2-4/GREM1 -0.28 0.28 -9999 0 -0.52 289 289
SMAD7 0.016 0.007 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.06 0.18 -9999 0 -0.85 21 21
SMAD1/SMAD6 0.033 0.043 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.005 -9999 0 -10000 0 0
BMP7 -0.002 0.051 -9999 0 -10000 0 0
BMP6 -0.24 0.35 -9999 0 -0.72 180 180
MAP3K7IP2 0.015 0.032 -9999 0 -0.72 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.14 0.21 -9999 0 -0.51 95 95
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.033 0.043 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0.003 -9999 0 -10000 0 0
CTDSPL 0.013 0.045 -9999 0 -0.72 2 2
PPP1CA 0.01 0.032 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0.045 -9999 0 -0.72 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.15 0.22 -9999 0 -0.51 97 97
CHRD 0.013 0.022 -9999 0 -10000 0 0
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.19 0.25 -9999 0 -0.64 95 95
BMP4 -0.088 0.26 -9999 0 -0.72 73 73
FST 0.009 0.066 -9999 0 -0.72 4 4
BMP2-4/NOG -0.28 0.28 -9999 0 -0.51 290 290
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.04 0.064 -9999 0 -0.4 5 5
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.008 0.079 -10000 0 -0.72 6 6
EPHB2 0.005 0.04 -10000 0 -10000 0 0
EFNB1 0.027 0.036 -10000 0 -0.54 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.18 -10000 0 -0.35 197 197
Ephrin B2/EPHB1-2 -0.15 0.22 -10000 0 -0.43 198 198
neuron projection morphogenesis -0.12 0.17 -10000 0 -0.33 197 197
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.2 -10000 0 -0.38 197 197
DNM1 0.016 0.007 -10000 0 -10000 0 0
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.046 0.22 -10000 0 -0.65 58 58
YES1 -0.084 0.28 -10000 0 -0.91 52 52
Ephrin B1/EPHB1-2/NCK2 -0.13 0.2 -10000 0 -0.38 197 197
PI3K -0.082 0.25 -10000 0 -0.58 95 95
mol:GDP -0.14 0.19 -10000 0 -0.38 197 197
ITGA2B 0.016 0.01 -10000 0 -10000 0 0
endothelial cell proliferation -0.005 0.055 -10000 0 -0.47 7 7
FYN -0.084 0.27 -10000 0 -0.91 52 52
MAP3K7 -0.065 0.22 -10000 0 -0.72 52 52
FGR -0.085 0.27 -10000 0 -0.91 52 52
TIAM1 0.015 0.012 -10000 0 -10000 0 0
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion -0.057 0.23 -10000 0 -0.58 73 73
LYN -0.084 0.27 -10000 0 -0.91 52 52
Ephrin B1/EPHB1-2/Src Family Kinases -0.081 0.26 -10000 0 -0.85 52 52
Ephrin B1/EPHB1-2 -0.076 0.23 -10000 0 -0.78 52 52
SRC -0.085 0.27 -10000 0 -0.91 52 52
ITGB3 0.014 0.02 -10000 0 -10000 0 0
EPHB1 -0.26 0.36 -10000 0 -0.72 197 197
EPHB4 0.011 0.039 -10000 0 -0.72 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.005 0.055 -10000 0 -0.47 7 7
alphaIIb/beta3 Integrin -0.001 0.011 -10000 0 -10000 0 0
BLK -0.084 0.27 -10000 0 -0.91 52 52
HCK -0.085 0.27 -10000 0 -0.91 52 52
regulation of stress fiber formation 0.14 0.19 0.38 197 -10000 0 197
MAPK8 -0.035 0.21 -10000 0 -0.62 58 58
Ephrin B1/EPHB1-2/RGS3 -0.13 0.2 -10000 0 -0.38 197 197
endothelial cell migration -0.058 0.2 -10000 0 -0.6 57 57
NCK2 0.016 0.01 -10000 0 -10000 0 0
PTPN13 -0.073 0.25 -10000 0 -0.83 52 52
regulation of focal adhesion formation 0.14 0.19 0.38 197 -10000 0 197
chemotaxis 0.14 0.19 0.38 197 -10000 0 197
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.12 0.17 -10000 0 -0.34 197 197
angiogenesis -0.076 0.23 -10000 0 -0.77 52 52
LCK -0.083 0.27 -10000 0 -0.91 52 52
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.054 0.11 0.27 104 -10000 0 104
RFC1 0.054 0.11 0.27 104 -10000 0 104
PRKDC 0.052 0.11 0.27 99 -10000 0 99
RIPK1 0.023 0.004 -10000 0 -10000 0 0
CASP7 -0.047 0.054 -10000 0 -0.99 1 1
FASLG/FAS/FADD/FAF1 -0.033 0.1 0.25 10 -0.37 25 35
MAP2K4 -0.17 0.16 -10000 0 -0.47 39 39
mol:ceramide -0.1 0.13 -10000 0 -0.46 32 32
GSN -0.073 0.23 0.28 76 -0.42 138 214
FASLG/FAS/FADD/FAF1/Caspase 8 -0.047 0.097 -10000 0 -0.35 22 22
FAS -0.045 0.18 -10000 0 -0.74 35 35
BID -0.002 0.008 -10000 0 -10000 0 0
MAP3K1 -0.074 0.11 -10000 0 -0.32 23 23
MAP3K7 0.004 0.012 -10000 0 -10000 0 0
RB1 0.053 0.11 0.27 103 -0.35 2 105
CFLAR 0.02 0.044 -10000 0 -0.69 2 2
HGF/MET -0.089 0.2 -10000 0 -0.49 97 97
ARHGDIB 0.052 0.11 0.28 102 -0.45 1 103
FADD -0.01 0.049 -10000 0 -10000 0 0
actin filament polymerization 0.072 0.23 0.42 138 -0.27 76 214
NFKB1 -0.15 0.093 -10000 0 -10000 0 0
MAPK8 -0.29 0.23 -10000 0 -0.42 391 391
DFFA 0.054 0.11 0.27 104 -10000 0 104
DNA fragmentation during apoptosis 0.054 0.11 0.27 104 -10000 0 104
FAS/FADD/MET -0.083 0.19 -10000 0 -0.52 80 80
CFLAR/RIP1 -0.002 0.031 -10000 0 -0.5 2 2
FAIM3 0.015 0.03 -10000 0 -10000 0 0
FAF1 0.005 0.008 -10000 0 -10000 0 0
PARP1 0.047 0.11 0.28 87 -10000 0 87
DFFB 0.054 0.11 0.27 104 -10000 0 104
CHUK -0.13 0.084 -10000 0 -0.59 1 1
FASLG -0.011 0.056 -10000 0 -0.73 1 1
FAS/FADD -0.044 0.14 -10000 0 -0.57 35 35
HGF 0.016 0.01 -10000 0 -10000 0 0
LMNA 0.05 0.1 0.25 101 -10000 0 101
CASP6 0.054 0.11 0.27 102 -10000 0 102
CASP10 0.004 0.011 -10000 0 -10000 0 0
CASP3 0.064 0.13 0.33 104 -10000 0 104
PTPN13 -0.057 0.22 -10000 0 -0.72 52 52
CASP8 -0.002 0.009 -10000 0 -10000 0 0
IL6 -0.97 0.6 -10000 0 -1.3 391 391
MET -0.057 0.22 -10000 0 -0.72 52 52
ICAD/CAD 0.051 0.1 0.26 104 -10000 0 104
FASLG/FAS/FADD/FAF1/Caspase 10 -0.1 0.13 -10000 0 -0.47 32 32
activation of caspase activity by cytochrome c -0.002 0.008 -10000 0 -10000 0 0
PAK2 0.054 0.11 0.27 104 -10000 0 104
BCL2 -0.13 0.29 -10000 0 -0.72 104 104
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.089 0.26 -9999 0 -0.72 75 75
LAT2 -0.048 0.18 -9999 0 -0.48 53 53
AP1 -0.32 0.25 -9999 0 -0.58 215 215
mol:PIP3 -0.047 0.23 -9999 0 -0.46 101 101
IKBKB -0.016 0.14 -9999 0 -0.28 72 72
AKT1 -0.07 0.24 -9999 0 -0.62 57 57
IKBKG -0.016 0.14 -9999 0 -0.28 72 72
MS4A2 -0.12 0.28 -9999 0 -0.72 92 92
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.007 -9999 0 -10000 0 0
MAP3K1 -0.013 0.16 -9999 0 -0.42 46 46
mol:Ca2+ -0.027 0.18 -9999 0 -0.34 101 101
LYN 0.014 0.012 -9999 0 -10000 0 0
CBLB -0.047 0.18 -9999 0 -0.4 92 92
SHC1 0.016 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.18 0.21 -9999 0 -0.42 225 225
positive regulation of cell migration -0.14 0.25 -9999 0 -0.55 147 147
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.085 0.24 -9999 0 -0.46 139 139
PTPN13 -0.072 0.22 -9999 0 -0.49 80 80
PTPN11 0.015 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.017 0.18 -9999 0 -0.39 57 57
SYK 0.009 0.031 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.2 -9999 0 -0.47 101 101
LAT -0.048 0.18 -9999 0 -0.39 92 92
PAK2 -0.021 0.17 -9999 0 -0.44 49 49
NFATC2 -0.041 0.073 -9999 0 -0.61 1 1
HRAS -0.034 0.18 -9999 0 -0.48 52 52
GAB2 0.015 0.016 -9999 0 -10000 0 0
PLA2G1B 0.039 0.021 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.27 -9999 0 -0.58 138 138
Antigen/IgE/Fc epsilon R1 -0.14 0.25 -9999 0 -0.53 138 138
mol:GDP -0.043 0.19 -9999 0 -0.49 53 53
JUN -0.12 0.29 -9999 0 -0.72 97 97
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.056 0.22 -9999 0 -0.72 51 51
FOS -0.51 0.34 -9999 0 -0.72 374 374
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.092 0.17 -9999 0 -0.42 92 92
CHUK -0.016 0.14 -9999 0 -0.29 68 68
KLRG1 -0.047 0.17 -9999 0 -0.46 51 51
VAV1 -0.051 0.18 -9999 0 -0.4 93 93
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.047 0.18 -9999 0 -0.39 92 92
negative regulation of mast cell degranulation -0.076 0.14 -9999 0 -0.44 49 49
BTK -0.048 0.19 -9999 0 -0.49 53 53
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.087 0.26 -9999 0 -0.46 138 138
GAB2/PI3K/SHP2 -0.14 0.23 -9999 0 -0.7 57 57
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.064 0.21 -9999 0 -0.61 48 48
RAF1 0.023 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.24 -9999 0 -0.5 138 138
FCER1G 0.016 0.017 -9999 0 -10000 0 0
FCER1A -0.11 0.28 -9999 0 -0.74 88 88
Antigen/IgE/Fc epsilon R1/Fyn -0.13 0.24 -9999 0 -0.5 138 138
MAPK3 0.037 0.021 -9999 0 -10000 0 0
MAPK1 0.037 0.021 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.011 0.077 -9999 0 -0.42 8 8
DUSP1 -0.3 0.36 -9999 0 -0.72 225 225
NF-kappa-B/RelA -0.037 0.06 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.046 0.18 -9999 0 -0.48 52 52
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.1 0.18 -9999 0 -0.51 63 63
FER -0.047 0.18 -9999 0 -0.39 92 92
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.021 0.049 -9999 0 -0.56 2 2
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.039 0.2 -9999 0 -0.51 52 52
cytokine secretion -0.027 0.044 -9999 0 -10000 0 0
SPHK1 -0.052 0.19 -9999 0 -0.41 95 95
PTK2 -0.049 0.19 -9999 0 -0.5 52 52
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.21 -9999 0 -0.49 101 101
EDG1 -0.14 0.25 -9999 0 -0.55 147 147
mol:DAG -0.082 0.26 -9999 0 -0.58 84 84
MAP2K2 0.032 0.022 -9999 0 -10000 0 0
MAP2K1 0.032 0.022 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.074 0.14 -9999 0 -0.46 42 42
MAP2K4 0.011 0.11 -9999 0 -0.92 7 7
Fc epsilon R1/FcgammaRIIB -0.14 0.26 -9999 0 -0.53 138 138
mol:Choline -0.084 0.24 -9999 0 -0.45 139 139
SHC/Grb2/SOS1 -0.07 0.15 -9999 0 -0.48 42 42
FYN 0.013 0.045 -9999 0 -0.72 2 2
DOK1 0.014 0.019 -9999 0 -10000 0 0
PXN -0.035 0.18 -9999 0 -0.49 42 42
HCLS1 -0.047 0.18 -9999 0 -0.48 53 53
PRKCB -0.041 0.18 -9999 0 -0.36 106 106
FCGR2B 0.01 0.065 -9999 0 -0.72 4 4
IGHE -0.001 0.007 -9999 0 -10000 0 0
KLRG1/SHIP -0.078 0.14 -9999 0 -0.44 49 49
LCP2 0.012 0.024 -9999 0 -10000 0 0
PLA2G4A -0.29 0.26 -9999 0 -0.44 354 354
RASA1 0.015 0.012 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.084 0.24 -9999 0 -0.45 139 139
IKK complex 0.007 0.11 -9999 0 -0.22 45 45
WIPF1 0.013 0.024 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.07 0.18 -10000 0 -0.39 118 118
ER alpha/Gai/GDP/Gbeta gamma -0.14 0.2 -10000 0 -0.42 120 120
AKT1 -0.18 0.35 -10000 0 -0.82 117 117
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.18 0.36 -10000 0 -0.83 117 117
mol:Ca2+ -0.05 0.16 -10000 0 -0.39 77 77
IGF1R -0.023 0.15 -10000 0 -0.72 23 23
E2/ER alpha (dimer)/Striatin -0.091 0.21 -10000 0 -0.47 118 118
SHC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.16 0.34 0.77 118 -10000 0 118
RhoA/GTP -0.069 0.15 -10000 0 -0.34 117 117
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.15 0.2 -10000 0 -0.48 120 120
regulation of stress fiber formation 0.02 0.13 0.31 16 -10000 0 16
E2/ERA-ERB (dimer) -0.089 0.2 -10000 0 -0.47 117 117
KRAS 0.012 0.025 -10000 0 -10000 0 0
G13/GTP -0.081 0.19 -10000 0 -0.43 117 117
pseudopodium formation -0.02 0.13 -10000 0 -0.31 16 16
E2/ER alpha (dimer)/PELP1 -0.089 0.2 -10000 0 -0.47 117 117
GRB2 0.013 0.022 -10000 0 -10000 0 0
GNG2 0.015 0.032 -10000 0 -0.72 1 1
GNAO1 0.016 0 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.12 0.22 -10000 0 -0.5 120 120
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.092 0.21 -10000 0 -0.49 117 117
mol:NADP -0.12 0.22 -10000 0 -0.5 120 120
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
mol:IP3 -0.053 0.17 -10000 0 -0.41 77 77
IGF-1R heterotetramer -0.023 0.15 -10000 0 -0.72 23 23
PLCB1 -0.064 0.17 -10000 0 -0.43 77 77
PLCB2 -0.006 0.095 -10000 0 -0.63 6 6
IGF1 -0.35 0.37 -10000 0 -0.72 262 262
mol:L-citrulline -0.12 0.22 -10000 0 -0.5 120 120
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.096 0.13 -10000 0 -0.77 2 2
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.016 0 -10000 0 -10000 0 0
ESR2 0.016 0 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.72 117 117
Gq family/GDP/Gbeta gamma 0.032 0.052 -10000 0 -0.78 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.043 0.13 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.15 0.2 -10000 0 -0.48 120 120
GNAZ 0.008 0.078 -10000 0 -0.72 6 6
E2/ER alpha (dimer) -0.14 0.22 -10000 0 -0.55 117 117
STRN 0.014 0.034 -10000 0 -0.72 1 1
GNAL 0.012 0.056 -10000 0 -0.72 3 3
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.024 0 -10000 0 -10000 0 0
GNAI2 0.016 0.007 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.25 0.35 -10000 0 -0.72 189 189
HBEGF -0.12 0.18 -10000 0 -0.38 123 123
cAMP biosynthetic process -0.076 0.17 -10000 0 -0.38 119 119
SRC -0.12 0.19 -10000 0 -0.39 120 120
PI3K -0.052 0.16 -10000 0 -0.54 51 51
GNB1 0.016 0.01 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.077 0.19 -10000 0 -0.42 118 118
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.27 0.24 -10000 0 -0.49 247 247
Gs family/GTP -0.075 0.17 -10000 0 -0.38 119 119
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.003 0.016 -10000 0 -10000 0 0
vasodilation -0.12 0.22 -10000 0 -0.48 120 120
mol:DAG -0.053 0.17 -10000 0 -0.41 77 77
Gs family/GDP/Gbeta gamma -0.079 0.17 -10000 0 -0.39 120 120
MSN -0.023 0.14 -10000 0 -0.33 16 16
Gq family/GTP -0.032 0.094 -10000 0 -0.68 6 6
mol:PI-3-4-5-P3 -0.17 0.34 -10000 0 -0.79 117 117
NRAS 0.014 0.019 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.12 0.22 0.48 120 -10000 0 120
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.083 0.2 -10000 0 -0.45 117 117
NOS3 -0.13 0.24 -10000 0 -0.53 120 120
GNA11 0.016 0 -10000 0 -10000 0 0
MAPKKK cascade -0.12 0.27 -10000 0 -0.6 118 118
E2/ER alpha (dimer)/PELP1/Src -0.16 0.21 -10000 0 -0.51 120 120
ruffle organization -0.02 0.13 -10000 0 -0.31 16 16
ROCK2 -0.036 0.15 -10000 0 -0.37 16 16
GNA14 -0.008 0.09 -10000 0 -0.72 6 6
GNA15 0.014 0.02 -10000 0 -10000 0 0
GNA13 0.015 0.014 -10000 0 -10000 0 0
MMP9 -0.13 0.18 -10000 0 -0.4 120 120
MMP2 -0.11 0.18 -10000 0 -0.37 123 123
IL4-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
BCL2L1 -0.21 0.48 -10000 0 -0.97 102 102
STAT6 (cleaved dimer) -0.3 0.38 -10000 0 -0.89 124 124
IGHG1 -0.046 0.22 -10000 0 -0.32 99 99
IGHG3 -0.22 0.46 -10000 0 -0.88 121 121
AKT1 -0.069 0.28 -10000 0 -0.51 59 59
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.009 0.2 -10000 0 -0.47 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.084 0.3 -10000 0 -0.56 71 71
THY1 -0.21 0.48 -10000 0 -0.97 102 102
MYB -0.049 0.2 -10000 0 -0.72 41 41
HMGA1 0.011 0.028 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.083 0.3 -10000 0 -0.5 96 96
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.058 0.26 -10000 0 -0.46 53 53
SP1 0.023 0.01 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.018 0.036 -10000 0 -0.72 1 1
STAT6 (dimer)/ETS1 -0.28 0.37 -10000 0 -0.9 112 112
SOCS1 -0.098 0.34 -10000 0 -0.62 99 99
SOCS3 -0.07 0.33 -10000 0 -1.3 16 16
FCER2 -0.21 0.42 -10000 0 -0.72 122 122
PARP14 0.011 0.033 -10000 0 -10000 0 0
CCL17 -0.21 0.48 -10000 0 -0.97 102 102
GRB2 0.013 0.022 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.032 0.22 -10000 0 -0.43 18 18
T cell proliferation -0.24 0.49 -10000 0 -0.95 123 123
IL4R/JAK1 -0.22 0.48 -10000 0 -0.99 103 103
EGR2 -0.63 0.81 -10000 0 -1.4 265 265
JAK2 0.014 0.054 -10000 0 -0.76 1 1
JAK3 0.021 0.008 -10000 0 -10000 0 0
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
JAK1 0.016 0.051 -10000 0 -0.72 2 2
COL1A2 -0.041 0.22 -10000 0 -1.6 3 3
CCL26 -0.21 0.48 -10000 0 -0.97 102 102
IL4R -0.23 0.52 -10000 0 -1 103 103
PTPN6 0.02 0.021 -10000 0 -10000 0 0
IL13RA2 -0.22 0.5 -10000 0 -0.99 108 108
IL13RA1 0.016 0.043 -10000 0 -10000 0 0
IRF4 0.017 0.13 -10000 0 -10000 0 0
ARG1 -0.007 0.2 -10000 0 -1.3 4 4
CBL -0.068 0.28 -10000 0 -0.47 96 96
GTF3A 0.012 0.015 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 0.021 0.072 -10000 0 -0.58 1 1
IRF4/BCL6 -0.027 0.17 -10000 0 -0.52 26 26
CD40LG 0.025 0.022 -10000 0 -10000 0 0
MAPK14 -0.069 0.29 -10000 0 -0.49 98 98
mitosis -0.064 0.27 -10000 0 -0.49 59 59
STAT6 -0.24 0.55 -10000 0 -1.1 111 111
SPI1 0.019 0.031 -10000 0 -10000 0 0
RPS6KB1 -0.055 0.26 -10000 0 -0.49 46 46
STAT6 (dimer) -0.24 0.55 -10000 0 -1.1 111 111
STAT6 (dimer)/PARP14 -0.23 0.49 -10000 0 -0.98 112 112
mast cell activation 0.001 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.041 0.25 -10000 0 -0.47 28 28
FRAP1 -0.069 0.28 -10000 0 -0.51 59 59
LTA -0.21 0.48 -10000 0 -0.97 102 102
FES 0.013 0.045 -10000 0 -0.72 2 2
T-helper 1 cell differentiation 0.23 0.54 1 111 -10000 0 111
CCL11 -0.22 0.46 -10000 0 -0.94 103 103
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.041 0.25 -10000 0 -0.47 27 27
IL2RG 0.011 0.041 -10000 0 -10000 0 0
IL10 -0.21 0.48 -10000 0 -0.97 102 102
IRS1 -0.081 0.25 -10000 0 -0.72 69 69
IRS2 -0.18 0.32 -10000 0 -0.72 137 137
IL4 -0.007 0.16 -10000 0 -10000 0 0
IL5 -0.21 0.48 -10000 0 -0.97 102 102
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.16 0.41 -10000 0 -0.77 100 100
COL1A1 -0.053 0.21 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.22 0.49 -10000 0 -1 103 103
IL2R gamma/JAK3 0.033 0.021 -10000 0 -10000 0 0
TFF3 -0.36 0.67 -10000 0 -1.3 153 153
ALOX15 -0.21 0.49 -10000 0 -0.98 102 102
MYBL1 -0.022 0.069 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.16 0.42 -10000 0 -0.76 113 113
SHC1 0.016 0 -10000 0 -10000 0 0
CEBPB 0.022 0.035 -10000 0 -0.72 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.1 0.29 -10000 0 -0.52 92 92
mol:PI-3-4-5-P3 -0.069 0.28 -10000 0 -0.51 59 59
PI3K -0.074 0.29 -10000 0 -0.54 59 59
DOK2 0.013 0.046 -10000 0 -0.72 2 2
ETS1 0.017 0.038 -10000 0 -0.68 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.023 0.21 -10000 0 -0.43 14 14
ITGB3 -0.21 0.48 -10000 0 -0.97 102 102
PIGR -0.57 0.8 -10000 0 -1.4 224 224
IGHE 0.001 0.064 -10000 0 -10000 0 0
MAPKKK cascade -0.022 0.21 -10000 0 -0.42 14 14
BCL6 -0.06 0.22 -10000 0 -0.72 53 53
OPRM1 -0.21 0.48 -10000 0 -0.97 102 102
RETNLB -0.21 0.48 -10000 0 -0.97 102 102
SELP -0.44 0.78 -10000 0 -1.5 163 163
AICDA -0.21 0.46 -10000 0 -0.94 104 104
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.01 0.026 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.35 0.2 -9999 0 -0.46 403 403
PTK2 -0.096 0.11 -9999 0 -0.56 1 1
IGF1R -0.023 0.15 -9999 0 -0.72 23 23
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 -0.023 0.16 -9999 0 -0.72 26 26
SRC 0.016 0.007 -9999 0 -10000 0 0
CDKN1B -0.14 0.12 -9999 0 -0.93 9 9
VEGFA -0.005 0.054 -9999 0 -10000 0 0
ILK -0.12 0.068 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.095 0.078 -9999 0 -10000 0 0
PTK2B 0.04 0.032 -9999 0 -0.38 1 1
alphaV/beta3 Integrin/JAM-A -0.29 0.16 -9999 0 -0.38 403 403
CBL 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.001 0.023 -9999 0 -0.46 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.28 0.31 -9999 0 -0.52 280 280
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.053 0.013 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Syndecan-1 0.021 0.043 -9999 0 -0.46 1 1
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.54 0.34 -9999 0 -0.66 412 412
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.028 0.062 -9999 0 -0.46 4 4
RPS6KB1 -0.49 0.3 -9999 0 -0.61 412 412
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.57 0.33 -9999 0 -0.74 403 403
GPR124 -0.015 0.15 -9999 0 -0.72 22 22
MAPK1 -0.57 0.33 -9999 0 -0.74 403 403
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
alphaV/beta3 Integrin/Tumstatin 0.001 0.023 -9999 0 -0.46 1 1
cell adhesion -0.023 0.096 -9999 0 -0.36 37 37
ANGPTL3 0.016 0.001 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.011 0.027 -9999 0 -10000 0 0
IGF-1R heterotetramer -0.023 0.15 -9999 0 -0.72 23 23
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.037 0.19 -9999 0 -0.72 38 38
ITGB3 0.014 0.02 -9999 0 -10000 0 0
IGF1 -0.35 0.37 -9999 0 -0.72 262 262
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.094 -9999 0 -0.46 23 23
apoptosis 0.014 0.034 -9999 0 -0.72 1 1
CD47 0.001 0.11 -9999 0 -0.72 11 11
alphaV/beta3 Integrin/CD47 -0.009 0.069 -9999 0 -0.46 12 12
VCL 0.016 0.007 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.012 0.1 -9999 0 -0.46 25 25
CSF1 0.016 0.007 -9999 0 -10000 0 0
PIK3C2A -0.12 0.068 -9999 0 -10000 0 0
PI4 Kinase/Pyk2 -0.24 0.14 -9999 0 -0.37 55 55
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.012 0.036 -9999 0 -0.41 1 1
FAK1/Vinculin -0.073 0.091 -9999 0 -0.43 1 1
alphaV beta3/Integrin/ppsTEM5 -0.018 0.095 -9999 0 -0.46 23 23
RHOA 0.016 0 -9999 0 -10000 0 0
VTN 0.015 0.012 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
FGF2 -0.55 0.31 -9999 0 -0.72 403 403
F11R -0.41 0.24 -9999 0 -0.54 403 403
alphaV/beta3 Integrin/Lactadherin -0.021 0.1 -9999 0 -0.46 27 27
alphaV/beta3 Integrin/TGFBR2 -0.033 0.12 -9999 0 -0.46 39 39
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0 0.019 -9999 0 -0.41 1 1
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.001 0.021 -9999 0 -0.42 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.098 0.074 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.041 0.032 -9999 0 -0.38 1 1
SDC1 -0.027 0.072 -9999 0 -10000 0 0
VAV3 0.037 0.089 -9999 0 -0.38 22 22
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 -0.081 0.25 -9999 0 -0.72 69 69
FAK1/Paxillin -0.073 0.091 -9999 0 -0.43 1 1
cell migration -0.06 0.087 -9999 0 -0.39 1 1
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
PI3K -0.29 0.19 -9999 0 -0.63 64 64
SPP1 -0.057 0.094 -9999 0 -0.72 3 3
KDR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.014 0.034 -9999 0 -0.72 1 1
COL4A3 0.016 0 -9999 0 -10000 0 0
angiogenesis -0.55 0.33 -9999 0 -0.71 403 403
Rac1/GTP -0.004 0.077 -9999 0 -0.34 22 22
EDIL3 -0.036 0.16 -9999 0 -0.72 24 24
cell proliferation -0.033 0.12 -9999 0 -0.46 39 39
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.36 0.21 -9999 0 -0.47 407 407
fibroblast growth factor receptor signaling pathway -0.36 0.21 -9999 0 -0.47 407 407
LAMA1 0.016 0.01 -9999 0 -10000 0 0
PRNP -0.003 0.12 -9999 0 -0.72 14 14
GPC1/SLIT2 -0.071 0.18 -9999 0 -0.54 69 69
SMAD2 0.009 0.12 -9999 0 -0.41 38 38
GPC1/PrPc/Cu2+ -0.012 0.076 -9999 0 -0.47 14 14
GPC1/Laminin alpha1 -0.001 0.008 -9999 0 -10000 0 0
TDGF1 0.016 0 -9999 0 -10000 0 0
CRIPTO/GPC1 0 0.006 -9999 0 -10000 0 0
APP/GPC1 -0.007 0.053 -9999 0 -0.54 5 5
mol:NO 0 0 -9999 0 -10000 0 0
YES1 0.034 0.022 -9999 0 -0.46 1 1
FLT1 0.016 0.01 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.032 0.12 -9999 0 -0.46 38 38
SERPINC1 0.012 0.025 -9999 0 -10000 0 0
FYN 0.033 0.031 -9999 0 -0.46 2 2
FGR 0.035 0.006 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.061 0.021 -9999 0 -10000 0 0
SLIT2 -0.081 0.25 -9999 0 -0.72 69 69
GPC1/NRG -0.07 0.18 -9999 0 -0.54 67 67
NRG1 -0.079 0.25 -9999 0 -0.72 67 67
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.011 0.028 -9999 0 -10000 0 0
LYN 0.035 0.008 -9999 0 -10000 0 0
mol:Spermine 0.014 0.008 -9999 0 -10000 0 0
cell growth -0.36 0.21 -9999 0 -0.47 407 407
BMP signaling pathway -0.015 0.012 -9999 0 -10000 0 0
SRC 0.035 0.007 -9999 0 -10000 0 0
TGFBR1 0.014 0.017 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.1 0.26 -9999 0 -0.72 79 79
GPC1 0.015 0.012 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.014 0.017 -9999 0 -10000 0 0
VEGFA -0.005 0.054 -9999 0 -10000 0 0
BLK 0.028 0.025 -9999 0 -10000 0 0
HCK 0.033 0.014 -9999 0 -10000 0 0
FGF2 -0.55 0.31 -9999 0 -0.72 403 403
FGFR1 -0.007 0.12 -9999 0 -0.72 15 15
VEGFR1 homodimer 0.016 0.01 -9999 0 -10000 0 0
TGFBR2 -0.037 0.19 -9999 0 -0.72 38 38
cell death -0.007 0.053 -9999 0 -0.54 5 5
ATIII/GPC1 -0.002 0.013 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.086 0.19 -9999 0 -0.54 79 79
LCK 0.027 0.026 -9999 0 -10000 0 0
neuron differentiation -0.069 0.18 -9999 0 -0.54 67 67
PrPc/Cu2+ -0.015 0.089 -9999 0 -0.55 14 14
APP 0.006 0.074 -9999 0 -0.72 5 5
TGFBR2 (dimer) -0.037 0.19 -9999 0 -0.72 38 38
p75(NTR)-mediated signaling

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0 0.003 -9999 0 -10000 0 0
Necdin/E2F1 -0.15 0.24 -9999 0 -0.56 135 135
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.087 0.18 -9999 0 -0.42 110 110
NGF (dimer)/p75(NTR)/BEX1 -0.078 0.19 -9999 0 -0.48 94 94
NT-4/5 (dimer)/p75(NTR) -0.098 0.21 -9999 0 -0.55 94 94
IKBKB 0.014 0.02 -9999 0 -10000 0 0
AKT1 -0.076 0.21 -9999 0 -0.43 131 131
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF 0.006 0.057 -9999 0 -0.72 2 2
MGDIs/NGR/p75(NTR)/LINGO1 -0.072 0.19 -9999 0 -0.47 94 94
FURIN 0.013 0.024 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.081 0.18 -9999 0 -0.46 96 96
LINGO1 -0.01 0.059 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.002 0.016 -9999 0 -10000 0 0
proBDNF (dimer) 0.006 0.057 -9999 0 -0.72 2 2
NTRK1 0.014 0.019 -9999 0 -10000 0 0
RTN4R 0.007 0.037 -9999 0 -10000 0 0
neuron apoptosis -0.015 0.17 -9999 0 -0.43 5 5
IRAK1 0.014 0.02 -9999 0 -10000 0 0
SHC1 -0.064 0.19 -9999 0 -0.47 94 94
ARHGDIA 0.015 0.014 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0.004 0.027 -9999 0 -0.38 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.086 0.18 -9999 0 -0.44 103 103
MAGEH1 -0.003 0.12 -9999 0 -0.72 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.18 0.27 -9999 0 -0.52 186 186
Mammalian IAPs/DIABLO -0.025 0.11 -9999 0 -0.42 35 35
proNGF (dimer) 0 0 -9999 0 -10000 0 0
MAGED1 0.006 0.04 -9999 0 -10000 0 0
APP 0.006 0.074 -9999 0 -0.72 5 5
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.015 0.014 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.045 0.16 -9999 0 -0.4 94 94
NGF 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.062 0.15 -9999 0 -0.38 94 94
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.02 0.13 -9999 0 -0.3 94 94
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.084 0.18 -9999 0 -0.47 94 94
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.086 0.2 -9999 0 -0.5 96 96
PSENEN 0.014 0.019 -9999 0 -10000 0 0
mol:ceramide -0.047 0.17 -9999 0 -0.42 94 94
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.009 0.11 -9999 0 -0.24 94 94
p75(NTR)/beta APP -0.1 0.22 -9999 0 -0.55 97 97
BEX1 -0.006 0.056 -9999 0 -10000 0 0
mol:GDP -0.076 0.19 -9999 0 -0.48 94 94
NGF (dimer) -0.068 0.16 -9999 0 -0.42 86 86
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.059 0.17 -9999 0 -0.42 94 94
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
RAC1/GTP -0.073 0.16 -9999 0 -0.41 94 94
MYD88 0.016 0.01 -9999 0 -10000 0 0
CHUK 0.015 0.032 -9999 0 -0.72 1 1
NGF (dimer)/p75(NTR)/PKA -0.087 0.2 -9999 0 -0.5 96 96
RHOB 0.013 0.046 -9999 0 -0.72 2 2
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.01 0.026 -9999 0 -10000 0 0
NT3 (dimer) -0.2 0.33 -9999 0 -0.72 150 150
TP53 -0.02 0.16 -9999 0 -0.41 5 5
PRDM4 -0.048 0.17 -9999 0 -0.42 94 94
BDNF (dimer) -0.032 0.2 -9999 0 -0.46 89 89
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
SORT1 0.016 0.007 -9999 0 -10000 0 0
activation of caspase activity -0.086 0.17 -9999 0 -0.41 110 110
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.075 0.16 -9999 0 -0.42 94 94
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.014 0.17 -9999 0 -0.36 94 94
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.048 0.17 -9999 0 -0.42 94 94
APH1B 0.015 0.033 -9999 0 -0.72 1 1
APH1A 0.01 0.032 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.084 0.18 -9999 0 -0.47 94 94
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.003 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.25 0.31 -9999 0 -0.6 216 216
MAPK8 -0.008 0.17 -9999 0 -0.36 94 94
MAPK9 -0.007 0.17 -9999 0 -0.36 94 94
APAF1 0.016 0.007 -9999 0 -10000 0 0
NTF3 -0.2 0.33 -9999 0 -0.72 150 150
NTF4 0 0 -9999 0 -10000 0 0
NDN -0.17 0.32 -9999 0 -0.72 135 135
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.067 0.16 -9999 0 -0.39 97 97
p75 CTF/Sortilin/TRAF6/NRIF 0.001 0.009 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.086 0.2 -9999 0 -0.5 96 96
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.065 0.15 -9999 0 -0.38 96 96
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.072 0.16 -9999 0 -0.41 96 96
PRKACB -0.007 0.099 -9999 0 -0.72 8 8
proBDNF (dimer)/p75 ECD -0.006 0.037 -9999 0 -0.54 2 2
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.038 0.18 -9999 0 -0.72 35 35
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.14 0.23 -9999 0 -0.55 105 105
BAD -0.003 0.17 -9999 0 -0.36 94 94
RIPK2 0.014 0.02 -9999 0 -10000 0 0
NGFR -0.12 0.28 -9999 0 -0.72 94 94
CYCS -0.04 0.16 -9999 0 -0.39 94 94
ADAM17 0.016 0.007 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.075 0.16 -9999 0 -0.42 94 94
BCL2L11 -0.003 0.17 -9999 0 -0.36 94 94
BDNF (dimer)/p75(NTR) -0.1 0.21 -9999 0 -0.54 96 96
PI3K -0.12 0.21 -9999 0 -0.46 131 131
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.075 0.16 -9999 0 -0.42 94 94
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.015 0.032 -9999 0 -0.72 1 1
PRKCI 0.013 0.022 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.098 0.21 -9999 0 -0.55 94 94
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.072 0.17 -9999 0 -0.43 94 94
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG 0.015 0.032 -9999 0 -0.72 1 1
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.048 0.18 -9999 0 -0.43 96 96
SQSTM1 0.016 0.007 -9999 0 -10000 0 0
NGFRAP1 -0.016 0.15 -9999 0 -0.72 23 23
CASP3 0.001 0.16 -9999 0 -0.33 94 94
E2F1 -0.006 0.055 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.03 0.07 -9999 0 -0.37 1 1
NGF (dimer)/TRKA -0.001 0.011 -9999 0 -10000 0 0
MMP7 -0.1 0.27 -9999 0 -0.72 85 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.069 0.15 -9999 0 -0.39 94 94
MMP3 -0.078 0.11 -9999 0 -0.72 8 8
APAF-1/Caspase 9 -0.068 0.14 -9999 0 -0.59 10 10
Nectin adhesion pathway

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
PDGFRB 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.002 0.026 -9999 0 -0.54 1 1
PTK2 -0.083 0.19 -9999 0 -0.49 89 89
positive regulation of JNK cascade -0.054 0.12 -9999 0 -0.32 89 89
CDC42/GDP -0.008 0.19 -9999 0 -0.43 89 89
Rac1/GDP -0.006 0.19 -9999 0 -0.42 89 89
RAP1B 0.016 0.01 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.065 -9999 0 -0.72 4 4
CDC42/GTP -0.066 0.15 -9999 0 -0.39 89 89
nectin-3/I-afadin -0.095 0.21 -9999 0 -0.56 89 89
RAPGEF1 -0.022 0.21 -9999 0 -0.48 89 89
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.04 0.24 -9999 0 -0.56 89 89
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
TLN1 -0.02 0.16 -9999 0 -0.64 23 23
Rap1/GTP -0.056 0.13 -9999 0 -0.33 89 89
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.007 0.058 -9999 0 -0.42 10 10
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.095 0.21 -9999 0 -0.56 89 89
PVR 0.014 0.017 -9999 0 -10000 0 0
Necl-5(dimer) 0.014 0.017 -9999 0 -10000 0 0
mol:GDP -0.025 0.23 -9999 0 -0.53 89 89
MLLT4 0.002 0.1 -9999 0 -0.72 10 10
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PI3K -0.1 0.2 -9999 0 -0.44 124 124
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.011 0.074 -9999 0 -0.54 10 10
positive regulation of lamellipodium assembly -0.056 0.12 -9999 0 -0.33 89 89
PVRL1 0.016 0.01 -9999 0 -10000 0 0
PVRL3 -0.1 0.27 -9999 0 -0.72 83 83
PVRL2 0.01 0.032 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
CDH1 -0.032 0.18 -9999 0 -0.72 33 33
CLDN1 -0.055 0.2 -9999 0 -0.72 42 42
JAM-A/CLDN1 -0.1 0.22 -9999 0 -0.48 116 116
SRC -0.1 0.24 -9999 0 -0.63 89 89
ITGB3 0.014 0.02 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin -0.011 0.074 -9999 0 -0.54 10 10
FARP2 -0.03 0.22 -9999 0 -0.52 89 89
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.08 0.18 -9999 0 -0.48 89 89
nectin-1/I-afadin -0.011 0.074 -9999 0 -0.54 10 10
nectin-2/I-afadin -0.014 0.075 -9999 0 -0.54 10 10
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.081 0.18 -9999 0 -0.48 89 89
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.012 0.027 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.054 0.12 -9999 0 -0.32 89 89
alphaV/beta3 Integrin/Talin 0 0.15 -9999 0 -0.61 21 21
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.014 0.075 -9999 0 -0.54 10 10
nectin-2(dimer)/I-afadin/I-afadin -0.014 0.075 -9999 0 -0.54 10 10
PIP5K1C -0.032 0.17 -9999 0 -0.33 96 96
VAV2 -0.032 0.23 -9999 0 -0.53 89 89
RAP1/GDP -0.066 0.15 -9999 0 -0.39 89 89
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.079 0.19 -9999 0 -0.48 89 89
nectin-3(dimer)/I-afadin/I-afadin -0.095 0.21 -9999 0 -0.56 89 89
Rac1/GTP -0.068 0.15 -9999 0 -0.4 89 89
PTPRM -0.048 0.19 -9999 0 -0.37 96 96
E-cadherin/beta catenin/alpha catenin -0.027 0.11 -9999 0 -0.37 46 46
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.074 0.24 -10000 0 -0.72 64 64
HRAS 0.015 0.012 -10000 0 -10000 0 0
EGFR -0.38 0.37 -10000 0 -0.72 277 277
AKT 0.023 0.044 -10000 0 -0.26 2 2
FOXO3 0.016 0.007 -10000 0 -10000 0 0
AKT1 0.014 0.02 -10000 0 -10000 0 0
FOXO1 -0.085 0.25 -10000 0 -0.72 72 72
AKT3 0.014 0.017 -10000 0 -10000 0 0
FOXO4 0.016 0 -10000 0 -10000 0 0
MET -0.057 0.22 -10000 0 -0.72 52 52
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
PIK3CB 0.016 0.01 -10000 0 -10000 0 0
NRAS 0.014 0.019 -10000 0 -10000 0 0
PIK3CG 0.013 0.023 -10000 0 -10000 0 0
PIK3R3 0.006 0.039 -10000 0 -10000 0 0
PIK3R2 0.014 0.019 -10000 0 -10000 0 0
NF1 0.016 0 -10000 0 -10000 0 0
RAS -0.11 0.15 -10000 0 -0.22 301 301
ERBB2 -0.004 0.06 -10000 0 -0.72 1 1
proliferation/survival/translation -0.009 0.073 0.23 22 -0.19 4 26
PI3K -0.1 0.16 0.22 9 -0.22 289 298
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
KRAS 0.012 0.025 -10000 0 -10000 0 0
FOXO 0.028 0.04 0.2 6 -0.23 1 7
AKT2 0.016 0 -10000 0 -10000 0 0
PTEN -0.002 0.12 -10000 0 -0.72 13 13
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.008 0.13 -10000 0 -0.37 51 51
adherens junction organization 0.013 0.096 -10000 0 -0.28 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.17 0.22 -10000 0 -0.57 58 58
FMN1 0.011 0.09 -10000 0 -0.28 38 38
mol:IP3 -0.041 0.1 -10000 0 -0.34 51 51
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.011 0.094 -10000 0 -0.29 38 38
CTNNB1 0.01 0.065 -10000 0 -0.72 4 4
AKT1 0.009 0.12 -10000 0 -0.33 51 51
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.016 0.13 -10000 0 -0.46 37 37
CTNND1 0.015 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.02 0.089 -10000 0 -0.49 1 1
VASP 0.016 0.091 -10000 0 -0.37 4 4
ZYX 0.02 0.091 -10000 0 -0.43 2 2
JUB 0.006 0.12 -10000 0 -0.42 20 20
EGFR(dimer) -0.19 0.23 -10000 0 -0.39 277 277
E-cadherin/beta catenin-gamma catenin -0.026 0.12 -10000 0 -0.44 38 38
mol:PI-3-4-5-P3 -0.046 0.11 -10000 0 -0.35 51 51
PIK3CA 0.015 0.009 -10000 0 -10000 0 0
PI3K -0.046 0.11 -10000 0 -0.36 51 51
FYN 0.023 0.11 -10000 0 -0.48 3 3
mol:Ca2+ 0.003 0.12 -10000 0 -0.33 51 51
JUP 0.014 0.035 -10000 0 -0.72 1 1
PIK3R1 -0.054 0.22 -10000 0 -0.72 51 51
mol:DAG -0.041 0.1 -10000 0 -0.34 51 51
CDH1 -0.033 0.18 -10000 0 -0.72 33 33
RhoA/GDP -0.17 0.22 -10000 0 -0.57 58 58
establishment of polarity of embryonic epithelium 0.016 0.09 -10000 0 -0.36 4 4
SRC 0.016 0.007 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR -0.38 0.37 -10000 0 -0.72 277 277
CASR 0.013 0.12 -10000 0 -0.47 1 1
RhoA/GTP -0.036 0.092 -10000 0 -0.46 1 1
AKT2 0.009 0.12 -10000 0 -0.33 51 51
actin cable formation 0.015 0.089 -10000 0 -0.36 4 4
apoptosis 0.044 0.11 0.35 51 -10000 0 51
CTNNA1 0.016 0.005 -10000 0 -10000 0 0
mol:GDP -0.19 0.24 -10000 0 -0.6 62 62
PIP5K1A 0.019 0.09 -10000 0 -0.5 1 1
PLCG1 -0.042 0.11 -10000 0 -0.34 51 51
Rac1/GTP -0.19 0.18 -10000 0 -0.35 277 277
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.023 0.013 -9999 0 -10000 0 0
RAS family/GTP -0.022 0.11 -9999 0 -0.32 25 25
NFATC4 -0.019 0.098 -9999 0 -0.29 15 15
ERBB2IP 0.017 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.016 0.01 -9999 0 -10000 0 0
mammary gland morphogenesis -0.034 0.13 -9999 0 -0.35 68 68
JUN -0.035 0.083 -9999 0 -10000 0 0
HRAS 0.014 0.012 -9999 0 -10000 0 0
DOCK7 -0.029 0.12 -9999 0 -0.33 67 67
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.056 0.14 -9999 0 -0.41 68 68
AKT1 0.012 0.014 -9999 0 -10000 0 0
BAD 0.024 0.011 -9999 0 -10000 0 0
MAPK10 -0.025 0.07 -9999 0 -0.3 12 12
mol:GTP -0.002 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.036 0.14 -9999 0 -0.38 68 68
RAF1 -0.022 0.11 -9999 0 -0.34 20 20
ErbB2/ErbB3/neuregulin 2 -0.3 0.21 -9999 0 -0.44 354 354
STAT3 0.004 0.009 -9999 0 -10000 0 0
cell migration 0.017 0.078 -9999 0 -0.29 4 4
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.24 0.28 -9999 0 -0.62 134 134
FOS -0.34 0.29 -9999 0 -0.52 375 375
NRAS 0.013 0.019 -9999 0 -10000 0 0
mol:Ca2+ -0.034 0.13 -9999 0 -0.35 68 68
MAPK3 -0.15 0.21 -9999 0 -0.47 111 111
MAPK1 -0.15 0.21 -9999 0 -0.48 101 101
JAK2 -0.029 0.12 -9999 0 -0.34 55 55
NF2 0.001 0.008 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.015 0.12 -9999 0 -0.33 67 67
NRG1 -0.08 0.25 -9999 0 -0.72 67 67
GRB2/SOS1 -0.001 0.011 -9999 0 -10000 0 0
MAPK8 -0.023 0.11 -9999 0 -0.3 68 68
MAPK9 -0.02 0.056 -9999 0 -0.2 2 2
ERBB2 -0.013 0.041 -9999 0 -0.56 1 1
ERBB3 0.008 0.03 -9999 0 -10000 0 0
SHC1 0.015 0.001 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
apoptosis 0.013 0.014 -9999 0 -10000 0 0
STAT3 (dimer) 0.004 0.009 -9999 0 -10000 0 0
RNF41 0.03 0.013 -9999 0 -10000 0 0
FRAP1 0.024 0.011 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.031 0.079 -9999 0 -0.26 14 14
ErbB2/ErbB2/HSP90 (dimer) -0.009 0.03 -9999 0 -0.47 1 1
CHRNA1 -0.11 0.17 -9999 0 -0.36 97 97
myelination 0.011 0.1 -9999 0 -0.32 2 2
PPP3CB -0.027 0.11 -9999 0 -0.31 67 67
KRAS 0.011 0.025 -9999 0 -10000 0 0
RAC1-CDC42/GDP 0.006 0.1 -9999 0 -0.29 5 5
NRG2 -0.48 0.35 -9999 0 -0.72 353 353
mol:GDP -0.015 0.12 -9999 0 -0.32 67 67
SOS1 0.015 0.001 -9999 0 -10000 0 0
MAP2K2 -0.026 0.12 -9999 0 -0.36 20 20
SRC 0.016 0.007 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.029 0.12 -9999 0 -0.33 53 53
MAP2K1 -0.16 0.2 -9999 0 -0.42 133 133
heart morphogenesis -0.034 0.13 -9999 0 -0.35 68 68
RAS family/GDP -0.016 0.1 -9999 0 -0.32 10 10
GRB2 0.012 0.022 -9999 0 -10000 0 0
PRKACA -0.002 0.008 -9999 0 -10000 0 0
CHRNE 0.007 0.02 -9999 0 -10000 0 0
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.014 -9999 0 -10000 0 0
nervous system development -0.034 0.13 -9999 0 -0.35 68 68
CDC42 0.016 0 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.002 0.11 -10000 0 -0.29 60 60
epithelial cell differentiation -0.026 0.1 -10000 0 -0.39 37 37
CYFIP2 -0.002 0.051 -10000 0 -10000 0 0
ENAH 0.058 0.085 -10000 0 -0.43 2 2
EGFR -0.38 0.37 -10000 0 -0.72 277 277
EPHA2 0.005 0.09 -10000 0 -0.72 8 8
MYO6 0.019 0.11 -10000 0 -0.37 38 38
CTNNB1 0.01 0.065 -10000 0 -0.72 4 4
ABI1/Sra1/Nap1 0.009 0.026 -10000 0 -10000 0 0
AQP5 -0.18 0.26 -10000 0 -0.56 155 155
CTNND1 0.016 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.1 -10000 0 -0.36 37 37
regulation of calcium-dependent cell-cell adhesion -0.015 0.15 -10000 0 -0.37 79 79
EGF -0.24 0.35 -10000 0 -0.72 178 178
NCKAP1 0.016 0 -10000 0 -10000 0 0
AQP3 -0.081 0.2 -10000 0 -0.56 65 65
cortical microtubule organization -0.026 0.1 -10000 0 -0.39 37 37
GO:0000145 0.019 0.099 -10000 0 -0.34 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.026 0.1 -10000 0 -0.39 37 37
MLLT4 0.002 0.1 -10000 0 -0.72 10 10
ARF6/GDP -0.025 0.085 -10000 0 -0.64 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.053 -10000 0 -0.41 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.034 0.1 -10000 0 -0.33 37 37
PVRL2 0.01 0.032 -10000 0 -10000 0 0
ZYX 0.018 0.11 -10000 0 -0.36 38 38
ARF6/GTP -0.003 0.048 -10000 0 -0.37 8 8
CDH1 -0.032 0.18 -10000 0 -0.72 33 33
EGFR/EGFR/EGF/EGF -0.33 0.26 -10000 0 -0.46 382 382
RhoA/GDP -0.024 0.092 -10000 0 -0.36 37 37
actin cytoskeleton organization 0.026 0.1 -10000 0 -0.34 38 38
IGF-1R heterotetramer -0.023 0.15 -10000 0 -0.72 23 23
GIT1 0.015 0.016 -10000 0 -10000 0 0
IGF1R -0.023 0.15 -10000 0 -0.72 23 23
IGF1 -0.35 0.37 -10000 0 -0.72 262 262
DIAPH1 0.012 0.026 -10000 0 -10000 0 0
Wnt receptor signaling pathway 0.026 0.1 0.39 37 -10000 0 37
RHOA 0.016 0 -10000 0 -10000 0 0
RhoA/GTP -0.025 0.086 -10000 0 -0.64 2 2
CTNNA1 0.016 0 -10000 0 -10000 0 0
VCL 0.026 0.11 -10000 0 -0.35 38 38
EFNA1 0.013 0.022 -10000 0 -10000 0 0
LPP 0.029 0.1 -10000 0 -0.34 37 37
Ephrin A1/EPHA2 -0.028 0.1 -10000 0 -0.36 43 43
SEC6/SEC8 -0.027 0.091 -10000 0 -0.44 4 4
MGAT3 -0.015 0.15 -10000 0 -0.38 79 79
HGF/MET -0.057 0.14 -10000 0 -0.37 84 84
HGF 0.016 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.002 0.11 -10000 0 -0.3 60 60
actin cable formation 0.08 0.081 -10000 0 -0.35 2 2
KIAA1543 0.028 0.1 -10000 0 -0.4 1 1
KIFC3 0.019 0.1 -10000 0 -0.36 37 37
NCK1 0.016 0 -10000 0 -10000 0 0
EXOC3 0.016 0 -10000 0 -10000 0 0
ACTN1 0.019 0.1 -10000 0 -0.36 37 37
NCK1/GIT1 -0.001 0.008 -10000 0 -10000 0 0
mol:GDP -0.026 0.1 -10000 0 -0.39 37 37
EXOC4 0.016 0 -10000 0 -10000 0 0
STX4 0.019 0.1 -10000 0 -0.36 37 37
PIP5K1C 0.019 0.1 -10000 0 -0.36 37 37
LIMA1 -0.016 0.15 -10000 0 -0.72 23 23
ABI1 0.016 0 -10000 0 -10000 0 0
ROCK1 -0.02 0.075 -10000 0 -0.54 2 2
adherens junction assembly 0.05 0.097 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.21 0.22 -10000 0 -0.39 290 290
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.014 0.075 -10000 0 -0.54 10 10
MET -0.057 0.22 -10000 0 -0.72 52 52
PLEKHA7 0.019 0.1 -10000 0 -0.36 37 37
mol:GTP -0.004 0.052 -10000 0 -0.41 8 8
establishment of epithelial cell apical/basal polarity 0.044 0.11 -10000 0 -0.62 1 1
cortical actin cytoskeleton stabilization 0.002 0.11 -10000 0 -0.29 60 60
regulation of cell-cell adhesion 0.026 0.1 -10000 0 -0.34 38 38
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.002 0.11 -10000 0 -0.3 60 60
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.25 0.23 -9999 0 -0.42 311 311
TC10/GTP -0.2 0.18 -9999 0 -0.35 292 292
Insulin Receptor/Insulin/IRS1/Shp2 -0.053 0.14 -9999 0 -0.42 69 69
HRAS 0.015 0.012 -9999 0 -10000 0 0
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.091 0.23 -9999 0 -0.72 57 57
FOXO3 -0.016 0.031 -9999 0 -10000 0 0
AKT1 -0.06 0.2 -9999 0 -0.51 41 41
INSR 0.019 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.046 0.036 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.011 0.064 -9999 0 -0.72 4 4
SORBS1 -0.39 0.37 -9999 0 -0.72 292 292
CRK 0.015 0.032 -9999 0 -0.72 1 1
PTPN1 0.045 0.036 -9999 0 -10000 0 0
CAV1 -0.33 0.25 -9999 0 -0.46 394 394
CBL/APS/CAP/Crk-II/C3G -0.22 0.2 -9999 0 -0.39 292 292
Insulin Receptor/Insulin/IRS1/NCK2 -0.054 0.14 -9999 0 -0.42 69 69
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.083 0.16 -9999 0 -0.38 113 113
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.016 0.098 -9999 0 -10000 0 0
RPS6KB1 -0.046 0.19 -9999 0 -0.55 25 25
PARD6A 0.015 0.016 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.002 0.012 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.093 0.16 -9999 0 -0.57 25 25
HRAS/GTP -0.04 0.1 -9999 0 -0.36 4 4
Insulin Receptor 0.018 0.002 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.047 0.13 -9999 0 -0.38 69 69
PRKCI -0.02 0.058 -9999 0 -0.63 2 2
Insulin Receptor/Insulin/GRB14/PDK1 -0.11 0.19 -9999 0 -0.54 46 46
SHC1 0.016 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.002 0.013 -9999 0 -10000 0 0
PI3K -0.084 0.17 -9999 0 -0.39 113 113
NCK2 0.016 0.01 -9999 0 -10000 0 0
RHOQ 0.015 0.032 -9999 0 -0.72 1 1
mol:H2O2 -0.001 0.004 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.007 -9999 0 -10000 0 0
AKT2 -0.06 0.2 -9999 0 -0.63 24 24
PRKCZ -0.026 0.059 -9999 0 -0.64 2 2
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.014 0.14 -9999 0 -0.37 69 69
F2RL2 -0.007 0.075 -9999 0 -0.72 3 3
TRIP10 0.015 0.032 -9999 0 -0.72 1 1
Insulin Receptor/Insulin/Shc 0.001 0.005 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst -0.002 0.029 -9999 0 -0.47 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.004 0.015 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.23 0.21 -9999 0 -0.42 292 292
TC10/GDP -0.001 0.024 -9999 0 -0.55 1 1
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.037 -9999 0 -0.42 4 4
INPP5D -0.026 0.15 -9999 0 -0.4 69 69
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.01 0.016 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 -0.081 0.25 -9999 0 -0.72 69 69
p62DOK/RasGAP 0.002 0.013 -9999 0 -10000 0 0
INS 0.019 0.002 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.025 0.14 -9999 0 -0.4 69 69
GRB2 0.013 0.022 -9999 0 -10000 0 0
EIF4EBP1 -0.049 0.19 -9999 0 -0.54 28 28
PTPRA 0.019 0.002 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
TC10/GTP/CIP4 -0.002 0.029 -9999 0 -0.47 2 2
PDPK1 0.016 0.007 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.006 0.11 -9999 0 -0.28 69 69
Insulin Receptor/Insulin/IRS1 -0.055 0.14 -9999 0 -0.43 69 69
Insulin Receptor/Insulin/IRS3 0.001 0.003 -9999 0 -10000 0 0
Par3/Par6 0.007 0.047 -9999 0 -0.39 5 5
ErbB4 signaling events

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.003 0.09 -10000 0 -0.42 8 8
epithelial cell differentiation 0.026 0.08 -10000 0 -10000 0 0
ITCH 0.025 0.02 -10000 0 -10000 0 0
WWP1 0.008 0.077 -10000 0 -10000 0 0
FYN 0.013 0.045 -10000 0 -0.72 2 2
EGFR -0.38 0.37 -10000 0 -0.72 277 277
PRL 0.016 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.012 0.14 -10000 0 -0.5 2 2
PTPRZ1 -0.5 0.34 -10000 0 -0.72 370 370
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.12 -10000 0 -0.47 10 10
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.04 0.16 -10000 0 -0.43 70 70
ADAM17 0.024 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 0 0.097 -10000 0 -0.46 4 4
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.005 0.087 -10000 0 -0.41 6 6
NCOR1 0.015 0.032 -10000 0 -0.72 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.031 0.16 -10000 0 -0.41 67 67
GRIN2B -0.028 0.16 -10000 0 -0.38 79 79
ErbB4/ErbB2/betacellulin 0 0.11 -10000 0 -0.42 26 26
STAT1 -0.011 0.061 -10000 0 -10000 0 0
HBEGF 0.011 0.064 -10000 0 -0.72 4 4
PRLR -0.026 0.071 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.054 0.19 -10000 0 -0.5 71 71
axon guidance 0.12 0.12 -10000 0 -10000 0 0
NEDD4 0.017 0.073 -10000 0 -0.7 5 5
Prolactin receptor/Prolactin receptor/Prolactin -0.02 0.034 -10000 0 -10000 0 0
CBFA2T3 -0.084 0.25 -10000 0 -0.72 70 70
ErbB4/ErbB2/HBEGF 0.017 0.075 -10000 0 -0.4 6 6
MAPK3 0.002 0.14 -10000 0 -0.43 10 10
STAT1 (dimer) 0.007 0.095 -10000 0 -0.4 4 4
MAPK1 0.002 0.14 -10000 0 -0.44 8 8
JAK2 0.015 0.033 -10000 0 -0.72 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.038 0.16 -10000 0 -0.41 69 69
NRG1 -0.04 0.19 -10000 0 -0.55 67 67
NRG3 0.009 0.052 -10000 0 -0.72 2 2
NRG2 -0.48 0.35 -10000 0 -0.72 353 353
NRG4 0.015 0.014 -10000 0 -10000 0 0
heart development 0.12 0.12 -10000 0 -10000 0 0
neural crest cell migration -0.037 0.16 -10000 0 -0.4 69 69
ERBB2 0.021 0.044 -10000 0 -0.53 1 1
WWOX/E4ICDs 0.007 0.083 -10000 0 -0.4 4 4
SHC1 0.016 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.23 0.18 -10000 0 -0.4 281 281
apoptosis 0.017 0.066 0.36 6 -10000 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.31 0.22 -10000 0 -0.45 354 354
ErbB4/ErbB2/epiregulin 0.019 0.076 -10000 0 -0.42 4 4
ErbB4/ErbB4/betacellulin/betacellulin -0.015 0.13 -10000 0 -0.45 28 28
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.004 0.083 -10000 0 -0.41 4 4
MDM2 0.009 0.084 -10000 0 -0.4 4 4
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.061 0.14 -10000 0 -0.41 67 67
STAT5A 0.12 0.11 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.25 0.26 -10000 0 -0.46 290 290
DLG4 0.016 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.061 -10000 0 -0.38 6 6
STAT5A (dimer) 0.032 0.093 -10000 0 -10000 0 0
MAP3K7IP2 0.015 0.032 -10000 0 -0.72 1 1
STAT5B (dimer) 0.11 0.1 -10000 0 -10000 0 0
LRIG1 -0.019 0.16 -10000 0 -0.72 25 25
EREG -0.001 0.064 -10000 0 -0.72 2 2
BTC -0.019 0.16 -10000 0 -0.72 24 24
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.12 0.12 -10000 0 -10000 0 0
ERBB4 0 0.097 -10000 0 -0.47 4 4
STAT5B 0.016 0.007 -10000 0 -10000 0 0
YAP1 -0.011 0.058 -10000 0 -0.63 4 4
GRB2 0.013 0.022 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.02 0.069 -10000 0 -0.46 2 2
glial cell differentiation 0.024 0.061 0.38 6 -10000 0 6
WWOX 0.009 0.033 -10000 0 -10000 0 0
cell proliferation 0.022 0.16 -10000 0 -0.47 14 14
Syndecan-3-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
CTTN 0.009 0.034 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.25 0.18 -9999 0 -0.36 374 374
Syndecan-3/Neurocan -0.004 0.073 -9999 0 -0.66 6 6
POMC 0.012 0.038 -9999 0 -0.72 1 1
EGFR -0.38 0.37 -9999 0 -0.72 277 277
Syndecan-3/EGFR -0.21 0.21 -9999 0 -0.4 278 278
AGRP 0.016 0.01 -9999 0 -10000 0 0
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.014 0.019 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.015 0.033 -9999 0 -0.72 1 1
APH1A 0.01 0.032 -9999 0 -10000 0 0
NCAN 0.01 0.03 -9999 0 -10000 0 0
long-term memory -0.003 0.072 -9999 0 -0.55 8 8
Syndecan-3/IL8 0.003 0.079 -9999 0 -0.63 7 7
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin -0.004 0.016 -9999 0 -10000 0 0
FYN 0.013 0.045 -9999 0 -0.72 2 2
limb bud formation -0.007 0.073 -9999 0 -0.69 6 6
MC4R 0.015 0.012 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
PTN -0.51 0.34 -9999 0 -0.72 373 373
FGFR/FGF/Syndecan-3 -0.008 0.074 -9999 0 -0.7 6 6
neuron projection morphogenesis -0.24 0.17 -9999 0 -0.46 40 40
Syndecan-3/AgRP -0.006 0.071 -9999 0 -0.66 6 6
Syndecan-3/AgRP/MC4R -0.005 0.069 -9999 0 -0.64 6 6
Fyn/Cortactin -0.006 0.037 -9999 0 -0.54 2 2
SDC3 -0.008 0.075 -9999 0 -0.71 6 6
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.077 -9999 0 -0.62 7 7
IL8 -0.006 0.063 -9999 0 -0.72 1 1
Syndecan-3/Fyn/Cortactin -0.003 0.074 -9999 0 -0.57 8 8
Syndecan-3/CASK -0.007 0.072 -9999 0 -0.67 6 6
alpha-MSH/MC4R -0.003 0.026 -9999 0 -0.54 1 1
Gamma Secretase 0.004 0.027 -9999 0 -0.38 1 1
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0.004 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0.009 0.039 -9999 0 -0.47 2 2
PDE6G/GNAT1/GTP 0.001 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.016 0.007 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.16 0.18 -9999 0 -0.36 238 238
mol:Na + -0.15 0.18 -9999 0 -0.57 11 11
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.018 0.13 -9999 0 -0.47 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.16 0.18 -9999 0 -0.6 11 11
CNGB1 0.016 0 -9999 0 -10000 0 0
RDH5 -0.58 0.29 -9999 0 -0.72 428 428
SAG -0.013 0.074 -9999 0 -0.72 2 2
mol:Ca2+ -0.11 0.2 -9999 0 -0.55 11 11
Na + (4 Units) -0.14 0.16 -9999 0 -0.53 11 11
RGS9 -0.03 0.18 -9999 0 -0.72 32 32
GNB1/GNGT1 -0.018 0.034 -9999 0 -10000 0 0
GNAT1/GDP -0.013 0.11 -9999 0 -0.4 35 35
GUCY2D 0.016 0 -9999 0 -10000 0 0
GNGT1 -0.022 0.068 -9999 0 -10000 0 0
GUCY2F 0.012 0.047 -9999 0 -0.72 2 2
GNB5 0.015 0.032 -9999 0 -0.72 1 1
mol:GMP (4 units) 0.029 0.069 -9999 0 -0.39 14 14
mol:11-cis-retinal -0.58 0.29 -9999 0 -0.72 428 428
mol:cGMP -0.01 0.073 -9999 0 -0.44 13 13
GNB1 0.016 0.01 -9999 0 -10000 0 0
Rhodopsin -0.44 0.21 -9999 0 -0.54 428 428
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.31 0.36 -9999 0 -0.72 230 230
Metarhodopsin II 0 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.009 0.069 -9999 0 -0.44 12 12
RGS9BP -0.015 0.076 -9999 0 -0.72 2 2
Metarhodopsin II/Transducin 0.029 0.005 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.009 0.071 -9999 0 -0.46 12 12
PDE6A/B -0.015 0.087 -9999 0 -0.54 14 14
mol:Pi -0.018 0.12 -9999 0 -0.47 35 35
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.018 0.033 -9999 0 -10000 0 0
PDE6B -0.005 0.12 -9999 0 -0.72 14 14
PDE6A 0.016 0.01 -9999 0 -10000 0 0
PDE6G 0.015 0.012 -9999 0 -10000 0 0
RHO 0.016 0 -9999 0 -10000 0 0
PDE6 -0.02 0.12 -9999 0 -0.39 47 47
GUCA1A 0.003 0.096 -9999 0 -0.72 9 9
GC2/GCAP Family -0.01 0.078 -9999 0 -0.47 13 13
GUCA1C 0.011 0.057 -9999 0 -0.72 3 3
GUCA1B 0.015 0.033 -9999 0 -0.72 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.054 0.16 -10000 0 -0.54 52 52
CRKL 0.018 0.1 -10000 0 -0.29 53 53
mol:PIP3 -0.014 0.1 0.62 13 -10000 0 13
AKT1 0.008 0.068 0.42 13 -10000 0 13
PTK2B 0.016 0 -10000 0 -10000 0 0
RAPGEF1 0.027 0.098 -10000 0 -0.37 1 1
RANBP10 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.044 0.14 -10000 0 -0.46 52 52
MAP3K5 0.013 0.14 -10000 0 -0.38 35 35
HGF/MET/CIN85/CBL/ENDOPHILINS -0.041 0.12 -10000 0 -0.41 53 53
AP1 -0.42 0.32 -10000 0 -0.6 375 375
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
apoptosis -0.54 0.37 -10000 0 -0.76 375 375
STAT3 (dimer) 0.023 0.097 -10000 0 -0.27 52 52
GAB1/CRKL/SHP2/PI3K -0.054 0.12 -10000 0 -0.59 7 7
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.026 0.099 -10000 0 -0.35 2 2
PTPN11 0.016 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.007 -10000 0 -10000 0 0
PTEN -0.002 0.12 -10000 0 -0.72 13 13
ELK1 -0.022 0.076 -10000 0 -0.25 52 52
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.017 0.052 -10000 0 -0.2 2 2
PAK1 0.005 0.067 0.39 13 -10000 0 13
HGF/MET/RANBP10 -0.045 0.14 -10000 0 -0.46 52 52
HRAS -0.022 0.22 -10000 0 -0.68 52 52
DOCK1 0.024 0.1 -10000 0 -0.35 5 5
GAB1 0.008 0.11 -10000 0 -0.31 53 53
CRK 0.017 0.1 -10000 0 -0.29 54 54
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.062 0.19 -10000 0 -0.64 52 52
JUN -0.12 0.29 -10000 0 -0.72 97 97
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.032 0.098 -10000 0 -0.33 52 52
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
cell morphogenesis 0.022 0.15 -10000 0 -0.57 7 7
GRB2/SHC 0.007 0.094 -10000 0 -0.28 52 52
FOS -0.51 0.34 -10000 0 -0.72 374 374
GLMN 0 0.002 -10000 0 -10000 0 0
cell motility -0.022 0.076 -10000 0 -0.25 52 52
HGF/MET/MUC20 -0.046 0.14 -10000 0 -0.47 52 52
cell migration 0.007 0.093 -10000 0 -0.27 52 52
GRB2 0.013 0.022 -10000 0 -10000 0 0
CBL 0.016 0 -10000 0 -10000 0 0
MET/RANBP10 -0.053 0.16 -10000 0 -0.54 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.1 -10000 0 -0.29 52 52
MET/MUC20 -0.055 0.16 -10000 0 -0.55 52 52
RAP1B 0.035 0.093 -10000 0 -0.34 1 1
RAP1A 0.035 0.093 -10000 0 -0.34 1 1
HGF/MET/RANBP9 -0.045 0.14 -10000 0 -0.46 52 52
RAF1 -0.01 0.21 -10000 0 -0.63 52 52
STAT3 0.023 0.098 -10000 0 -0.27 52 52
cell proliferation 0.023 0.14 -10000 0 -0.41 52 52
RPS6KB1 0.005 0.04 -10000 0 -10000 0 0
MAPK3 -0.027 0.069 -10000 0 -0.24 52 52
MAPK1 -0.027 0.069 -10000 0 -10000 0 0
RANBP9 0.016 0.007 -10000 0 -10000 0 0
MAPK8 0.027 0.12 -10000 0 -0.39 14 14
SRC 0.025 0.095 -10000 0 -0.26 52 52
PI3K -0.033 0.16 -10000 0 -0.35 96 96
MET/Glomulin -0.035 0.15 -10000 0 -0.49 52 52
SOS1 0.016 0 -10000 0 -10000 0 0
MAP2K1 0.002 0.19 -10000 0 -0.57 52 52
MET -0.057 0.22 -10000 0 -0.72 52 52
MAP4K1 0.03 0.098 -10000 0 -0.37 1 1
PTK2 0.015 0.014 -10000 0 -10000 0 0
MAP2K2 0.002 0.19 -10000 0 -0.57 52 52
BAD 0.016 0.062 0.4 13 -10000 0 13
MAP2K4 0.018 0.14 -10000 0 -0.43 16 16
SHP2/GRB2/SOS1/GAB1 -0.041 0.13 -10000 0 -0.42 53 53
INPPL1 0.015 0.012 -10000 0 -10000 0 0
PXN 0.016 0 -10000 0 -10000 0 0
SH3KBP1 0.015 0.033 -10000 0 -0.72 1 1
HGS -0.003 0.097 -10000 0 -0.3 52 52
PLCgamma1/PKC 0 0.004 -10000 0 -10000 0 0
HGF 0.016 0.01 -10000 0 -10000 0 0
RASA1 0.015 0.012 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
PTPRJ 0.014 0.019 -10000 0 -10000 0 0
NCK/PLCgamma1 0.01 0.092 -10000 0 -0.27 52 52
PDPK1 -0.002 0.078 0.48 13 -10000 0 13
HGF/MET/SHIP -0.046 0.14 -10000 0 -0.47 52 52
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.002 0.01 -10000 0 -10000 0 0
HDAC1 0.014 0.011 -10000 0 -10000 0 0
AES 0.016 0.004 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 0.012 0.056 -10000 0 -0.72 3 3
LRP6/FZD1 -0.001 0.024 -10000 0 -0.54 1 1
TLE1 -0.009 0.13 -10000 0 -0.72 18 18
AP1 -0.26 0.2 -10000 0 -0.38 374 374
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.015 0.012 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.015 0.094 -10000 0 -0.58 2 2
NICD/RBPSUH 0.002 0.009 -10000 0 -10000 0 0
WIF1 -0.53 0.32 -10000 0 -0.72 392 392
NOTCH1 0.002 0.008 -10000 0 -10000 0 0
PSENEN 0.014 0.019 -10000 0 -10000 0 0
KREMEN2 -0.076 0.08 -10000 0 -10000 0 0
DKK1 -0.075 0.21 -10000 0 -0.72 46 46
beta catenin/beta TrCP1 -0.004 0.053 -10000 0 -0.48 4 4
APH1B 0.015 0.033 -10000 0 -0.72 1 1
APH1A 0.01 0.032 -10000 0 -10000 0 0
AXIN1 0.006 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.027 0.074 0.3 2 -0.3 18 20
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.51 0.34 -10000 0 -0.72 374 374
JUN -0.12 0.29 -10000 0 -0.72 97 97
MAP3K7 0.015 0.011 -10000 0 -10000 0 0
CTNNB1 -0.015 0.055 -10000 0 -0.51 4 4
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.04 0.068 -10000 0 -0.5 5 5
HNF1A 0.015 0.012 -10000 0 -10000 0 0
CTBP1 0.015 0.008 -10000 0 -10000 0 0
MYC -0.055 0.34 -10000 0 -1.5 29 29
NKD1 0.014 0.018 -10000 0 -10000 0 0
FZD1 0.015 0.032 -10000 0 -0.72 1 1
NOTCH1 precursor/Deltex homolog 1 0 0.03 -10000 0 -0.38 3 3
apoptosis -0.26 0.2 -10000 0 -0.38 374 374
Delta 1/NOTCHprecursor 0.002 0.009 -10000 0 -10000 0 0
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.022 0.027 -10000 0 -10000 0 0
Gamma Secretase 0.004 0.027 -10000 0 -0.38 1 1
APC 0.006 0.006 -10000 0 -10000 0 0
DVL1 -0.041 0.025 -10000 0 -10000 0 0
CSNK2A1 0.016 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0.015 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.027 0.16 -10000 0 -0.5 46 46
LRP6 0.015 0.012 -10000 0 -10000 0 0
CSNK1A1 0.016 0.004 -10000 0 -10000 0 0
NLK 0.029 0.015 -10000 0 -10000 0 0
CCND1 -0.02 0.23 -10000 0 -1.5 12 12
WNT1 0.016 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.006 0.045 -10000 0 -0.33 1 1
DKK2 0.007 0.074 -10000 0 -0.72 5 5
NOTCH1 precursor/DVL1 -0.008 0.012 -10000 0 -10000 0 0
GSK3B 0.015 0.01 -10000 0 -10000 0 0
FRAT1 0.015 0.01 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0 0.03 -10000 0 -0.38 2 2
PPP2R5D -0.021 0.016 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.31 0.18 -10000 0 -0.41 392 392
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.018 0.033 -10000 0 -0.73 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.011 0.038 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.13 0.17 -9999 0 -0.47 81 81
JUN -0.074 0.19 -9999 0 -0.42 98 98
HRAS 0.015 0.012 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.01 0.18 -9999 0 -0.43 72 72
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.011 0.039 -9999 0 -0.72 1 1
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.013 0.18 -9999 0 -0.42 68 68
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
RET9/GFRalpha1/GDNF/Enigma -0.017 0.16 -9999 0 -0.42 68 68
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP 0.01 0.15 -9999 0 -0.37 68 68
GRB7 0.001 0.048 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.015 0.18 -9999 0 -0.42 68 68
MAPKKK cascade -0.003 0.13 -9999 0 -0.38 14 14
BCAR1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.074 0.25 -9999 0 -0.53 109 109
lamellipodium assembly -0.12 0.17 -9999 0 -0.41 102 102
RET51/GFRalpha1/GDNF/SHC 0.015 0.18 -9999 0 -0.42 68 68
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.017 0.16 -9999 0 -0.42 68 68
RET9/GFRalpha1/GDNF/Shank3 -0.017 0.16 -9999 0 -0.42 68 68
MAPK3 -0.057 0.12 -9999 0 -0.35 68 68
DOK1 0.014 0.019 -9999 0 -10000 0 0
DOK6 0.009 0.06 -9999 0 -0.72 3 3
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.034 0.12 -9999 0 -0.44 3 3
DOK5 -0.018 0.15 -9999 0 -0.72 23 23
GFRA1 -0.16 0.23 -9999 0 -0.72 68 68
MAPK8 -0.005 0.1 -9999 0 -0.42 1 1
HRAS/GTP 0.01 0.16 -9999 0 -0.39 68 68
tube development -0.013 0.15 -9999 0 -0.39 68 68
MAPK1 -0.057 0.12 -9999 0 -0.4 13 13
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.01 0.11 -9999 0 -0.29 69 69
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
PDLIM7 0.016 0.007 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.018 0.17 -9999 0 -0.41 69 69
SHC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.015 0.18 -9999 0 -0.42 68 68
RET51/GFRalpha1/GDNF/Dok5 -0.009 0.21 -9999 0 -0.45 88 88
PRKCA 0.016 0.01 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.007 -9999 0 -10000 0 0
CREB1 -0.011 0.12 -9999 0 -0.32 68 68
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.01 0.11 -9999 0 -0.29 69 69
RET51/GFRalpha1/GDNF/Grb7 0.011 0.18 -9999 0 -0.44 68 68
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.062 0.081 -9999 0 -10000 0 0
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade -0.072 0.19 -9999 0 -0.41 98 98
RET9/GFRalpha1/GDNF/FRS2 -0.017 0.16 -9999 0 -0.42 69 69
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.009 0.11 -9999 0 -0.3 68 68
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.009 0.11 -9999 0 -0.31 13 13
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.007 0.11 -9999 0 -0.29 68 68
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.006 0.11 -9999 0 -0.3 13 13
PI3K -0.16 0.3 -9999 0 -0.68 102 102
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.01 0.15 -9999 0 -0.39 68 68
GRB10 0.011 0.064 -9999 0 -0.72 4 4
activation of MAPKK activity -0.012 0.1 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2 0.012 0.18 -9999 0 -0.42 69 69
GAB1 0.014 0.034 -9999 0 -0.72 1 1
IRS1 -0.081 0.25 -9999 0 -0.72 69 69
IRS2 -0.18 0.32 -9999 0 -0.72 137 137
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.007 0.11 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/PKC alpha 0.015 0.18 -9999 0 -0.42 68 68
GRB2 0.013 0.022 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.016 0.007 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.044 0.27 -9999 0 -0.54 109 109
Rac1/GTP -0.14 0.21 -9999 0 -0.55 81 81
RET9/GFRalpha1/GDNF -0.027 0.17 -9999 0 -0.47 68 68
GFRalpha1/GDNF -0.11 0.17 -9999 0 -0.54 68 68
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.003 0.028 -10000 0 -0.47 1 1
cell-cell adhesion 0.12 0.16 0.45 21 -10000 0 21
Ephrin B/EPHB2/RasGAP 0.001 0.053 -10000 0 -0.38 8 8
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.001 0.03 -10000 0 -0.47 2 2
Ephrin B1/EPHB1 -0.18 0.23 -10000 0 -0.47 197 197
HRAS/GDP -0.12 0.16 -10000 0 -0.59 11 11
Ephrin B/EPHB1/GRB7 -0.15 0.2 -10000 0 -0.4 198 198
Endophilin/SYNJ1 0.038 0.052 -10000 0 -0.36 8 8
KRAS 0.012 0.025 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.15 0.2 -10000 0 -0.39 198 198
endothelial cell migration -0.041 0.13 -10000 0 -0.4 56 56
GRB2 0.013 0.022 -10000 0 -10000 0 0
GRB7 0.001 0.048 -10000 0 -10000 0 0
PAK1 0.053 0.059 -10000 0 -0.38 8 8
HRAS 0.015 0.012 -10000 0 -10000 0 0
RRAS 0.038 0.052 -10000 0 -0.36 8 8
DNM1 0.016 0.007 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.11 0.21 -10000 0 -0.37 199 199
lamellipodium assembly -0.12 0.16 -10000 0 -0.45 21 21
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.08 0.18 -10000 0 -0.3 198 198
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
EPHB2 0.006 0.04 -10000 0 -10000 0 0
EPHB3 0.014 0.017 -10000 0 -10000 0 0
EPHB1 -0.26 0.36 -10000 0 -0.72 197 197
EPHB4 0.011 0.039 -10000 0 -0.72 1 1
mol:GDP -0.1 0.14 -10000 0 -0.62 10 10
Ephrin B/EPHB2 0 0.052 -10000 0 -0.39 8 8
Ephrin B/EPHB3 -0.005 0.049 -10000 0 -0.39 8 8
JNK cascade -0.12 0.21 -10000 0 -0.38 197 197
Ephrin B/EPHB1 -0.15 0.2 -10000 0 -0.4 198 198
RAP1/GDP -0.083 0.12 -10000 0 -0.52 10 10
EFNB2 0.008 0.079 -10000 0 -0.72 6 6
EFNB3 0.016 0 -10000 0 -10000 0 0
EFNB1 0.013 0.045 -10000 0 -0.72 2 2
Ephrin B2/EPHB1-2 -0.16 0.22 -10000 0 -0.43 198 198
RAP1B 0.016 0.01 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.16 -10000 0 -0.65 8 8
Rap1/GTP -0.12 0.15 -10000 0 -0.62 7 7
axon guidance 0.003 0.028 -10000 0 -0.47 1 1
MAPK3 -0.053 0.16 -10000 0 -0.66 7 7
MAPK1 -0.053 0.16 -10000 0 -0.66 7 7
Rac1/GDP -0.054 0.16 -10000 0 -0.55 10 10
actin cytoskeleton reorganization -0.088 0.12 -10000 0 -0.46 9 9
CDC42/GDP -0.054 0.16 -10000 0 -0.55 10 10
PI3K -0.041 0.13 -10000 0 -0.4 56 56
EFNA5 0.014 0.034 -10000 0 -0.72 1 1
Ephrin B2/EPHB4 -0.005 0.055 -10000 0 -0.47 7 7
Ephrin B/EPHB2/Intersectin/N-WASP 0.041 0.043 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.15 -10000 0 -0.57 8 8
PTK2 0.039 0.051 -10000 0 -10000 0 0
MAP4K4 -0.12 0.21 -10000 0 -0.38 197 197
SRC 0.016 0.007 -10000 0 -10000 0 0
KALRN 0.016 0 -10000 0 -10000 0 0
Intersectin/N-WASP -0.001 0.023 -10000 0 -0.54 1 1
neuron projection morphogenesis -0.032 0.16 -10000 0 -0.46 9 9
MAP2K1 -0.066 0.17 -10000 0 -0.7 7 7
WASL 0.015 0.032 -10000 0 -0.72 1 1
Ephrin B1/EPHB1-2/NCK1 -0.15 0.21 -10000 0 -0.42 197 197
cell migration -0.07 0.18 -10000 0 -0.72 7 7
NRAS 0.014 0.019 -10000 0 -10000 0 0
SYNJ1 0.038 0.052 -10000 0 -0.36 8 8
PXN 0.016 0 -10000 0 -10000 0 0
TF 0.033 0.088 -10000 0 -0.35 26 26
HRAS/GTP -0.12 0.17 -10000 0 -0.5 16 16
Ephrin B1/EPHB1-2 -0.16 0.21 -10000 0 -0.43 197 197
cell adhesion mediated by integrin -0.028 0.063 0.36 8 -10000 0 8
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.13 0.18 -10000 0 -0.36 198 198
RAC1-CDC42/GTP -0.11 0.15 -10000 0 -0.59 8 8
RASA1 0.015 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.083 0.12 -10000 0 -0.52 10 10
ruffle organization -0.072 0.19 -10000 0 -0.62 8 8
NCK1 0.016 0 -10000 0 -10000 0 0
receptor internalization 0.047 0.051 -10000 0 -0.34 8 8
Ephrin B/EPHB2/KALRN 0 0.052 -10000 0 -0.38 8 8
ROCK1 0.03 0.029 -10000 0 -0.42 2 2
RAS family/GDP -0.074 0.1 -10000 0 -0.47 8 8
Rac1/GTP -0.12 0.17 -10000 0 -0.48 21 21
Ephrin B/EPHB1/Src/Paxillin -0.085 0.18 -10000 0 -0.77 7 7
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.055 0.26 -10000 0 -0.55 103 103
IHH 0.009 0.047 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 -0.14 0.2 -10000 0 -0.43 169 169
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.14 0.2 0.42 169 -10000 0 169
SMO/beta Arrestin2 -0.003 0.16 -10000 0 -0.65 8 8
SMO -0.012 0.17 -10000 0 -0.59 12 12
AKT1 -0.014 0.17 -10000 0 -0.61 25 25
ARRB2 0.016 0 -10000 0 -10000 0 0
BOC -0.15 0.31 -10000 0 -0.72 117 117
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.011 0.17 -10000 0 -0.58 12 12
STIL 0.011 0.12 -10000 0 -0.42 7 7
DHH N/PTCH2 0 0 -10000 0 -10000 0 0
DHH N/PTCH1 0.001 0.12 -10000 0 -0.39 3 3
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
DHH 0.016 0 -10000 0 -10000 0 0
PTHLH -0.15 0.47 -10000 0 -1.1 103 103
determination of left/right symmetry -0.011 0.17 -10000 0 -0.58 12 12
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
skeletal system development -0.15 0.46 -10000 0 -1.1 103 103
IHH N/Hhip 0.023 0.023 -10000 0 -10000 0 0
DHH N/Hhip 0 0.006 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.011 0.17 -10000 0 -0.58 12 12
pancreas development 0.015 0.012 -10000 0 -10000 0 0
HHAT 0.006 0.074 -10000 0 -0.72 5 5
PI3K -0.052 0.16 -10000 0 -0.54 51 51
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.22 0.34 -10000 0 -0.72 166 166
somite specification -0.011 0.17 -10000 0 -0.58 12 12
SHH Np/Cholesterol/PTCH1 0.008 0.12 -10000 0 -0.38 8 8
SHH Np/Cholesterol/PTCH2 -0.005 0.041 -10000 0 -0.42 5 5
SHH Np/Cholesterol/Megalin -0.12 0.2 -10000 0 -0.43 149 149
SHH 0.022 0.057 -10000 0 -0.54 5 5
catabolic process -0.009 0.14 -10000 0 -0.38 9 9
SMO/Vitamin D3 0.004 0.14 -10000 0 -0.5 10 10
SHH Np/Cholesterol/Hhip -0.004 0.041 -10000 0 -0.42 5 5
LRP2 -0.19 0.33 -10000 0 -0.72 147 147
receptor-mediated endocytosis -0.12 0.17 -10000 0 -0.52 48 48
SHH Np/Cholesterol/BOC -0.098 0.18 -10000 0 -0.43 121 121
SHH Np/Cholesterol/CDO -0.007 0.057 -10000 0 -0.48 7 7
mesenchymal cell differentiation 0.004 0.041 0.42 5 -10000 0 5
mol:Vitamin D3 0.012 0.12 -10000 0 -0.38 8 8
IHH N/PTCH2 0.023 0.022 -10000 0 -10000 0 0
CDON 0.012 0.056 -10000 0 -0.72 3 3
IHH N/PTCH1 -0.007 0.14 -10000 0 -0.38 9 9
Megalin/LRPAP1 -0.15 0.24 -10000 0 -0.54 147 147
PTCH2 0.016 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.003 0.043 -10000 0 -0.43 5 5
PTCH1 -0.009 0.14 -10000 0 -0.38 9 9
HHIP 0.015 0.012 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.078 0.11 0.6 2 -10000 0 2
GNAI2 0.016 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0 -10000 0 -10000 0 0
RhoA/GTP -0.08 0.11 -10000 0 -0.62 2 2
negative regulation of cAMP metabolic process -0.067 0.14 -10000 0 -0.25 193 193
GNAZ 0.008 0.078 -10000 0 -0.72 6 6
GNAI3 0.016 0 -10000 0 -10000 0 0
GNA12 0.016 0 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.068 0.14 -10000 0 -0.25 193 193
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.25 0.35 -10000 0 -0.72 189 189
TCGA08_retinoblastoma

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
CDKN2B 0.007 0.061 -10000 0 -0.69 3 3
CDKN2C -0.043 0.2 -10000 0 -0.7 44 44
CDKN2A -0.008 0.066 -10000 0 -10000 0 0
CCND2 0.016 0.059 0.2 42 -0.17 7 49
RB1 -0.018 0.063 0.18 3 -0.22 42 45
CDK4 0.021 0.066 0.23 45 -10000 0 45
CDK6 0.017 0.067 0.22 42 -0.26 4 46
G1/S progression 0.002 0.068 0.22 42 -0.18 3 45
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.026 0.17 -10000 0 -0.54 51 51
MAP4K4 0.044 0.066 -10000 0 -10000 0 0
BAG4 0.011 0.029 -10000 0 -10000 0 0
PKC zeta/ceramide -0.03 0.073 0.16 36 -10000 0 36
NFKBIA 0.015 0.032 -10000 0 -0.72 1 1
BIRC3 -0.038 0.18 -10000 0 -0.72 35 35
BAX -0.003 0.039 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.028 0.024 -10000 0 -10000 0 0
BAD -0.018 0.076 0.19 36 -10000 0 36
SMPD1 0.032 0.027 -10000 0 -0.23 1 1
RB1 -0.019 0.078 0.19 35 -0.3 2 37
FADD/Caspase 8 0.052 0.066 -10000 0 -10000 0 0
MAP2K4 -0.019 0.093 -10000 0 -0.42 11 11
NSMAF 0.012 0.056 -10000 0 -0.72 3 3
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.072 -10000 0 -10000 0 0
EGF -0.24 0.35 -10000 0 -0.72 178 178
mol:ceramide -0.03 0.082 0.2 36 -0.12 153 189
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.034 0.19 -10000 0 -0.57 54 54
ASAH1 0.005 0.086 -10000 0 -0.72 7 7
negative regulation of cell cycle -0.02 0.077 0.19 35 -0.3 2 37
cell proliferation -0.17 0.16 -10000 0 -0.34 224 224
BID 0.031 0.052 -10000 0 -10000 0 0
MAP3K1 -0.024 0.085 0.19 35 -0.43 4 39
EIF2A -0.003 0.071 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 0.007 0.068 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.068 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.026 0.076 0.18 35 -10000 0 35
FADD 0.038 0.07 -10000 0 -0.27 6 6
KSR1 -0.018 0.076 0.19 36 -10000 0 36
MAPK8 -0.015 0.08 0.18 34 -0.27 11 45
PRKRA -0.018 0.076 0.19 36 -10000 0 36
PDGFA -0.055 0.22 -10000 0 -0.72 51 51
TRAF2 0.015 0.012 -10000 0 -10000 0 0
IGF1 -0.35 0.37 -10000 0 -0.72 262 262
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.03 0.081 0.19 36 -0.12 153 189
CTSD 0.001 0.047 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.17 0.19 -10000 0 -0.37 224 224
PRKCD 0.014 0.019 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.034 0.19 -10000 0 -0.57 54 54
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0.037 -10000 0 -0.72 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.036 0.069 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.004 0.019 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.026 0.17 -10000 0 -0.54 51 51
MAP2K1 0.002 0.069 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS 0.026 0.087 0.2 66 -10000 0 66
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.003 0.014 -10000 0 -10000 0 0
EIF2AK2 -0.013 0.074 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0 0.037 -10000 0 -0.46 3 3
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.046 0.041 -10000 0 -10000 0 0
MAP2K2 0.002 0.069 -10000 0 -10000 0 0
SMPD3 0.035 0.03 -10000 0 -0.22 1 1
TNF 0.012 0.025 -10000 0 -10000 0 0
PKC zeta/PAR4 -0.002 0.026 -10000 0 -0.55 1 1
mol:PHOSPHOCHOLINE 0.098 0.14 0.26 214 -10000 0 214
NF kappa B1/RelA/I kappa B alpha 0 0.026 -10000 0 -0.39 2 2
AIFM1 0.026 0.087 0.2 66 -10000 0 66
BCL2 -0.13 0.29 -10000 0 -0.72 104 104
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0 0.013 -9999 0 -10000 0 0
VDR 0.013 0.046 -9999 0 -0.72 2 2
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.074 0.041 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.084 0.043 -9999 0 -0.36 2 2
MED1 0.006 0.039 -9999 0 -10000 0 0
mol:9cRA 0.008 0.004 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.035 0.17 -9999 0 -0.72 10 10
RXRs/NUR77 0.034 0.11 -9999 0 -0.4 31 31
RXRs/PPAR -0.19 0.16 -9999 0 -0.28 388 388
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.034 -9999 0 -0.55 2 2
RARs/VDR/DNA/Vit D3 -0.064 0.15 -9999 0 -0.39 86 86
RARA 0.015 0.016 -9999 0 -10000 0 0
NCOA1 0.015 0.032 -9999 0 -0.72 1 1
VDR/VDR/DNA 0.013 0.046 -9999 0 -0.72 2 2
RARs/RARs/DNA/9cRA -0.063 0.15 -9999 0 -0.4 85 85
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.023 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.034 0.16 -9999 0 -0.32 117 117
THRA -0.031 0.18 -9999 0 -0.72 33 33
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.034 -9999 0 -0.55 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.048 0.049 -9999 0 -0.4 5 5
NR1H4 0.016 0.01 -9999 0 -10000 0 0
RXRs/LXRs/DNA 0.08 0.049 -9999 0 -0.35 6 6
NR1H2 0.024 0.003 -9999 0 -10000 0 0
NR1H3 0.024 0.032 -9999 0 -0.71 1 1
RXRs/VDR/DNA/Vit D3 0.051 0.05 -9999 0 -0.38 7 7
NR4A1 -0.02 0.16 -9999 0 -0.72 26 26
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.049 0.029 -9999 0 -10000 0 0
RXRG 0.016 0.072 -9999 0 -0.72 5 5
RXR alpha/CCPG 0.027 0.01 -9999 0 -10000 0 0
RXRA 0.024 0.003 -9999 0 -10000 0 0
RXRB 0.025 0.004 -9999 0 -10000 0 0
THRB 0.006 0.085 -9999 0 -0.72 7 7
PPARG -0.53 0.32 -9999 0 -0.72 388 388
PPARD 0.016 0.01 -9999 0 -10000 0 0
TNF 0.089 0.041 -9999 0 -10000 0 0
mol:Oxysterols 0.008 0.004 -9999 0 -10000 0 0
cholesterol transport 0.084 0.043 -9999 0 -0.36 2 2
PPARA 0.015 0.032 -9999 0 -0.72 1 1
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.1 0.27 -9999 0 -0.72 85 85
RXRs/NUR77/BCL2 -0.04 0.16 -9999 0 -0.3 129 129
SREBF1 0.088 0.042 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.048 0.049 -9999 0 -0.4 5 5
ABCA1 0.087 0.082 -9999 0 -1.1 2 2
RARs/THRs -0.09 0.18 -9999 0 -0.41 117 117
RXRs/FXR 0.057 0.045 -9999 0 -0.4 5 5
BCL2 -0.13 0.29 -9999 0 -0.72 104 104
Neurotrophic factor-mediated Trk 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
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.059 0.094 -10000 0 -0.31 5 5
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.55 161 161
NT3 (dimer)/TRKB -0.42 0.39 -10000 0 -0.67 329 329
SHC/Grb2/SOS1/GAB1/PI3K 0.015 0.1 -10000 0 -0.3 4 4
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF 0.006 0.057 -10000 0 -0.72 2 2
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 0.014 0.019 -10000 0 -10000 0 0
NTRK2 -0.34 0.37 -10000 0 -0.72 252 252
NTRK3 -0.006 0.13 -10000 0 -0.72 16 16
NT-4/5 (dimer)/TRKB -0.3 0.32 -10000 0 -0.58 274 274
neuron apoptosis 0.18 0.23 0.54 124 -10000 0 124
SHC 2-3/Grb2 -0.2 0.26 -10000 0 -0.6 124 124
SHC1 0.016 0 -10000 0 -10000 0 0
SHC2 -0.2 0.27 -10000 0 -0.64 120 120
SHC3 -0.17 0.24 -10000 0 -0.6 105 105
STAT3 (dimer) 0.019 0.059 -10000 0 -0.36 12 12
NT3 (dimer)/TRKA -0.21 0.27 -10000 0 -0.51 216 216
RIN/GDP -0.002 0.099 -10000 0 -0.24 11 11
GIPC1 0.015 0.012 -10000 0 -10000 0 0
KRAS 0.012 0.025 -10000 0 -10000 0 0
DNAJA3 -0.09 0.18 -10000 0 -0.44 94 94
RIN/GTP -0.001 0.024 -10000 0 -0.55 1 1
CCND1 -0.001 0.15 -10000 0 -0.94 12 12
MAGED1 0.006 0.04 -10000 0 -10000 0 0
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0.012 0.026 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.002 0.011 -10000 0 -10000 0 0
GRB2 0.013 0.022 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.003 0.015 -10000 0 -10000 0 0
TRKA/NEDD4-2 -0.017 0.09 -10000 0 -0.54 15 15
ELMO1 0.016 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 -0.004 0.041 -10000 0 -0.47 4 4
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
DOCK1 0.011 0.064 -10000 0 -0.72 4 4
GAB2 0.015 0.016 -10000 0 -10000 0 0
RIT2 0.015 0.032 -10000 0 -0.72 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.011 0.039 -10000 0 -0.72 1 1
DNM1 0.016 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0.032 -10000 0 -0.72 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.087 0.18 -10000 0 -0.43 94 94
mol:GDP -0.017 0.14 -10000 0 -0.34 15 15
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.002 0.098 -10000 0 -0.24 10 10
TIAM1 0.015 0.012 -10000 0 -10000 0 0
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
BDNF (dimer)/TRKB -0.22 0.23 -10000 0 -0.46 254 254
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0.006 -10000 0 -10000 0 0
FRS2 family/SHP2 0.001 0.023 -10000 0 -0.46 1 1
SHC/GRB2/SOS1/GAB1 0.001 0.022 -10000 0 -0.41 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.2 0.33 -10000 0 -0.72 150 150
RAP1/GDP -0.035 0.057 -10000 0 -0.22 4 4
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) 0.006 0.057 -10000 0 -0.72 2 2
ubiquitin-dependent protein catabolic process -0.012 0.078 -10000 0 -0.47 15 15
Schwann cell development -0.044 0.037 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.003 0.025 -10000 0 -0.41 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.05 0.018 -10000 0 -10000 0 0
RAP1B 0.016 0.01 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.27 0.26 -10000 0 -0.68 110 110
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.07 0.075 -10000 0 -10000 0 0
STAT3 0.02 0.059 -10000 0 -0.36 12 12
axon guidance -0.26 0.25 -10000 0 -0.64 110 110
MAPK3 0.029 0.016 -10000 0 -10000 0 0
MAPK1 0.029 0.016 -10000 0 -10000 0 0
CDC42/GDP -0.002 0.098 -10000 0 -0.24 9 9
NTF3 -0.2 0.33 -10000 0 -0.72 150 150
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.001 0.009 -10000 0 -10000 0 0
PI3K -0.052 0.16 -10000 0 -0.54 51 51
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0.007 -10000 0 -10000 0 0
GAB1 0.014 0.034 -10000 0 -0.72 1 1
RASGRF1 -0.092 0.18 -10000 0 -0.44 94 94
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L -0.12 0.24 -10000 0 -0.47 161 161
RGS19 0.012 0.027 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.07 -10000 0 -10000 0 0
Rac1/GDP -0.002 0.098 -10000 0 -0.24 9 9
NGF (dimer)/TRKA/GRIT 0.003 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.053 0.19 -10000 0 -0.68 18 18
NGF (dimer)/TRKA/NEDD4-2 -0.012 0.079 -10000 0 -0.47 15 15
MAP2K1 0.048 0.022 -10000 0 -0.38 1 1
NGFR -0.12 0.28 -10000 0 -0.72 94 94
NGF (dimer)/TRKA/GIPC/GAIP 0.039 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.007 0.099 -10000 0 -0.3 51 51
FRS2 family/SHP2/GRB2/SOS1 0.003 0.024 -10000 0 -0.38 1 1
NRAS 0.014 0.019 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
PRKCI 0.013 0.022 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.042 0.047 -10000 0 -10000 0 0
RASA1 0.015 0.012 -10000 0 -10000 0 0
TRKA/c-Abl -0.001 0.009 -10000 0 -10000 0 0
SQSTM1 0.016 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.2 0.21 -10000 0 -0.41 254 254
NGF (dimer)/TRKA/p62/Atypical PKCs 0.002 0.013 -10000 0 -10000 0 0
MATK 0.011 0.029 -10000 0 -10000 0 0
NEDD4L -0.005 0.12 -10000 0 -0.72 15 15
RAS family/GDP -0.033 0.053 -10000 0 -0.22 1 1
NGF (dimer)/TRKA -0.097 0.2 -10000 0 -0.47 94 94
Rac1/GTP -0.073 0.1 -10000 0 -0.34 40 40
FRS2 family/SHP2/CRK family 0 0.028 -10000 0 -0.41 2 2
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 0.046 0.11 -9999 0 -0.47 20 20
EPHB2 0.006 0.04 -9999 0 -10000 0 0
Syndecan-2/TACI 0.012 0.093 -9999 0 -0.46 20 20
LAMA1 0.016 0.01 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.16 0.22 -9999 0 -0.42 196 196
HRAS 0.015 0.012 -9999 0 -10000 0 0
Syndecan-2/CASK -0.018 0.089 -9999 0 -0.47 20 20
ITGA5 0.016 0.007 -9999 0 -10000 0 0
BAX 0.033 0.087 -9999 0 -10000 0 0
EPB41 0.016 0.007 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.017 0.081 -9999 0 -0.42 21 21
LAMA3 -0.23 0.35 -9999 0 -0.72 176 176
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.46 0.35 -9999 0 -0.72 338 338
Syndecan-2/MMP2 0.008 0.12 -9999 0 -0.54 21 21
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.02 0.1 -9999 0 -0.54 19 19
dendrite morphogenesis 0.015 0.094 -9999 0 -0.45 20 20
Syndecan-2/GM-CSF 0.013 0.096 -9999 0 -0.46 20 20
determination of left/right symmetry 0.003 0.11 -9999 0 -0.54 20 20
Syndecan-2/PKC delta 0.012 0.094 -9999 0 -0.46 20 20
GNB2L1 0.016 0 -9999 0 -10000 0 0
MAPK3 0.021 0.088 -9999 0 -0.41 20 20
MAPK1 0.021 0.088 -9999 0 -0.41 20 20
Syndecan-2/RACK1 -0.015 0.075 -9999 0 -0.39 20 20
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.003 0.11 -9999 0 -0.54 20 20
ITGA2 -0.011 0.14 -9999 0 -0.72 19 19
MAPK8 0.024 0.097 -9999 0 -0.45 21 21
Syndecan-2/alpha2/beta1 Integrin -0.027 0.11 -9999 0 -0.43 35 35
Syndecan-2/Kininogen 0.012 0.093 -9999 0 -0.46 20 20
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.031 0.078 -9999 0 -0.36 20 20
Syndecan-2/CASK/Protein 4.1 -0.016 0.08 -9999 0 -0.42 20 20
extracellular matrix organization 0.012 0.093 -9999 0 -0.45 20 20
actin cytoskeleton reorganization 0.046 0.11 -9999 0 -0.46 20 20
Syndecan-2/Caveolin-2/Ras -0.28 0.22 -9999 0 -0.44 338 338
Syndecan-2/Laminin alpha3 -0.15 0.25 -9999 0 -0.48 189 189
Syndecan-2/RasGAP -0.013 0.071 -9999 0 -0.36 20 20
alpha5/beta1 Integrin 0 0.003 -9999 0 -10000 0 0
PRKCD 0.014 0.019 -9999 0 -10000 0 0
Syndecan-2 dimer 0.015 0.095 -9999 0 -0.46 20 20
GO:0007205 0.004 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.077 -9999 0 -0.35 20 20
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.015 0.032 -9999 0 -0.72 1 1
TNFRSF13B 0.016 0.01 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.02 0.1 -9999 0 -0.54 19 19
Syndecan-2/Synbindin 0.012 0.093 -9999 0 -0.46 20 20
TGFB1 0.016 0.01 -9999 0 -10000 0 0
CASP3 0.023 0.087 -9999 0 -0.41 20 20
FN1 -0.098 0.074 -9999 0 -10000 0 0
Syndecan-2/IL8 0.017 0.1 -9999 0 -0.46 21 21
SDC2 0.003 0.11 -9999 0 -0.54 20 20
KNG1 0.016 0.007 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.012 0.093 -9999 0 -0.46 20 20
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 0.01 0.03 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.012 0.093 -9999 0 -0.46 20 20
Syndecan-2/Syntenin/PI-4-5-P2 -0.017 0.082 -9999 0 -0.42 21 21
Syndecan-2/Ezrin -0.016 0.08 -9999 0 -0.42 20 20
PRKACA 0.024 0.086 -9999 0 -0.41 20 20
angiogenesis 0.017 0.099 -9999 0 -0.46 21 21
MMP2 0.009 0.072 -9999 0 -0.72 5 5
IL8 -0.006 0.063 -9999 0 -0.72 1 1
calcineurin-NFAT signaling pathway 0.012 0.093 -9999 0 -0.45 20 20
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.019 0.011 -10000 0 -10000 0 0
HSPA8 0.016 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.13 0.23 0.3 1 -0.52 125 126
AKT1 0.017 0.02 -10000 0 -10000 0 0
GSC -0.097 0.43 -10000 0 -1.5 46 46
NKX2-5 -0.003 0.057 -10000 0 -0.23 7 7
muscle cell differentiation 0.035 0.11 0.41 31 -10000 0 31
SMAD2-3/SMAD4/SP1 0.026 0.094 -10000 0 -0.41 8 8
SMAD4 -0.013 0.082 -10000 0 -0.38 11 11
CBFB 0.016 0.01 -10000 0 -10000 0 0
SAP18 0.016 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.26 0.23 -10000 0 -0.46 302 302
SMAD3/SMAD4/VDR 0 0.065 -10000 0 -0.45 6 6
MYC -0.028 0.17 -10000 0 -0.73 29 29
CDKN2B 0.023 0.13 -10000 0 -1.5 3 3
AP1 -0.35 0.39 -10000 0 -0.63 244 244
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.065 0.04 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.016 0.11 -10000 0 -0.34 16 16
SP3 0.019 0.005 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 0.01 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.058 0.17 -10000 0 -0.55 49 49
GATA3 -0.067 0.19 -10000 0 -0.7 38 38
SKI/SIN3/HDAC complex/NCoR1 0.056 0.021 -10000 0 -10000 0 0
MEF2C/TIF2 -0.012 0.2 -10000 0 -0.72 33 33
endothelial cell migration -0.032 0.047 -10000 0 -10000 0 0
MAX 0.014 0.002 -10000 0 -10000 0 0
RBBP7 0.012 0.026 -10000 0 -10000 0 0
RBBP4 0.016 0.007 -10000 0 -10000 0 0
RUNX2 0.013 0.022 -10000 0 -10000 0 0
RUNX3 -0.045 0.2 -10000 0 -0.72 42 42
RUNX1 -0.006 0.12 -10000 0 -0.72 15 15
CTBP1 0.016 0.007 -10000 0 -10000 0 0
NR3C1 -0.051 0.21 -10000 0 -0.73 46 46
VDR 0.013 0.046 -10000 0 -0.72 2 2
CDKN1A 0.033 0.11 -10000 0 -1.4 2 2
KAT2B 0 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.019 0.1 -10000 0 -0.42 14 14
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.016 0.007 -10000 0 -10000 0 0
SERPINE1 0.03 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.013 0.067 -10000 0 -0.46 5 5
SMAD3/SMAD4/ATF3 -0.18 0.25 -10000 0 -0.52 175 175
SAP30 0.016 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.01 0.039 -10000 0 -0.42 1 1
JUN -0.34 0.38 -10000 0 -0.72 185 185
SMAD3/SMAD4/IRF7 -0.011 0.068 -10000 0 -0.45 5 5
TFE3 0.015 0.036 -10000 0 -10000 0 0
COL1A2 0.043 0.12 -10000 0 -1.1 3 3
mesenchymal cell differentiation 0.014 0.068 0.46 5 -10000 0 5
DLX1 0.006 0.04 -10000 0 -10000 0 0
TCF3 0.014 0.019 -10000 0 -10000 0 0
FOS -0.52 0.35 -10000 0 -0.74 374 374
SMAD3/SMAD4/Max -0.015 0.067 -10000 0 -0.46 5 5
Cbp/p300/SNIP1 0.004 0.026 -10000 0 -0.44 1 1
ZBTB17 0.014 0.005 -10000 0 -10000 0 0
LAMC1 -0.009 0.21 -10000 0 -0.75 37 37
TGIF2/HDAC complex/SMAD3/SMAD4 -0.014 0.067 -10000 0 -0.46 5 5
IRF7 0.018 0.023 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.73 117 117
HNF4A 0.016 0 -10000 0 -10000 0 0
MEF2C -0.004 0.21 -10000 0 -0.76 34 34
SMAD2-3/SMAD4 -0.02 0.081 -10000 0 -0.4 11 11
Cbp/p300/Src-1 0.006 0.036 -10000 0 -0.44 2 2
IGHV3OR16-13 -0.011 0.032 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0.01 -10000 0 -10000 0 0
CREBBP 0.016 0.032 -10000 0 -0.7 1 1
SKIL -0.001 0.049 -10000 0 -10000 0 0
HDAC1 0.016 0.001 -10000 0 -10000 0 0
HDAC2 0.014 0.017 -10000 0 -10000 0 0
SNIP1 0.015 0.004 -10000 0 -10000 0 0
GCN5L2 0.018 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.02 0.1 -10000 0 -0.4 29 29
MSG1/HSC70 -0.31 0.27 -10000 0 -0.54 302 302
SMAD2 0.014 0.035 -10000 0 -10000 0 0
SMAD3 -0.003 0.058 -10000 0 -0.5 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.055 -10000 0 -0.35 3 3
SMAD2/SMAD2/SMAD4 0.011 0.041 -10000 0 -0.42 2 2
NCOR1 0.015 0.032 -10000 0 -0.72 1 1
NCOA2 0.015 0.014 -10000 0 -10000 0 0
NCOA1 0.015 0.032 -10000 0 -0.72 1 1
MYOD/E2A -0.004 0.035 -10000 0 -0.54 2 2
SMAD2-3/SMAD4/SP1/MIZ-1 0.045 0.089 -10000 0 -0.41 6 6
IFNB1 0.026 0.073 -10000 0 -0.46 3 3
SMAD3/SMAD4/MEF2C -0.027 0.21 -10000 0 -0.75 35 35
CITED1 -0.41 0.36 -10000 0 -0.72 302 302
SMAD2-3/SMAD4/ARC105 -0.013 0.071 -10000 0 -0.42 6 6
RBL1 0.007 0.037 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.023 0.12 -10000 0 -0.38 15 15
RUNX1-3/PEBPB2 -0.048 0.15 -10000 0 -0.48 55 55
SMAD7 -0.18 0.24 -10000 0 -0.54 114 114
MYC/MIZ-1 -0.029 0.13 -10000 0 -0.55 29 29
SMAD3/SMAD4 0.03 0.076 0.28 20 -0.33 1 21
IL10 -0.013 0.14 -10000 0 -0.46 39 39
PIASy/HDAC complex 0.014 0.016 -10000 0 -10000 0 0
PIAS3 0.017 0.003 -10000 0 -10000 0 0
CDK2 0.015 0.024 -10000 0 -10000 0 0
IL5 -0.013 0.14 -10000 0 -0.46 39 39
CDK4 0.017 0.018 -10000 0 -10000 0 0
PIAS4 0.014 0.016 -10000 0 -10000 0 0
ATF3 -0.22 0.34 -10000 0 -0.72 170 170
SMAD3/SMAD4/SP1 -0.006 0.073 -10000 0 -0.47 6 6
FOXG1 0.004 0.041 -10000 0 -10000 0 0
FOXO3 0.033 0.015 -10000 0 -10000 0 0
FOXO1 -0.045 0.2 -10000 0 -0.54 72 72
FOXO4 0.033 0.015 -10000 0 -10000 0 0
heart looping -0.003 0.21 -10000 0 -0.74 34 34
CEBPB 0.016 0.033 -10000 0 -0.72 1 1
SMAD3/SMAD4/DLX1 -0.016 0.072 -10000 0 -0.42 7 7
MYOD1 0.011 0.049 -10000 0 -0.72 2 2
SMAD3/SMAD4/HNF4 -0.013 0.067 -10000 0 -0.46 5 5
SMAD3/SMAD4/GATA3 -0.028 0.16 -10000 0 -0.53 40 40
SnoN/SIN3/HDAC complex/NCoR1 -0.001 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.046 0.15 -10000 0 -0.45 58 58
SMAD3/SMAD4/SP1-3 0.002 0.071 -10000 0 -0.46 6 6
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.026 0.014 -10000 0 -10000 0 0
SIN3B 0.015 0.016 -10000 0 -10000 0 0
SIN3A 0.016 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.014 0.13 -10000 0 -0.46 23 23
ITGB5 0.045 0.093 -10000 0 -0.68 5 5
TGIF/SIN3/HDAC complex/CtBP 0.059 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.079 0.19 -10000 0 -0.53 71 71
AR -0.082 0.25 -10000 0 -0.72 69 69
negative regulation of cell growth -0.041 0.12 -10000 0 -0.4 11 11
SMAD3/SMAD4/MYOD -0.016 0.073 -10000 0 -0.47 7 7
E2F5 -0.002 0.051 -10000 0 -10000 0 0
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.006 0.075 -10000 0 -0.37 8 8
SMAD2-3/SMAD4/FOXO1-3a-4 0.017 0.12 -10000 0 -0.36 18 18
TFDP1 0.012 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.35 0.4 -10000 0 -0.72 195 195
SMAD3/SMAD4/RUNX2 -0.014 0.068 -10000 0 -0.46 5 5
TGIF2 0.016 0.01 -10000 0 -10000 0 0
TGIF1 0.015 0.032 -10000 0 -0.72 1 1
ATF2 0.016 0 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.003 0.037 -9999 0 -0.34 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.026 -9999 0 -0.31 1 1
AP1 -0.34 0.25 -9999 0 -0.47 376 376
mol:PIP3 -0.21 0.2 -9999 0 -0.38 294 294
AKT1 0.028 0.1 -9999 0 -0.39 5 5
PTK2B 0.024 0.023 -9999 0 -0.2 5 5
RHOA 0.027 0.025 -9999 0 -10000 0 0
PIK3CB 0.015 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0.032 0.027 -9999 0 -0.37 1 1
MAGI3 0.003 0.066 -9999 0 -0.72 3 3
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis 0.018 0.027 -9999 0 -0.25 5 5
HRAS/GDP -0.001 0.007 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.038 0.036 -9999 0 -0.34 3 3
NF kappa B1 p50/RelA -0.003 0.024 -9999 0 -0.3 1 1
endothelial cell migration 0.017 0.081 -9999 0 -0.81 5 5
ADCY4 -0.038 0.12 -9999 0 -0.42 10 10
ADCY5 -0.036 0.12 -9999 0 -0.45 7 7
ADCY6 -0.036 0.12 -9999 0 -0.45 7 7
ADCY7 -0.036 0.12 -9999 0 -0.45 7 7
ADCY1 -0.036 0.12 -9999 0 -0.45 7 7
ADCY2 -0.039 0.12 -9999 0 -0.43 11 11
ADCY3 -0.036 0.12 -9999 0 -0.45 7 7
ADCY8 -0.036 0.12 -9999 0 -0.45 7 7
ADCY9 -0.036 0.12 -9999 0 -0.45 7 7
GSK3B 0.032 0.022 -9999 0 -0.21 1 1
arachidonic acid secretion -0.024 0.11 -9999 0 -0.45 6 6
GNG2 0.015 0.032 -9999 0 -0.72 1 1
TRIP6 0.024 0.023 -9999 0 -0.48 1 1
GNAO1 0.022 0.032 -9999 0 -0.3 5 5
HRAS 0.015 0.012 -9999 0 -10000 0 0
NFKBIA 0.044 0.033 -9999 0 -0.32 2 2
GAB1 0.014 0.034 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.003 0.009 -9999 0 -10000 0 0
JUN -0.12 0.29 -9999 0 -0.72 97 97
LPA/LPA2/NHERF2 -0.002 0.023 -9999 0 -0.47 1 1
TIAM1 0.003 0.008 -9999 0 -10000 0 0
PIK3R1 -0.056 0.22 -9999 0 -0.72 51 51
mol:IP3 0.033 0.028 -9999 0 -0.38 1 1
PLCB3 0.025 0.023 -9999 0 -0.42 1 1
FOS -0.51 0.34 -9999 0 -0.72 374 374
positive regulation of mitosis -0.024 0.11 -9999 0 -0.45 6 6
LPA/LPA1-2-3 -0.003 0.027 -9999 0 -0.28 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
stress fiber formation 0.031 0.024 -9999 0 -0.2 5 5
GNAZ 0.016 0.061 -9999 0 -0.39 11 11
EGFR/PI3K-beta/Gab1 -0.22 0.22 -9999 0 -0.39 294 294
positive regulation of dendritic cell cytokine production -0.003 0.027 -9999 0 -0.28 5 5
LPA/LPA2/MAGI-3 -0.007 0.04 -9999 0 -0.47 3 3
ARHGEF1 0.038 0.028 -9999 0 -10000 0 0
GNAI2 0.022 0.032 -9999 0 -0.3 5 5
GNAI3 0.022 0.032 -9999 0 -0.3 5 5
GNAI1 -0.16 0.24 -9999 0 -0.47 190 190
LPA/LPA3 -0.001 0.013 -9999 0 -0.13 5 5
LPA/LPA2 -0.001 0.013 -9999 0 -0.13 5 5
LPA/LPA1 -0.004 0.036 -9999 0 -0.36 5 5
HB-EGF/EGFR -0.26 0.25 -9999 0 -0.49 277 277
HBEGF -0.024 0.07 -9999 0 -0.54 4 4
mol:DAG 0.033 0.028 -9999 0 -0.38 1 1
cAMP biosynthetic process -0.03 0.12 -9999 0 -0.48 6 6
NFKB1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
GNB1 0.015 0.01 -9999 0 -10000 0 0
LYN 0.045 0.027 -9999 0 -0.27 1 1
GNAQ 0.004 0.011 -9999 0 -0.1 5 5
LPAR2 0 0 -9999 0 -10000 0 0
LPAR3 0 0 -9999 0 -10000 0 0
LPAR1 0.004 0.021 -9999 0 -0.2 5 5
IL8 -0.27 0.18 -9999 0 -0.42 285 285
PTK2 0.02 0.027 -9999 0 -0.25 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 0.018 0.027 -9999 0 -0.26 5 5
EGFR -0.38 0.37 -9999 0 -0.72 277 277
PLCG1 0.018 0.021 -9999 0 -0.15 6 6
PLD2 0.019 0.032 -9999 0 -0.28 6 6
G12/G13 -0.002 0.026 -9999 0 -0.26 5 5
PI3K-beta -0.033 0.097 -9999 0 -0.5 3 3
cell migration 0.004 0.016 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.034 -9999 0 -0.72 1 1
PXN 0.031 0.024 -9999 0 -0.21 5 5
HRAS/GTP -0.059 0.085 -9999 0 -0.46 6 6
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.059 0.081 -9999 0 -10000 0 0
PRKCE 0.016 0 -9999 0 -10000 0 0
PRKCD 0.04 0.028 -9999 0 -0.35 1 1
Gi(beta/gamma) -0.031 0.12 -9999 0 -0.52 6 6
mol:LPA 0.004 0.021 -9999 0 -0.2 5 5
TRIP6/p130 Cas/FAK1/Paxillin -0.001 0.023 -9999 0 -10000 0 0
MAPKKK cascade -0.024 0.11 -9999 0 -0.45 6 6
contractile ring contraction involved in cytokinesis 0.027 0.025 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 0.004 0.048 -9999 0 -0.37 7 7
GNA15 0.013 0.012 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
MAPT 0.038 0.037 -9999 0 -0.36 3 3
GNA11 0.014 0.011 -9999 0 -10000 0 0
Rac1/GTP 0.004 0.011 -9999 0 -10000 0 0
MMP2 0.017 0.082 -9999 0 -0.82 5 5
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.029 0.01 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.04 0.18 0.69 21 -0.51 1 22
IL27/IL27R/JAK1 -0.082 0.27 -10000 0 -1.1 22 22
TBX21 -0.059 0.24 -10000 0 -0.66 54 54
IL12B 0.013 0.024 -10000 0 -10000 0 0
IL12A 0.002 0.082 -10000 0 -0.55 11 11
IL6ST -0.02 0.15 -10000 0 -0.73 21 21
IL27RA/JAK1 -0.029 0.25 -10000 0 -1.3 19 19
IL27 -0.067 0.23 -10000 0 -0.73 58 58
TYK2 0.014 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.22 0.15 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.04 0.18 0.69 21 -0.51 1 22
T cell proliferation during immune response 0.04 0.18 0.69 21 -0.51 1 22
MAPKKK cascade -0.04 0.18 0.51 1 -0.69 21 22
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 -0.011 0.061 -10000 0 -10000 0 0
IL12RB1 0.017 0.001 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.047 0.21 -10000 0 -0.62 39 39
IL27/IL27R/JAK2/TYK2 -0.041 0.18 0.51 1 -0.7 21 22
positive regulation of T cell mediated cytotoxicity -0.04 0.18 0.51 1 -0.69 21 22
STAT1 (dimer) -0.075 0.31 0.5 22 -1 30 52
JAK2 0.011 0.034 -10000 0 -0.73 1 1
JAK1 0.013 0.046 -10000 0 -0.72 2 2
STAT2 (dimer) -0.031 0.17 0.44 1 -0.66 21 22
T cell proliferation -0.33 0.25 0.47 1 -0.53 191 192
IL12/IL12R/TYK2/JAK2 0.035 0.047 -10000 0 -10000 0 0
IL17A -0.22 0.15 -10000 0 -10000 0 0
mast cell activation 0.04 0.18 0.69 21 -0.51 1 22
IFNG 0.002 0.027 0.12 1 -0.081 21 22
T cell differentiation -0.004 0.007 0.034 1 -0.025 21 22
STAT3 (dimer) -0.031 0.17 0.44 1 -0.66 21 22
STAT5A (dimer) -0.032 0.17 0.44 1 -0.64 23 24
STAT4 (dimer) -0.036 0.18 0.44 1 -0.62 27 28
STAT4 0.005 0.086 -10000 0 -0.72 7 7
T cell activation -0.006 0.026 0.13 18 -10000 0 18
IL27R/JAK2/TYK2 -0.048 0.24 -10000 0 -1.2 19 19
GATA3 -0.094 0.37 -10000 0 -1.4 38 38
IL18 0.005 0.038 -10000 0 -0.55 1 1
positive regulation of mast cell cytokine production -0.03 0.16 0.44 1 -0.64 21 22
IL27/EBI3 -0.058 0.17 -10000 0 -0.55 58 58
IL27RA -0.053 0.26 0.44 1 -1.4 18 19
IL6 -0.52 0.32 -10000 0 -0.71 391 391
STAT5A 0.013 0.045 -10000 0 -0.72 2 2
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.019 0.11 0.5 18 -1.4 1 19
IL1B 0.006 0.062 -10000 0 -0.55 6 6
EBI3 0.013 0.013 -10000 0 -10000 0 0
TNF 0.012 0.017 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 -0.003 0.016 -9999 0 -10000 0 0
VLDLR -0.1 0.27 -9999 0 -0.72 83 83
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.013 0.045 -9999 0 -0.72 2 2
ITGA3 0.013 0.046 -9999 0 -0.72 2 2
RELN/VLDLR/Fyn -0.09 0.19 -9999 0 -0.48 100 100
MAPK8IP1/MKK7/MAP3K11/JNK1 0.002 0.022 -9999 0 -0.38 1 1
AKT1 -0.05 0.19 -9999 0 -0.68 23 23
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 0.016 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1 0.004 0.095 -9999 0 -0.44 20 20
LRPAP1/LRP8 -0.022 0.035 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.005 0.093 -9999 0 -0.41 22 22
DAB1/alpha3/beta1 Integrin -0.056 0.16 -9999 0 -0.46 30 30
long-term memory 0.001 0.11 -9999 0 -0.41 31 31
DAB1/LIS1 -0.053 0.17 -9999 0 -0.39 98 98
DAB1/CRLK/C3G -0.054 0.16 -9999 0 -0.46 28 28
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
DAB1/NCK2 -0.053 0.17 -9999 0 -0.39 98 98
ARHGEF2 0.012 0.026 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.016 0.007 -9999 0 -10000 0 0
CDK5R1 0.014 0.019 -9999 0 -10000 0 0
RELN -0.013 0.14 -9999 0 -0.72 20 20
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
RELN/LRP8/Fyn 0.001 0.11 -9999 0 -0.48 22 22
GRIN2A/RELN/LRP8/DAB1/Fyn 0.008 0.094 -9999 0 -0.4 22 22
MAPK8 0.015 0.032 -9999 0 -0.72 1 1
RELN/VLDLR/DAB1 -0.082 0.18 -9999 0 -0.44 98 98
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.087 0.22 -9999 0 -0.44 133 133
RELN/LRP8 0.003 0.1 -9999 0 -0.48 20 20
GRIN2B/RELN/LRP8/DAB1/Fyn -0.001 0.12 -9999 0 -0.43 31 31
PI3K -0.052 0.16 -9999 0 -0.54 51 51
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.034 -9999 0 -0.54 2 2
RAP1A -0.019 0.16 -9999 0 -0.42 28 28
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.016 0.007 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.002 0.11 -9999 0 -0.72 12 12
NCK2 0.016 0.01 -9999 0 -10000 0 0
neuron differentiation 0.044 0.049 -9999 0 -10000 0 0
neuron adhesion -0.001 0.16 -9999 0 -0.63 6 6
LRP8 -0.029 0.072 -9999 0 -10000 0 0
GSK3B -0.038 0.18 -9999 0 -0.64 23 23
RELN/VLDLR/DAB1/Fyn -0.077 0.16 -9999 0 -0.41 100 100
MAP3K11 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.063 0.2 -9999 0 -0.37 133 133
CDK5 0.012 0.027 -9999 0 -10000 0 0
MAPT 0.014 0.06 -9999 0 -0.66 3 3
neuron migration -0.018 0.18 -9999 0 -0.43 47 47
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.044 0.049 -9999 0 -10000 0 0
RELN/VLDLR -0.063 0.19 -9999 0 -0.45 98 98
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0.006 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.015 0.032 -9999 0 -0.72 1 1
ERC1 0.013 0.022 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.037 0.086 -9999 0 -0.35 21 21
IRAK/TOLLIP 0.031 0.012 -9999 0 -10000 0 0
IKBKB 0.014 0.02 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.008 0.045 -9999 0 -0.54 3 3
IL1A 0.014 0.02 -9999 0 -10000 0 0
IL1B -0.043 0.2 -9999 0 -0.57 62 62
IRAK/TRAF6/p62/Atypical PKCs 0.002 0.013 -9999 0 -10000 0 0
IL1R2 0.004 0.065 -9999 0 -0.72 3 3
IL1R1 -0.067 0.23 -9999 0 -0.72 59 59
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.14 -9999 0 -0.34 63 63
TOLLIP 0.016 0.007 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 -0.001 0.021 -9999 0 -0.46 1 1
IKK complex/ELKS 0.082 0.02 -9999 0 -0.34 1 1
JUN -0.01 0.16 -9999 0 -0.33 97 97
MAP3K7 0.016 0.01 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.12 0.24 -9999 0 -0.49 130 130
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.044 0.13 -9999 0 -0.41 59 59
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.04 0.12 -9999 0 -0.38 59 59
IL1 beta fragment/IL1R1/IL1RAP -0.098 0.21 -9999 0 -0.49 104 104
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.054 0.062 -9999 0 -0.32 14 14
IRAK1 0.022 0.012 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.071 0.17 -9999 0 -0.55 59 59
IRAK4 0.016 0.01 -9999 0 -10000 0 0
PRKCI 0.013 0.022 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PI3K -0.052 0.16 -9999 0 -0.54 51 51
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.017 0.15 -9999 0 -0.35 63 63
CHUK 0.015 0.032 -9999 0 -0.72 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.098 0.21 -9999 0 -0.49 104 104
IL1 beta/IL1R2 -0.057 0.17 -9999 0 -0.49 64 64
IRAK/TRAF6/TAK1/TAB1/TAB2 0.001 0.018 -9999 0 -0.34 1 1
NF kappa B1 p50/RelA -0.11 0.21 -9999 0 -0.67 45 45
IRAK3 0.012 0.039 -9999 0 -0.72 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.087 0.19 -9999 0 -0.44 104 104
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.11 -9999 0 -0.29 59 59
IL1 alpha/IL1R1/IL1RAP -0.05 0.14 -9999 0 -0.46 59 59
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
SQSTM1 0.016 0.007 -9999 0 -10000 0 0
MYD88 0.016 0.01 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.041 0.004 -9999 0 -10000 0 0
IL1RAP 0.016 0 -9999 0 -10000 0 0
UBE2N 0.016 0.01 -9999 0 -10000 0 0
IRAK/TRAF6 -0.07 0.16 -9999 0 -0.57 25 25
CASP1 -0.068 0.24 -9999 0 -0.72 60 60
IL1RN/IL1R2 -0.018 0.052 -9999 0 -0.54 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.09 0.2 -9999 0 -0.46 104 104
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.009 0.12 -9999 0 -0.34 59 59
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
IL1RN -0.006 0.056 -9999 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0 0.017 -9999 0 -0.36 1 1
MAP2K6 0.047 0.063 -9999 0 -0.35 13 13
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.027 0.056 -9999 0 -0.51 5 5
alphaM/beta2 Integrin/GPIbA -0.023 0.036 -9999 0 -10000 0 0
alphaM/beta2 Integrin/proMMP-9 -0.04 0.073 -9999 0 -10000 0 0
PLAUR -0.022 0.069 -9999 0 -10000 0 0
HMGB1 -0.017 0.022 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.023 0.029 -9999 0 -10000 0 0
AGER -0.018 0.04 -9999 0 -0.78 1 1
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG 0.014 0.034 -9999 0 -0.72 1 1
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.13 0.089 -9999 0 -0.63 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.059 0.081 -9999 0 -10000 0 0
CYR61 -0.21 0.34 -9999 0 -0.72 161 161
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.002 0.027 -9999 0 -0.36 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.33 -9999 0 -0.72 150 150
MYH2 0.047 0.057 -9999 0 -0.37 5 5
MST1R 0.005 0.041 -9999 0 -10000 0 0
leukocyte activation during inflammatory response -0.011 0.022 -9999 0 -10000 0 0
APOB 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.009 0.072 -9999 0 -0.72 5 5
JAM3 -0.038 0.19 -9999 0 -0.72 39 39
GP1BA 0.011 0.029 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.042 0.1 -9999 0 -0.52 22 22
alphaM/beta2 Integrin 0.027 0.039 -9999 0 -0.43 1 1
JAM3 homodimer -0.038 0.19 -9999 0 -0.72 39 39
ICAM2 0.004 0.096 -9999 0 -0.72 9 9
ICAM1 0.008 0.045 -9999 0 -0.72 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor 0.027 0.039 -9999 0 -0.43 1 1
cell adhesion -0.023 0.036 -9999 0 -10000 0 0
NFKB1 -0.22 0.18 -9999 0 -0.41 25 25
THY1 0.013 0.024 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.11 0.19 -9999 0 -0.45 118 118
IL6 -0.62 0.41 -9999 0 -0.86 391 391
ITGB2 -0.026 0.041 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration -0.022 0.069 -9999 0 -10000 0 0
alphaM/beta2 Integrin/JAM2/JAM3 -0.17 0.27 -9999 0 -0.56 152 152
JAM2 -0.19 0.33 -9999 0 -0.72 150 150
alphaM/beta2 Integrin/ICAM1 -0.005 0.04 -9999 0 -0.43 1 1
alphaM/beta2 Integrin/uPA/Plg -0.019 0.047 -9999 0 -0.46 1 1
RhoA/GTP 0.043 0.05 -9999 0 -0.43 2 2
positive regulation of phagocytosis 0.001 0.029 -9999 0 -10000 0 0
Ron/MSP -0.005 0.02 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA -0.022 0.071 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR -0.028 0.058 -9999 0 -10000 0 0
PLAU -0.009 0.059 -9999 0 -10000 0 0
PLAT -0.15 0.31 -9999 0 -0.72 118 118
actin filament polymerization 0.046 0.055 -9999 0 -0.36 5 5
MST1 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.01 0.023 -9999 0 -10000 0 0
TNF -0.2 0.17 -9999 0 -0.67 1 1
RAP1B 0.016 0.01 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.031 0.049 -9999 0 -10000 0 0
fibrinolysis -0.019 0.047 -9999 0 -0.46 1 1
HCK 0.013 0.024 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation 0.027 0.039 -9999 0 -0.43 1 1
VTN 0.015 0.012 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.17 0.23 -9999 0 -0.51 161 161
LPA 0.016 0 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
cell migration -0.044 0.063 -9999 0 -0.46 5 5
FN1 -0.098 0.074 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.024 0.033 -9999 0 -10000 0 0
MPO 0.015 0.016 -9999 0 -10000 0 0
KNG1 0.016 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.004 -9999 0 -10000 0 0
ROCK1 0.049 0.048 -9999 0 -0.49 1 1
ELA2 0.016 0 -9999 0 -10000 0 0
PLG 0.015 0.032 -9999 0 -0.72 1 1
CTGF -0.015 0.15 -9999 0 -0.72 22 22
alphaM/beta2 Integrin/Hck -0.024 0.034 -9999 0 -10000 0 0
ITGAM -0.017 0.025 -9999 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.14 0.21 -9999 0 -0.46 150 150
HP 0.016 0 -9999 0 -10000 0 0
leukocyte adhesion -0.21 0.23 -9999 0 -0.56 138 138
SELP -0.19 0.33 -9999 0 -0.72 150 150
Angiopoietin receptor Tie2-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
AKT1 0.051 0.24 -10000 0 -0.94 24 24
NCK1/PAK1/Dok-R -0.029 0.093 -10000 0 -0.43 24 24
NCK1/Dok-R -0.048 0.23 -10000 0 -1.1 24 24
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol -0.008 0.041 0.24 14 -10000 0 14
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.018 0.002 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.008 0.042 0.26 13 -10000 0 13
TNIP2 0.015 0.012 -10000 0 -10000 0 0
NF kappa B/RelA -0.045 0.21 -10000 0 -1 24 24
FN1 -0.098 0.074 -10000 0 -10000 0 0
PLD2 0.039 0.26 -10000 0 -1.1 24 24
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.091 0.23 -10000 0 -0.72 57 57
ELK1 0.054 0.24 -10000 0 -1 24 24
GRB7 0.001 0.048 -10000 0 -10000 0 0
PAK1 -0.01 0.06 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.051 0.26 -10000 0 -1.1 24 24
CDKN1A 0.05 0.19 -10000 0 -0.68 19 19
ITGA5 0.016 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.047 0.23 -10000 0 -1.1 24 24
CRK 0.015 0.032 -10000 0 -0.72 1 1
mol:NO 0.066 0.19 -10000 0 -0.67 24 24
PLG 0.039 0.26 -10000 0 -1.1 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.003 0.21 -10000 0 -0.9 24 24
GRB2 0.013 0.022 -10000 0 -10000 0 0
PIK3R1 -0.054 0.22 -10000 0 -0.72 51 51
ANGPT2 -0.027 0.2 -10000 0 -0.64 16 16
BMX -0.21 0.34 -10000 0 -1.4 24 24
ANGPT1 0.015 0.23 -10000 0 -1.4 14 14
tube development 0.042 0.21 -10000 0 -0.74 20 20
ANGPT4 0.016 0.001 -10000 0 -10000 0 0
response to hypoxia 0.004 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.001 0.31 -10000 0 -1.3 24 24
alpha5/beta1 Integrin 0 0.003 -10000 0 -10000 0 0
FGF2 -0.55 0.31 -10000 0 -0.72 403 403
STAT5A (dimer) 0.045 0.23 -10000 0 -0.87 19 19
mol:L-citrulline 0.066 0.19 -10000 0 -0.67 24 24
AGTR1 -0.31 0.35 -10000 0 -0.72 224 224
MAPK14 0.035 0.27 -10000 0 -1.2 24 24
Tie2/SHP2 -0.032 0.18 -10000 0 -1.2 12 12
TEK 0.027 0.21 -10000 0 -1.3 12 12
RPS6KB1 0.048 0.23 -10000 0 -0.9 24 24
Angiotensin II/AT1 -0.23 0.27 -10000 0 -0.55 224 224
Tie2/Ang1/GRB2 0.036 0.27 -10000 0 -1.2 24 24
MAPK3 0.049 0.24 -10000 0 -1 24 24
MAPK1 0.049 0.24 -10000 0 -1 24 24
Tie2/Ang1/GRB7 0.039 0.27 -10000 0 -1.2 24 24
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.039 0.26 -10000 0 -1.1 24 24
PI3K 0.034 0.27 -10000 0 -1.1 24 24
FES 0.033 0.27 -10000 0 -1.2 24 24
Crk/Dok-R -0.048 0.23 -10000 0 -1.1 24 24
Tie2/Ang1/ABIN2 0.035 0.27 -10000 0 -1.2 24 24
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.055 0.22 -10000 0 -0.83 24 24
STAT5A 0.014 0.045 -10000 0 -0.72 2 2
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.049 0.23 -10000 0 -0.9 24 24
Tie2/Ang2 0.024 0.26 -10000 0 -1.1 19 19
Tie2/Ang1 0.028 0.28 -10000 0 -1.2 24 24
FOXO1 0.04 0.26 -10000 0 -0.87 25 25
ELF1 0.026 0.018 -10000 0 -10000 0 0
ELF2 0.036 0.26 -10000 0 -1.1 24 24
mol:Choline 0.041 0.25 -10000 0 -1.1 24 24
cell migration -0.013 0.054 -10000 0 -0.24 24 24
FYN 0.037 0.23 -10000 0 -0.87 19 19
DOK2 0.013 0.046 -10000 0 -0.72 2 2
negative regulation of cell cycle 0.052 0.18 -10000 0 -0.61 19 19
ETS1 0.022 0.057 -10000 0 -0.89 1 1
PXN 0.061 0.2 -10000 0 -0.73 24 24
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 0.063 0.21 -10000 0 -0.78 24 24
RAC1 0.016 0 -10000 0 -10000 0 0
TNF 0.02 0.046 -10000 0 -10000 0 0
MAPKKK cascade 0.041 0.25 -10000 0 -1.1 24 24
RASA1 0.015 0.012 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.033 0.27 -10000 0 -1.2 24 24
NCK1 0.016 0 -10000 0 -10000 0 0
vasculogenesis 0.068 0.17 -10000 0 -0.6 24 24
mol:Phosphatidic acid 0.041 0.25 -10000 0 -1.1 24 24
mol:Angiotensin II 0.002 0.001 -10000 0 -10000 0 0
mol:NADP 0.066 0.19 -10000 0 -0.67 24 24
Rac1/GTP -0.053 0.18 -10000 0 -0.83 24 24
MMP2 0.036 0.27 -10000 0 -1.2 24 24
Wnt signaling

Figure 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
Noncanonical Wnts/FZD -0.016 0.18 -9999 0 -0.41 72 72
FZD6 -0.024 0.16 -9999 0 -0.72 26 26
WNT6 0.012 0.048 -9999 0 -0.72 2 2
WNT4 0.005 0.05 -9999 0 -0.72 1 1
FZD3 -0.019 0.16 -9999 0 -0.72 25 25
WNT5A -0.029 0.17 -9999 0 -0.72 28 28
WNT11 -0.001 0.1 -9999 0 -0.72 10 10
S1P4 pathway

Figure 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.08 0.11 -9999 0 -0.62 2 2
PLCG1 -0.054 0.13 -9999 0 -0.53 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0.007 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.007 -9999 0 -10000 0 0
cell migration -0.078 0.11 -9999 0 -0.6 2 2
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 -0.054 0.13 -9999 0 -0.51 3 3
MAPK1 -0.054 0.13 -9999 0 -0.64 2 2
S1P/S1P5/Gi -0.068 0.14 -9999 0 -0.25 193 193
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0 0 -9999 0 -10000 0 0
RHOA 0.03 0.006 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.068 0.14 -9999 0 -0.25 193 193
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.008 0.078 -9999 0 -0.72 6 6
S1P/S1P4/G12/G13 0.001 0.006 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.016 0.007 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.072 0.16 0.32 6 -0.36 106 112
FRAP1 0.009 0.049 -10000 0 -10000 0 0
AKT1 -0.032 0.15 0.25 6 -0.38 52 58
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.049 0.1 -10000 0 -0.31 52 52
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.014 0.033 -10000 0 -10000 0 0
TSC2 0.016 0 -10000 0 -10000 0 0
RHEB/GDP -0.042 0.092 0.18 1 -0.4 8 9
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.033 0.14 -10000 0 -0.39 69 69
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.017 0.039 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0.007 -10000 0 -10000 0 0
RPS6KB1 0.002 0.091 -10000 0 -0.31 7 7
MAP3K5 -0.015 0.11 -10000 0 -0.42 35 35
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
apoptosis -0.015 0.11 -10000 0 -0.42 35 35
mol:LY294002 0 0.001 -10000 0 -0.002 62 62
EIF4B 0.012 0.083 -10000 0 -0.27 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.026 0.058 -10000 0 -0.4 1 1
eIF4E/eIF4G1/eIF4A1 -0.005 0.015 -10000 0 -10000 0 0
KIAA1303 0.016 0.01 -10000 0 -10000 0 0
PI3K -0.057 0.18 -10000 0 -0.38 113 113
mTOR/RHEB/GTP/Raptor/GBL 0.031 0.071 -10000 0 -10000 0 0
FKBP1A 0.016 0.01 -10000 0 -10000 0 0
RHEB/GTP -0.042 0.091 0.23 1 -0.39 8 9
mol:Amino Acids 0 0.001 -10000 0 -0.002 62 62
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.066 0.14 0.26 6 -0.33 106 112
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C -0.02 0.16 -10000 0 -0.62 35 35
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.042 0.006 -10000 0 -10000 0 0
TSC1/TSC2 -0.052 0.11 -10000 0 -0.33 52 52
tumor necrosis factor receptor activity 0 0.001 0.002 62 -10000 0 62
RPS6 0.015 0.032 -10000 0 -0.72 1 1
PPP5C 0.014 0.02 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 -0.046 0.15 -10000 0 -0.42 69 69
INS 0.016 0 -10000 0 -10000 0 0
PTEN -0.002 0.11 -10000 0 -0.72 13 13
PDK2 -0.066 0.14 0.26 6 -0.34 106 112
EIF4EBP1 0.022 0.019 -10000 0 -10000 0 0
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
PPP2R5D 0.017 0.046 -10000 0 -10000 0 0
peptide biosynthetic process 0.032 0 -10000 0 -10000 0 0
RHEB 0.016 0.007 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 13 -0.003 51 64
EEF2 0.033 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.029 0.014 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.002 0.026 -9999 0 -0.54 1 1
AKT1 -0.006 0.2 -9999 0 -0.54 31 31
PTK2B 0.001 0.14 -9999 0 -0.51 25 25
VEGFR2 homodimer/Frs2 -0.006 0.14 -9999 0 -0.52 32 32
CAV1 -0.52 0.33 -9999 0 -0.72 385 385
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.057 0.15 -9999 0 -0.58 26 26
endothelial cell proliferation 0.015 0.19 -9999 0 -0.5 29 29
mol:Ca2+ -0.043 0.22 -9999 0 -0.69 29 29
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.05 0.13 -9999 0 -0.54 25 25
RP11-342D11.1 -0.054 0.22 -9999 0 -0.69 30 30
CDH5 0.016 0 -9999 0 -10000 0 0
VEGFA homodimer 0.003 0.053 -9999 0 -0.44 4 4
SHC1 0.016 0 -9999 0 -10000 0 0
SHC2 -0.023 0.17 -9999 0 -0.72 28 28
HRAS/GDP -0.078 0.16 -9999 0 -0.58 29 29
SH2D2A -0.006 0.056 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.063 0.15 -9999 0 -0.52 29 29
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.05 0.16 -9999 0 -0.58 26 26
VEGFR1 homodimer 0.016 0.01 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.084 0.18 -9999 0 -0.65 29 29
GRB10 -0.046 0.23 -9999 0 -0.73 30 30
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
PAK1 -0.01 0.06 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.047 0.13 -9999 0 -0.52 26 26
HRAS 0.015 0.012 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.026 0.085 -9999 0 -10000 0 0
HIF1A 0.008 0.067 -9999 0 -0.72 4 4
FRS2 0.011 0.039 -9999 0 -0.72 1 1
oxygen and reactive oxygen species metabolic process -0.049 0.13 -9999 0 -0.54 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak -0.013 0.029 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.059 0.15 -9999 0 -0.58 27 27
mol:GDP -0.083 0.17 -9999 0 -0.63 29 29
mol:NADP 0.007 0.16 -9999 0 -0.45 29 29
eNOS/Hsp90 0.015 0.16 -9999 0 -0.42 29 29
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
mol:IP3 -0.044 0.22 -9999 0 -0.7 29 29
HIF1A/ARNT -0.005 0.048 -9999 0 -0.54 4 4
SHB 0.013 0.037 -9999 0 -0.72 1 1
VEGFA -0.018 0.068 -9999 0 -10000 0 0
VEGFC -0.002 0.12 -9999 0 -0.72 13 13
FAK1/Vinculin 0.027 0.14 -9999 0 -0.49 23 23
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.049 0.14 -9999 0 -0.54 25 25
PTPN6 0.015 0.014 -9999 0 -10000 0 0
EPAS1 -0.03 0.18 -9999 0 -0.76 31 31
mol:L-citrulline 0.007 0.16 -9999 0 -0.45 29 29
ITGAV 0.014 0.034 -9999 0 -0.72 1 1
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.049 0.14 -9999 0 -0.54 26 26
VEGFR2 homodimer/VEGFA homodimer -0.11 0.21 -9999 0 -0.75 30 30
VEGFR2/3 heterodimer -0.006 0.14 -9999 0 -0.52 31 31
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.04 0.22 -9999 0 -0.69 30 30
VEGFR2 homodimer -0.016 0.16 -9999 0 -0.61 31 31
FLT1 0.016 0.01 -9999 0 -10000 0 0
NEDD4 -0.004 0.079 -9999 0 -0.74 5 5
MAPK3 -0.032 0.2 -9999 0 -0.63 29 29
MAPK1 -0.032 0.2 -9999 0 -0.63 29 29
VEGFA145/NRP2 -0.005 0.041 -9999 0 -10000 0 0
VEGFR1/2 heterodimer -0.005 0.14 -9999 0 -0.52 31 31
KDR -0.016 0.16 -9999 0 -0.61 31 31
VEGFA165/NRP1/VEGFR2 homodimer -0.092 0.19 -9999 0 -0.69 29 29
SRC 0.016 0.007 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.031 0.21 -9999 0 -0.64 29 29
PI3K -0.098 0.19 -9999 0 -0.65 33 33
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.057 0.14 -9999 0 -0.58 25 25
FES -0.047 0.23 -9999 0 -0.71 31 31
GAB1 -0.066 0.15 -9999 0 -0.6 26 26
VEGFR2 homodimer/VEGFA homodimer/Src -0.057 0.14 -9999 0 -0.58 25 25
CTNNB1 0.01 0.065 -9999 0 -0.72 4 4
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.23 0.24 -9999 0 -0.52 149 149
VEGFR2 homodimer/VEGFA homodimer/Yes -0.058 0.14 -9999 0 -0.58 26 26
PI3K/GAB1 -0.015 0.22 -9999 0 -0.55 47 47
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.037 0.14 -9999 0 -0.54 23 23
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.046 0.13 -9999 0 -0.5 37 37
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
CDC42 -0.045 0.22 -9999 0 -0.71 29 29
actin cytoskeleton reorganization -0.05 0.15 -9999 0 -0.58 26 26
PTK2 0.019 0.15 -9999 0 -0.53 23 23
EDG1 -0.17 0.4 -9999 0 -0.79 149 149
mol:DAG -0.044 0.22 -9999 0 -0.7 29 29
CaM/Ca2+ -0.09 0.17 -9999 0 -0.64 29 29
MAP2K3 -0.033 0.21 -9999 0 -0.67 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.099 0.21 -9999 0 -0.76 30 30
PLCG1 -0.045 0.22 -9999 0 -0.71 29 29
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.05 0.14 -9999 0 -0.54 26 26
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.015 0.032 -9999 0 -0.72 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.057 0.14 -9999 0 -0.58 25 25
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.056 0.14 -9999 0 -0.57 26 26
cell migration 0.059 0.13 -9999 0 -0.4 23 23
mol:PI-3-4-5-P3 -0.025 0.22 -9999 0 -0.59 35 35
FYN 0.013 0.045 -9999 0 -0.72 2 2
VEGFB/NRP1 -0.095 0.18 -9999 0 -0.65 29 29
mol:NO 0.007 0.16 -9999 0 -0.45 29 29
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.084 0.15 -9999 0 -0.58 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.042 0.24 -9999 0 -0.75 30 30
VHL 0.012 0.027 -9999 0 -10000 0 0
ITGB3 0.014 0.02 -9999 0 -10000 0 0
NOS3 0.003 0.18 -9999 0 -0.51 29 29
VEGFR2 homodimer/VEGFA homodimer/Sck -0.08 0.18 -9999 0 -0.61 39 39
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.031 0.21 -9999 0 -0.65 29 29
PRKCB -0.041 0.21 -9999 0 -0.66 29 29
VCL 0.016 0.007 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.048 0.22 -9999 0 -0.69 30 30
VEGFR1/2 heterodimer/VEGFA homodimer -0.056 0.14 -9999 0 -0.58 25 25
VEGFA165/NRP2 -0.005 0.041 -9999 0 -10000 0 0
MAPKKK cascade -0.072 0.17 -9999 0 -0.61 30 30
NRP2 0.015 0.016 -9999 0 -10000 0 0
VEGFC homodimer -0.002 0.11 -9999 0 -0.72 13 13
NCK1 0.016 0 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.028 0.14 -9999 0 -0.49 23 23
MAP3K13 -0.045 0.22 -9999 0 -0.71 29 29
PDPK1 -0.011 0.2 -9999 0 -0.52 33 33
Regulation of Telomerase

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
Telomerase catalytic core complex -0.067 0.13 -10000 0 -0.61 13 13
RAD9A 0.016 0 -10000 0 -10000 0 0
AP1 -0.46 0.35 -10000 0 -0.65 375 375
IFNAR2 0.018 0.003 -10000 0 -10000 0 0
AKT1 -0.034 0.12 -10000 0 -0.25 118 118
ER alpha/Oestrogen -0.14 0.22 -10000 0 -0.55 117 117
NFX1/SIN3/HDAC complex 0.06 0.01 -10000 0 -10000 0 0
EGF -0.23 0.35 -10000 0 -0.72 178 178
SMG5 0.014 0.02 -10000 0 -10000 0 0
SMG6 0.016 0 -10000 0 -10000 0 0
SP3/HDAC2 0.023 0.015 -10000 0 -10000 0 0
TERT/c-Abl -0.063 0.11 -10000 0 -0.56 13 13
SAP18 0.017 0.001 -10000 0 -10000 0 0
MRN complex 0 0.004 -10000 0 -10000 0 0
WT1 -0.04 0.077 -10000 0 -10000 0 0
WRN 0.016 0.01 -10000 0 -10000 0 0
SP1 0.019 0.003 -10000 0 -10000 0 0
SP3 0.017 0.003 -10000 0 -10000 0 0
TERF2IP 0.016 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.052 0.091 -10000 0 -0.56 8 8
Mad/Max 0.022 0.011 -10000 0 -10000 0 0
TERT -0.07 0.13 -10000 0 -0.63 13 13
CCND1 -0.072 0.2 -10000 0 -1.2 13 13
MAX 0.017 0.003 -10000 0 -10000 0 0
RBBP7 0.012 0.026 -10000 0 -10000 0 0
RBBP4 0.016 0.007 -10000 0 -10000 0 0
TERF2 -0.001 0.029 -10000 0 -0.66 1 1
PTGES3 0.015 0.032 -10000 0 -0.72 1 1
SIN3A 0.017 0.001 -10000 0 -10000 0 0
Telomerase/911 0.037 0.025 -10000 0 -10000 0 0
CDKN1B 0.011 0.12 -10000 0 -0.76 10 10
RAD1 0.015 0.012 -10000 0 -10000 0 0
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
SAP30 0.016 0.007 -10000 0 -10000 0 0
TRF2/PARP2 -0.001 0.023 -10000 0 -0.53 1 1
UBE3A 0.017 0.003 -10000 0 -10000 0 0
JUN -0.12 0.29 -10000 0 -0.72 97 97
E6 0.001 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.006 -10000 0 -10000 0 0
FOS -0.51 0.34 -10000 0 -0.72 374 374
IFN-gamma/IRF1 0 0.073 -10000 0 -0.35 10 10
PARP2 0.016 0 -10000 0 -10000 0 0
BLM -0.033 0.074 -10000 0 -10000 0 0
Telomerase 0.008 0.026 -10000 0 -10000 0 0
IRF1 0.01 0.046 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.72 117 117
KU/TER 0 0 -10000 0 -10000 0 0
ATM/TRF2 -0.001 0.019 -10000 0 -0.43 1 1
ubiquitin-dependent protein catabolic process 0.067 0.01 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.067 0.01 -10000 0 -10000 0 0
HDAC1 0.017 0.001 -10000 0 -10000 0 0
HDAC2 0.017 0.018 -10000 0 -10000 0 0
ATM 0 0.011 0.25 1 -10000 0 1
SMAD3 0.026 0.026 -10000 0 -0.54 1 1
ABL1 0.016 0 -10000 0 -10000 0 0
MXD1 0.017 0.008 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
HUS1 0.015 0.012 -10000 0 -10000 0 0
RPS6KB1 0.013 0.024 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.056 0.12 -10000 0 -0.6 12 12
NR2F2 -0.007 0.12 -10000 0 -0.72 14 14
MAPK3 0.03 0.026 -10000 0 -0.54 1 1
MAPK1 0.03 0.026 -10000 0 -0.54 1 1
TGFB1/TGF beta receptor Type II 0.015 0.01 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
HNRNPC 0.016 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0.011 0.25 1 -10000 0 1
NBN 0.016 0.007 -10000 0 -10000 0 0
EGFR -0.37 0.37 -10000 0 -0.72 277 277
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.45 0.33 -10000 0 -0.64 372 372
MYC -0.023 0.17 -10000 0 -0.72 29 29
IL2 0.018 0.033 -10000 0 -0.72 1 1
KU 0 0 -10000 0 -10000 0 0
RAD50 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
TGFB1 0.015 0.01 -10000 0 -10000 0 0
TRF2/BLM 0.022 0.042 -10000 0 -0.53 1 1
FRAP1 0.016 0 -10000 0 -10000 0 0
KU/TERT -0.056 0.11 -10000 0 -0.6 9 9
SP1/HDAC2 0.026 0.016 -10000 0 -10000 0 0
PINX1 0.016 0 -10000 0 -10000 0 0
Telomerase/EST1A -0.052 0.091 -10000 0 -0.56 8 8
Smad3/Myc 0.004 0.11 -10000 0 -0.46 30 30
911 complex 0 0.009 -10000 0 -10000 0 0
IFNG -0.016 0.074 -10000 0 -0.71 1 1
Telomerase/PinX1 -0.052 0.091 -10000 0 -0.56 8 8
Telomerase/AKT1/mTOR/p70S6K 0.015 0.062 -10000 0 -0.48 2 2
SIN3B 0.015 0.016 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
Telomerase/EST1B -0.053 0.092 -10000 0 -0.55 9 9
response to DNA damage stimulus 0.004 0.003 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.001 0.018 -10000 0 -0.4 1 1
TRF2/WRN -0.001 0.024 -10000 0 -0.53 1 1
Telomerase/hnRNP C1/C2 -0.052 0.091 -10000 0 -0.56 8 8
E2F1 -0.004 0.056 -10000 0 -10000 0 0
ZNFX1 0.014 0.022 -10000 0 -10000 0 0
PIF1 0.01 0.032 -10000 0 -10000 0 0
NCL 0.016 0 -10000 0 -10000 0 0
DKC1 0.015 0.014 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
E-cadherin signaling events

Figure 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
E-cadherin/beta catenin-gamma catenin -0.032 0.12 -9999 0 -0.46 38 38
E-cadherin/beta catenin -0.039 0.14 -9999 0 -0.54 37 37
CTNNB1 0.01 0.065 -9999 0 -0.72 4 4
JUP 0.014 0.035 -9999 0 -0.72 1 1
CDH1 -0.032 0.18 -9999 0 -0.72 33 33
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.032 0.16 -9999 0 -0.54 2 2
PCK1 -0.84 0.6 -9999 0 -1.2 400 400
HNF4A 0.042 0.16 -9999 0 -10000 0 0
KCNJ11 0.034 0.18 -9999 0 -0.6 2 2
AKT1 0.014 0.11 -9999 0 -0.33 3 3
response to starvation 0.008 0.002 -9999 0 -10000 0 0
DLK1 0.034 0.18 -9999 0 -0.6 2 2
NKX2-1 0.075 0.11 -9999 0 -10000 0 0
ACADM 0.024 0.2 -9999 0 -0.98 7 7
TAT -0.023 0.2 -9999 0 -0.81 10 10
CEBPB 0.021 0.033 -9999 0 -0.72 1 1
CEBPA 0.02 0.056 -9999 0 -0.72 3 3
TTR -0.035 0.24 -9999 0 -0.59 62 62
PKLR 0.032 0.16 -9999 0 -0.54 2 2
APOA1 0.041 0.19 -9999 0 -10000 0 0
CPT1C 0.032 0.16 -9999 0 -0.54 2 2
ALAS1 0.034 0.12 -9999 0 -10000 0 0
TFRC -0.004 0.19 -9999 0 -10000 0 0
FOXF1 -0.002 0.018 -9999 0 -10000 0 0
NF1 0.026 0 -9999 0 -10000 0 0
HNF1A (dimer) 0.041 0.016 -9999 0 -10000 0 0
CPT1A 0.033 0.16 -9999 0 -0.54 2 2
HMGCS1 0.032 0.16 -9999 0 -0.54 2 2
NR3C1 -0.031 0.21 -9999 0 -0.71 46 46
CPT1B 0.032 0.16 -9999 0 -0.54 2 2
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.025 0.008 -9999 0 -10000 0 0
GCK 0.032 0.16 -9999 0 -10000 0 0
CREB1 -0.16 0.11 -9999 0 -0.24 114 114
IGFBP1 0.008 0.15 -9999 0 -0.94 2 2
PDX1 0.043 0.14 -9999 0 -1.5 1 1
UCP2 0.033 0.16 -9999 0 -0.54 2 2
ALDOB 0.033 0.18 -9999 0 -0.6 2 2
AFP -0.095 0.15 -9999 0 -0.43 71 71
BDH1 0.032 0.16 -9999 0 -0.55 1 1
HADH 0.029 0.2 -9999 0 -1.1 3 3
F2 0.041 0.19 -9999 0 -10000 0 0
HNF1A 0.041 0.016 -9999 0 -10000 0 0
G6PC -0.083 0.11 -9999 0 -0.53 3 3
SLC2A2 0.04 0.15 -9999 0 -1.3 1 1
INS 0 0.009 -9999 0 -10000 0 0
FOXA1 -0.12 0.26 -9999 0 -0.71 80 80
FOXA3 -0.13 0.13 -9999 0 -0.38 39 39
FOXA2 0.038 0.23 -9999 0 -0.65 3 3
ABCC8 -0.1 0.43 -9999 0 -1 91 91
ALB -0.098 0.16 -9999 0 -0.5 29 29
Canonical Wnt signaling pathway

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
HDAC1 0.011 0.028 -10000 0 -10000 0 0
AES 0.01 0.023 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.001 0.024 -10000 0 -0.54 1 1
SMAD4 0.013 0.045 -10000 0 -0.72 2 2
DKK2 0.007 0.074 -10000 0 -0.72 5 5
TLE1 -0.016 0.14 -10000 0 -0.72 18 18
MACF1 0.017 0 -10000 0 -10000 0 0
CTNNB1 0.16 0.077 0.3 2 -10000 0 2
WIF1 -0.53 0.32 -10000 0 -0.72 392 392
beta catenin/RanBP3 0.04 0.13 0.46 46 -10000 0 46
KREMEN2 -0.076 0.08 -10000 0 -10000 0 0
DKK1 -0.075 0.21 -10000 0 -0.72 46 46
beta catenin/beta TrCP1 0.16 0.072 -10000 0 -10000 0 0
FZD1 0.016 0.032 -10000 0 -0.72 1 1
AXIN2 -0.018 0.21 -10000 0 -1.4 11 11
AXIN1 0.017 0.01 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.019 0.042 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.13 0.1 0.33 3 -0.52 3 6
Axin1/APC/GSK3 0.002 0.014 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.11 0.033 -10000 0 -10000 0 0
HNF1A 0.01 0.028 0.27 1 -10000 0 1
CTBP1 0.01 0.026 -10000 0 -10000 0 0
MYC -0.068 0.36 -10000 0 -1.5 29 29
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.04 0.068 -10000 0 -0.5 5 5
NKD1 0.013 0.019 -10000 0 -10000 0 0
TCF4 0 0.086 -10000 0 -0.71 7 7
TCF3 0.009 0.03 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.02 -10000 0 -0.4 1 1
Ran/GTP 0.002 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.032 0.15 0.47 44 -0.41 1 45
LEF1 -0.015 0.068 -10000 0 -10000 0 0
DVL1 0.11 0.062 -10000 0 -10000 0 0
CSNK2A1 0.017 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.12 0.11 -10000 0 -0.46 3 3
DKK1/LRP6/Kremen 2 -0.025 0.16 -10000 0 -0.5 46 46
LRP6 0.016 0.012 -10000 0 -10000 0 0
CSNK1A1 0.011 0.028 -10000 0 -10000 0 0
NLK 0.005 0.041 -10000 0 -10000 0 0
CCND1 -0.033 0.24 -10000 0 -1.6 12 12
WNT1 0.017 0.002 -10000 0 -10000 0 0
GSK3A 0.018 0.001 -10000 0 -10000 0 0
GSK3B 0.015 0.01 -10000 0 -10000 0 0
FRAT1 0.015 0.01 -10000 0 -10000 0 0
PPP2R5D 0.065 0.029 -10000 0 -10000 0 0
APC 0.054 0.02 -10000 0 -0.37 1 1
WNT1/LRP6/FZD1 0.2 0.12 0.27 391 -10000 0 391
CREBBP 0.009 0.041 -10000 0 -0.73 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.03 0 -9999 0 -10000 0 0
SMARCC1 0.011 0.026 -9999 0 -0.46 1 1
REL 0.011 0.027 -9999 0 -10000 0 0
HDAC7 -0.003 0.14 -9999 0 -0.58 8 8
JUN -0.12 0.29 -9999 0 -0.72 97 97
EP300 0.016 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0.088 -9999 0 -0.55 12 12
FOXO1 -0.085 0.25 -9999 0 -0.72 72 72
T-DHT/AR 0.002 0.15 -9999 0 -0.61 8 8
MAP2K6 -0.003 0.11 -9999 0 -0.73 12 12
BRM/BAF57 0 0.005 -9999 0 -10000 0 0
MAP2K4 0.005 0.085 -9999 0 -0.72 7 7
SMARCA2 0.017 0 -9999 0 -10000 0 0
PDE9A -0.093 0.28 -9999 0 -1.2 30 30
NCOA2 0.016 0.014 -9999 0 -10000 0 0
CEBPA 0.012 0.056 -9999 0 -0.72 3 3
EHMT2 0.017 0 -9999 0 -10000 0 0
cell proliferation 0.061 0.14 -9999 0 -0.45 6 6
NR0B1 -0.17 0.31 -9999 0 -0.72 124 124
EGR1 -0.6 0.28 -9999 0 -0.72 436 436
RXRs/9cRA -0.004 0.041 -9999 0 -0.42 5 5
AR/RACK1/Src 0.032 0.1 -9999 0 -0.39 19 19
AR/GR -0.043 0.17 -9999 0 -0.42 64 64
GNB2L1 0.017 0 -9999 0 -10000 0 0
PKN1 0.016 0.012 -9999 0 -10000 0 0
RCHY1 0.011 0.064 -9999 0 -0.72 4 4
epidermal growth factor receptor activity 0.001 0 -9999 0 -10000 0 0
MAPK8 0.018 0.072 -9999 0 -0.54 8 8
T-DHT/AR/TIF2/CARM1 0.029 0.1 -9999 0 -0.47 9 9
SRC 0.032 0.093 -9999 0 -0.41 19 19
NR3C1 -0.048 0.21 -9999 0 -0.72 46 46
KLK3 -0.068 0.09 -9999 0 -10000 0 0
APPBP2 0.012 0.016 -9999 0 -10000 0 0
TRIM24 0.016 0.014 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.034 0.087 -9999 0 -0.44 19 19
TMPRSS2 -0.28 0.5 -9999 0 -1.2 126 126
RXRG 0.009 0.072 -9999 0 -0.72 5 5
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.016 0 -9999 0 -10000 0 0
RXRB 0.016 0 -9999 0 -10000 0 0
CARM1 0.015 0.017 -9999 0 -10000 0 0
NR2C2 0.014 0.019 -9999 0 -10000 0 0
KLK2 0.05 0.088 -9999 0 -0.53 1 1
AR -0.011 0.13 -9999 0 -0.28 88 88
SENP1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
MDM2 0.01 0.025 -9999 0 -10000 0 0
SRY 0.006 0.073 -9999 0 -0.72 5 5
GATA2 0.007 0.037 -9999 0 -10000 0 0
MYST2 0.012 0.037 -9999 0 -0.72 1 1
HOXB13 -0.04 0.077 -9999 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.027 0.1 -9999 0 -0.4 19 19
positive regulation of transcription 0.007 0.037 -9999 0 -10000 0 0
DNAJA1 0.013 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.034 -9999 0 -0.36 4 4
NCOA1 0.022 0.034 -9999 0 -0.75 1 1
SPDEF -0.06 0.22 -9999 0 -0.72 54 54
T-DHT/AR/TIF2 0.038 0.066 -9999 0 -0.38 1 1
T-DHT/AR/Hsp90 0.013 0.1 -9999 0 -0.43 19 19
GSK3B 0.015 0.011 -9999 0 -10000 0 0
NR2C1 0.014 0.032 -9999 0 -0.72 1 1
mol:T-DHT 0.02 0.1 -9999 0 -0.45 19 19
SIRT1 0.016 0.007 -9999 0 -10000 0 0
ZMIZ2 0.015 0 -9999 0 -10000 0 0
POU2F1 0.024 0.024 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.086 0.21 -9999 0 -0.42 136 136
CREBBP 0.015 0.032 -9999 0 -0.72 1 1
SMARCE1 0.017 0.01 -9999 0 -10000 0 0
Aurora B signaling

Figure 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
Condensin I complex 0.024 0.024 -9999 0 -10000 0 0
STMN1 -0.008 0.068 -9999 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.018 0.077 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.18 0.13 -9999 0 -0.26 384 384
BIRC5 -0.087 0.078 -9999 0 -10000 0 0
DES 0.006 0.1 -9999 0 -0.61 13 13
Aurora C/Aurora B/INCENP 0.028 0.036 -9999 0 -10000 0 0
Aurora B/TACC1 -0.011 0.12 -9999 0 -0.49 31 31
Aurora B/PP2A 0.022 0.031 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.017 0.011 -9999 0 -0.19 1 1
mitotic metaphase/anaphase transition -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.053 0.078 -9999 0 -10000 0 0
Cul3 protein complex -0.34 0.22 -9999 0 -0.47 384 384
KIF2C 0.017 0.012 -9999 0 -10000 0 0
PEBP1 0.013 0.033 -9999 0 -0.74 1 1
KIF20A -0.091 0.077 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.023 0.03 -9999 0 -10000 0 0
SEPT1 0.013 0.023 -9999 0 -10000 0 0
SMC2 0.009 0.034 -9999 0 -10000 0 0
SMC4 -0.002 0.051 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.036 0.012 -9999 0 -10000 0 0
PSMA3 0.016 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.001 -9999 0 -10000 0 0
H3F3B 0.014 0.024 -9999 0 -0.41 1 1
AURKB -0.015 0.064 -9999 0 -10000 0 0
AURKC 0.013 0.022 -9999 0 -10000 0 0
CDCA8 -0.064 0.081 -9999 0 -10000 0 0
cytokinesis -0.009 0.03 -9999 0 -10000 0 0
Aurora B/Septin1 0.009 0.035 -9999 0 -10000 0 0
AURKA -0.05 0.08 -9999 0 -10000 0 0
INCENP 0 0.046 -9999 0 -10000 0 0
KLHL13 -0.52 0.33 -9999 0 -0.72 382 382
BUB1 -0.12 0.059 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.009 0.098 -9999 0 -10000 0 0
EVI5 0.015 0.032 -9999 0 -0.73 1 1
RhoA/GTP 0.018 0.069 -9999 0 -10000 0 0
SGOL1 -0.029 0.073 -9999 0 -10000 0 0
CENPA 0.012 0.019 -9999 0 -10000 0 0
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.023 0.029 -9999 0 -10000 0 0
NCAPD2 0.009 0.034 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.023 0.029 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.036 0.076 -9999 0 -10000 0 0
NPM1 0.017 0.009 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
KLHL9 0.004 0.096 -9999 0 -0.72 9 9
mitotic prometaphase -0.002 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.029 -9999 0 -10000 0 0
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.003 0.079 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.017 0.009 -9999 0 -10000 0 0
MYLK -0.11 0.19 -9999 0 -0.41 151 151
KIF23 -0.081 0.08 -9999 0 -10000 0 0
VIM -0.044 0.17 -9999 0 -0.56 49 49
RACGAP1 -0.029 0.074 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.017 0.009 -9999 0 -10000 0 0
Chromosomal passenger complex 0.004 0.031 -9999 0 -0.23 1 1
Chromosomal passenger complex/EVI5 0.077 0.091 -9999 0 -0.59 1 1
TACC1 -0.028 0.17 -9999 0 -0.72 31 31
PPP2R5D 0.015 0.012 -9999 0 -10000 0 0
CUL3 0.012 0.056 -9999 0 -0.72 3 3
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.012 0.074 -10000 0 -0.3 5 5
TBX21 -0.095 0.39 -10000 0 -1.3 39 39
B2M 0.016 0.033 -10000 0 -0.72 1 1
TYK2 0.009 0.017 -10000 0 -10000 0 0
IL12RB1 0.009 0.017 -10000 0 -10000 0 0
GADD45B -0.036 0.25 -10000 0 -0.78 34 34
IL12RB2 -0.018 0.076 -10000 0 -0.72 2 2
GADD45G -0.03 0.22 -10000 0 -0.7 32 32
natural killer cell activation -0.004 0.019 -10000 0 -10000 0 0
RELB 0.013 0.024 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.007 0.055 -10000 0 -0.73 1 1
IL2RA 0.006 0.039 -10000 0 -10000 0 0
IFNG -0.021 0.074 -10000 0 -0.72 1 1
STAT3 (dimer) -0.019 0.21 -10000 0 -0.55 36 36
HLA-DRB5 0.005 0.008 -10000 0 -10000 0 0
FASLG -0.045 0.24 -10000 0 -0.81 19 19
NF kappa B2 p52/RelB -0.09 0.19 -10000 0 -0.52 73 73
CD4 0.005 0.008 -10000 0 -10000 0 0
SOCS1 0.015 0.012 -10000 0 -10000 0 0
EntrezGene:6955 -0.017 0.014 -10000 0 -10000 0 0
CD3D -0.002 0.037 -10000 0 -10000 0 0
CD3E 0.005 0.011 -10000 0 -10000 0 0
CD3G -0.022 0.11 -10000 0 -0.73 10 10
IL12Rbeta2/JAK2 -0.002 0.065 -10000 0 -0.55 3 3
CCL3 -0.042 0.24 -10000 0 -0.78 19 19
CCL4 -0.042 0.24 -10000 0 -0.78 19 19
HLA-A 0.014 0.025 -10000 0 -10000 0 0
IL18/IL18R 0.027 0.16 -10000 0 -0.49 45 45
NOS2 -0.045 0.24 -10000 0 -0.53 76 76
IL12/IL12R/TYK2/JAK2/SPHK2 0.012 0.074 -10000 0 -0.28 7 7
IL1R1 -0.14 0.46 -10000 0 -1.2 69 69
IL4 0.022 0.017 -10000 0 -10000 0 0
JAK2 0.008 0.037 -10000 0 -0.74 1 1
EntrezGene:6957 -0.015 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.076 -10000 0 -0.44 7 7
RAB7A 0.009 0.21 -10000 0 -0.6 33 33
lysosomal transport 0.011 0.2 -10000 0 -0.57 33 33
FOS -0.88 0.64 -10000 0 -1.3 374 374
STAT4 (dimer) -0.006 0.24 -10000 0 -0.67 39 39
STAT5A (dimer) -0.089 0.21 0.24 6 -0.54 75 81
GZMA -0.051 0.23 -10000 0 -0.54 74 74
GZMB -0.046 0.24 -10000 0 -0.82 20 20
HLX 0.013 0.045 -10000 0 -0.72 2 2
LCK -0.053 0.25 -10000 0 -0.57 73 73
TCR/CD3/MHC II/CD4 -0.12 0.13 -10000 0 -0.44 26 26
IL2/IL2R 0.007 0.039 -10000 0 -0.33 2 2
MAPK14 -0.008 0.24 -10000 0 -0.71 35 35
CCR5 -0.033 0.22 -10000 0 -0.71 32 32
IL1B -0.001 0.083 -10000 0 -0.74 6 6
STAT6 -0.028 0.16 -10000 0 -0.45 39 39
STAT4 0.005 0.086 -10000 0 -0.72 7 7
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 -0.011 0.061 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
NFKB2 0.015 0.012 -10000 0 -10000 0 0
IL12B 0.007 0.029 -10000 0 -10000 0 0
CD8A 0.002 0.002 -10000 0 -10000 0 0
CD8B 0.014 0.027 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.012 0.073 0.29 5 -10000 0 5
IL2RB 0.013 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.23 -10000 0 -0.62 39 39
IL2RG 0.006 0.039 -10000 0 -10000 0 0
IL12 0 0.087 -10000 0 -0.55 11 11
STAT5A 0.013 0.045 -10000 0 -0.72 2 2
CD247 -0.041 0.16 -10000 0 -0.73 25 25
IL2 0.015 0.033 -10000 0 -0.72 1 1
SPHK2 0.016 0 -10000 0 -10000 0 0
FRAP1 0.016 0 -10000 0 -10000 0 0
IL12A -0.008 0.11 -10000 0 -0.73 11 11
IL12/IL12R/TYK2/JAK2 -0.053 0.26 -10000 0 -0.6 74 74
MAP2K3 -0.013 0.24 -10000 0 -0.72 35 35
RIPK2 0.014 0.02 -10000 0 -10000 0 0
MAP2K6 -0.017 0.24 -10000 0 -0.69 39 39
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.033 -10000 0 -0.74 1 1
IL18RAP -0.043 0.21 -10000 0 -0.73 45 45
IL12Rbeta1/TYK2 0.011 0.025 -10000 0 -10000 0 0
EOMES 0.016 0.031 -10000 0 -10000 0 0
STAT1 (dimer) -0.011 0.21 -10000 0 -0.55 36 36
T cell proliferation -0.004 0.2 -10000 0 -0.55 38 38
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.036 -10000 0 -0.73 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.07 0.18 -10000 0 -0.64 38 38
ATF2 0.003 0.23 -10000 0 -0.66 34 34
Osteopontin-mediated 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
IKK alpha homodimer 0.039 0.052 -9999 0 -0.36 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.016 0.036 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin/Src 0.033 0.066 -9999 0 -0.52 4 4
AP1 -0.29 0.25 -9999 0 -0.69 103 103
ILK 0.031 0.051 -9999 0 -0.38 4 4
bone resorption 0.062 0.049 -9999 0 -0.36 1 1
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.047 0.065 -9999 0 -10000 0 0
ITGAV 0.02 0.033 -9999 0 -0.71 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.003 0.034 -9999 0 -0.54 2 2
alphaV/beta3 Integrin/Osteopontin 0.041 0.065 -9999 0 -0.43 4 4
MAP3K1 0.028 0.066 -9999 0 -0.41 8 8
JUN -0.12 0.29 -9999 0 -0.72 97 97
MAPK3 0.044 0.052 -9999 0 -0.34 4 4
MAPK1 0.044 0.052 -9999 0 -0.34 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.034 0.065 -9999 0 -0.37 9 9
ITGB3 0.019 0.019 -9999 0 -10000 0 0
NFKBIA 0.056 0.052 -9999 0 -10000 0 0
FOS -0.51 0.34 -9999 0 -0.72 374 374
CD44 0.014 0.034 -9999 0 -0.72 1 1
CHUK 0.015 0.032 -9999 0 -0.72 1 1
PLAU 0.033 0.058 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.018 0.04 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.001 0.026 -9999 0 -0.52 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.027 0.055 -9999 0 -0.38 4 4
VAV3 0.013 0.1 -9999 0 -0.4 25 25
MAP3K14 0.035 0.051 -9999 0 -0.38 4 4
ROCK2 0.015 0.033 -9999 0 -0.72 1 1
SPP1 -0.049 0.092 -9999 0 -0.71 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.011 0.081 -9999 0 -0.36 23 23
MMP2 -0.22 0.22 -9999 0 -0.54 104 104
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.002 0.048 -10000 0 -10000 0 0
GNB1/GNG2 -0.017 0.051 -10000 0 -0.17 52 52
AKT1 0.072 0.088 -10000 0 -0.2 15 15
EGF -0.24 0.35 -10000 0 -0.72 178 178
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.06 0.036 -10000 0 -10000 0 0
mol:Ca2+ 0.075 0.12 -10000 0 -0.28 52 52
LYN 0.06 0.036 -10000 0 -0.27 1 1
RhoA/GTP -0.011 0.035 -10000 0 -0.13 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.08 0.14 -10000 0 -0.32 52 52
GNG2 0.015 0.032 -10000 0 -0.72 1 1
ARRB2 0.016 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.041 0.037 -10000 0 -0.45 2 2
G beta5/gamma2 -0.022 0.066 -10000 0 -0.22 52 52
PRKCH 0.073 0.14 -10000 0 -0.34 52 52
DNM1 0.016 0.007 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 -0.001 0.005 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.006 0.081 -10000 0 -0.72 6 6
G12 family/GTP -0.027 0.086 -10000 0 -0.28 52 52
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.014 0.045 -10000 0 -0.72 2 2
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.064 0.079 0.35 5 -10000 0 5
mol:NADP 0.016 0 -10000 0 -10000 0 0
RAB11A 0.016 0.01 -10000 0 -10000 0 0
PRKG1 0.016 0 -10000 0 -10000 0 0
mol:IP3 0.077 0.14 -10000 0 -0.35 52 52
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.076 0.18 -10000 0 -0.47 52 52
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.063 0.038 -10000 0 -0.27 1 1
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.061 0.036 -10000 0 -0.27 1 1
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.016 0 -10000 0 -10000 0 0
PRKCB1 0.074 0.14 -10000 0 -0.35 52 52
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.076 0.19 -10000 0 -0.5 52 52
LCK 0.064 0.038 -10000 0 -0.27 1 1
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.002 0.028 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.04 0.014 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.002 0.028 -10000 0 -10000 0 0
MAPK14 0.076 0.098 -10000 0 -0.22 16 16
TGM2/GTP 0.082 0.16 -10000 0 -0.38 52 52
MAPK11 0.076 0.098 -10000 0 -0.21 52 52
ARHGEF1 0.061 0.076 -10000 0 -0.18 7 7
GNAI2 0.016 0.007 -10000 0 -10000 0 0
JNK cascade 0.078 0.15 -10000 0 -0.37 52 52
RAB11/GDP 0.014 0.01 -10000 0 -10000 0 0
ICAM1 0.071 0.12 -10000 0 -0.28 52 52
cAMP biosynthetic process 0.074 0.13 -10000 0 -0.32 52 52
Gq family/GTP/EBP50 0.021 0.027 -10000 0 -0.22 6 6
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.06 0.036 -10000 0 -0.27 1 1
GNB5 0.015 0.032 -10000 0 -0.72 1 1
GNB1 0.016 0.01 -10000 0 -10000 0 0
EGF/EGFR -0.038 0.096 -10000 0 -0.3 8 8
VCAM1 0.068 0.13 -10000 0 -0.31 52 52
TP beta/Gq family/GDP/G beta5/gamma2 0.041 0.037 -10000 0 -0.45 2 2
platelet activation 0.098 0.13 -10000 0 -0.28 52 52
PGI2/IP 0 0.001 -10000 0 -10000 0 0
PRKACA 0.024 0.039 -10000 0 -0.34 6 6
Gq family/GDP/G beta5/gamma2 0.039 0.037 -10000 0 -0.43 2 2
TXA2/TP beta/beta Arrestin2 0 0.003 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.034 0.037 -10000 0 -0.31 6 6
mol:DAG 0.075 0.16 -10000 0 -0.4 52 52
EGFR -0.38 0.37 -10000 0 -0.72 277 277
TXA2/TP alpha 0.084 0.17 -10000 0 -0.43 52 52
Gq family/GTP -0.003 0.03 -10000 0 -0.28 6 6
YES1 0.06 0.043 -10000 0 -0.4 2 2
GNAI2/GTP -0.004 0.032 -10000 0 -0.3 3 3
PGD2/DP -0.008 0.059 -10000 0 -0.55 6 6
SLC9A3R1 -0.022 0.069 -10000 0 -10000 0 0
FYN 0.059 0.043 -10000 0 -0.3 3 3
mol:NO 0.016 0 -10000 0 -10000 0 0
GNA15 0.014 0.02 -10000 0 -10000 0 0
PGK/cGMP 0 0 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.007 0.043 -10000 0 -0.33 1 1
NOS3 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.075 0.14 -10000 0 -0.33 52 52
PRKCB 0.068 0.14 -10000 0 -0.34 52 52
PRKCE 0.076 0.14 -10000 0 -0.34 52 52
PRKCD 0.073 0.15 -10000 0 -0.37 52 52
PRKCG 0.074 0.15 -10000 0 -0.36 52 52
muscle contraction 0.081 0.18 -10000 0 -0.46 52 52
PRKCZ 0.074 0.14 -10000 0 -0.33 52 52
ARR3 0.016 0 -10000 0 -10000 0 0
TXA2/TP beta -0.004 0.035 -10000 0 -0.34 2 2
PRKCQ 0.073 0.14 -10000 0 -0.34 52 52
MAPKKK cascade 0.076 0.16 -10000 0 -0.41 52 52
SELE 0.058 0.16 -10000 0 -0.4 52 52
TP beta/GNAI2/GDP/G beta/gamma -0.003 0.032 -10000 0 -0.33 1 1
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 -0.008 0.09 -10000 0 -0.72 6 6
chemotaxis 0.071 0.23 -10000 0 -0.6 52 52
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.015 0.014 -10000 0 -10000 0 0
GNA11 0.016 0 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.006 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.003 0.1 -9999 0 -0.72 10 10
SVIL 0.001 0.11 -9999 0 -0.72 12 12
ZNF318 0.007 0.006 -9999 0 -10000 0 0
JMJD2C 0.026 0.001 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.061 0.17 -9999 0 -0.48 69 69
CARM1 0.015 0.017 -9999 0 -10000 0 0
PRDX1 0.014 0.016 -9999 0 -10000 0 0
PELP1 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.012 0.065 -9999 0 -0.72 4 4
AKT1 0.013 0.02 -9999 0 -10000 0 0
PTK2B 0.017 0 -9999 0 -10000 0 0
MED1 0.005 0.039 -9999 0 -10000 0 0
MAK -0.001 0.034 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.018 0.007 -9999 0 -10000 0 0
GSN -0.18 0.33 -9999 0 -0.72 143 143
NCOA2 0.015 0.014 -9999 0 -10000 0 0
NCOA6 0.018 0.007 -9999 0 -10000 0 0
DNA-PK 0.003 0.014 -9999 0 -10000 0 0
NCOA4 0.014 0.045 -9999 0 -0.72 2 2
PIAS3 0.018 0 -9999 0 -10000 0 0
cell proliferation -0.02 0.033 -9999 0 -10000 0 0
XRCC5 0.015 0 -9999 0 -10000 0 0
UBE3A 0.019 0.001 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.072 0.17 -9999 0 -0.42 88 88
FHL2 -0.15 0.36 -9999 0 -1.1 58 58
RANBP9 0.018 0.007 -9999 0 -10000 0 0
JMJD1A -0.008 0.062 -9999 0 -10000 0 0
CDK6 0.005 0.086 -9999 0 -0.72 7 7
TGFB1I1 0.014 0.056 -9999 0 -0.72 3 3
T-DHT/AR/CyclinD1 -0.07 0.2 -9999 0 -0.5 81 81
XRCC6 0.015 0 -9999 0 -10000 0 0
T-DHT/AR -0.076 0.2 -9999 0 -0.46 88 88
CTDSP1 0.017 0 -9999 0 -10000 0 0
CTDSP2 0.013 0.001 -9999 0 -10000 0 0
BRCA1 0.014 0.025 -9999 0 -10000 0 0
TCF4 0.004 0.085 -9999 0 -0.72 7 7
CDKN2A -0.013 0.061 -9999 0 -10000 0 0
SRF 0.01 0.043 -9999 0 -10000 0 0
NKX3-1 -0.08 0.11 -9999 0 -0.25 133 133
KLK3 0.013 0.038 -9999 0 -10000 0 0
TMF1 0.017 0 -9999 0 -10000 0 0
HNRNPA1 0.015 0 -9999 0 -10000 0 0
AOF2 0.018 0.007 -9999 0 -10000 0 0
APPL1 0.025 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.084 0.16 -9999 0 -0.48 69 69
AR -0.096 0.25 -9999 0 -0.73 69 69
UBA3 0.001 0 -9999 0 -10000 0 0
PATZ1 0.014 0.007 -9999 0 -10000 0 0
PAWR 0.013 0.037 -9999 0 -0.72 1 1
PRKDC 0.009 0.03 -9999 0 -10000 0 0
PA2G4 0.014 0.007 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.056 0.16 -9999 0 -0.45 69 69
RPS6KA3 0.015 0.046 -9999 0 -0.72 2 2
T-DHT/AR/ARA70 -0.062 0.18 -9999 0 -0.48 71 71
LATS2 0.001 0.1 -9999 0 -0.72 10 10
T-DHT/AR/PRX1 -0.077 0.15 -9999 0 -0.45 69 69
Cyclin D3/CDK11 p58 0 0.004 -9999 0 -10000 0 0
VAV3 -0.031 0.15 -9999 0 -0.72 21 21
KLK2 0.001 0.076 -9999 0 -10000 0 0
CASP8 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.043 0.16 -9999 0 -0.44 69 69
TMPRSS2 -0.25 0.49 -9999 0 -1.1 126 126
CCND1 -0.027 0.12 -9999 0 -0.72 12 12
PIAS1 0.019 0.007 -9999 0 -10000 0 0
mol:T-DHT -0.018 0.041 -9999 0 -0.081 146 146
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.019 0.016 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.09 0.17 -9999 0 -0.49 76 76
CMTM2 0.016 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.001 0.037 -9999 0 -10000 0 0
CCND3 0.016 0.007 -9999 0 -10000 0 0
TGIF1 0.013 0.032 -9999 0 -0.72 1 1
FKBP4 0.012 0.031 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.002 0.11 -9999 0 -0.72 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.006 0.085 -9999 0 -0.72 7 7
RAC1-CDC42/GTP/PAK family -0.14 0.14 -9999 0 -0.25 321 321
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.015 0.032 -9999 0 -0.72 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.013 0.045 -9999 0 -0.72 2 2
MAP3K12 0.016 0 -9999 0 -10000 0 0
FGR 0.016 0 -9999 0 -10000 0 0
p38 alpha/TAB1 0.02 0.04 -9999 0 -0.35 1 1
PRKG1 0.016 0 -9999 0 -10000 0 0
DUSP8 0.016 0.007 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.005 0.028 -9999 0 -0.34 1 1
apoptosis -0.005 0.028 -9999 0 -0.34 1 1
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.016 0.01 -9999 0 -10000 0 0
DUSP1 -0.3 0.36 -9999 0 -0.72 225 225
PAK1 -0.01 0.06 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.004 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.036 0.06 -9999 0 -0.28 12 12
BLK 0.002 0.045 -9999 0 -10000 0 0
HCK 0.013 0.024 -9999 0 -10000 0 0
MAP2K3 0.016 0.007 -9999 0 -10000 0 0
DUSP16 0.014 0.034 -9999 0 -0.72 1 1
DUSP10 0.013 0.037 -9999 0 -0.72 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.045 0.047 -9999 0 -0.38 1 1
positive regulation of innate immune response 0.044 0.066 -9999 0 -0.34 2 2
LCK 0 0.049 -9999 0 -10000 0 0
p38alpha-beta/MKP7 0.051 0.066 -9999 0 -0.34 2 2
p38alpha-beta/MKP5 0.051 0.066 -9999 0 -0.34 2 2
PGK/cGMP 0 0 -9999 0 -10000 0 0
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.1 0.19 -9999 0 -0.34 150 150
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.43 0.36 -9999 0 -0.72 321 321
S1P3 pathway

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
PDGFRB 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.15 0.22 -9999 0 -0.39 195 195
GNAO1 0.018 0.001 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.025 0.005 -9999 0 -10000 0 0
AKT1 -0.022 0.042 -9999 0 -10000 0 0
AKT3 0.005 0.08 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
GNAI2 0.018 0.007 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 -0.25 0.36 -9999 0 -0.72 189 189
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.002 0.001 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.19 0.33 -9999 0 -0.72 147 147
mol:Ca2+ -0.054 0.14 -9999 0 -0.28 19 19
MAPK3 -0.041 0.13 -9999 0 -0.62 2 2
MAPK1 -0.041 0.13 -9999 0 -0.62 2 2
JAK2 -0.038 0.13 -9999 0 -0.52 3 3
CXCR4 -0.046 0.13 -9999 0 -0.33 12 12
FLT1 0.019 0.01 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC -0.041 0.13 -9999 0 -0.62 2 2
S1P/S1P3/Gi -0.054 0.14 -9999 0 -0.28 19 19
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.075 0.1 -9999 0 -0.6 2 2
VEGFA -0.001 0.054 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.059 0.14 -9999 0 -0.24 193 193
VEGFR1 homodimer/VEGFA homodimer 0.041 0.02 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.021 0.036 -9999 0 -0.31 6 6
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0.078 -9999 0 -0.72 6 6
G12/G13 -0.001 0.007 -9999 0 -10000 0 0
GNA14 -0.008 0.09 -9999 0 -0.72 6 6
GNA15 0.014 0.02 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
GNA11 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.075 0.1 -9999 0 -0.6 2 2
Sphingosine 1-phosphate (S1P) pathway

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.016 0 -9999 0 -10000 0 0
SPHK1 0.004 0.071 -9999 0 -0.72 4 4
GNAI2 0.016 0.007 -9999 0 -10000 0 0
mol:S1P 0.025 0.032 -9999 0 -0.34 4 4
GNAO1 0.016 0 -9999 0 -10000 0 0
mol:Sphinganine-1-P 0.021 0.053 -9999 0 -0.54 4 4
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0 0.023 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.007 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.19 0.33 -9999 0 -0.72 147 147
S1P1/S1P -0.1 0.22 -9999 0 -0.46 147 147
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
S1P/S1P5/G12 -0.001 0.023 -9999 0 -0.26 4 4
S1P/S1P3/Gq 0.03 0.041 -9999 0 -0.32 6 6
S1P/S1P4/Gi -0.057 0.14 -9999 0 -0.34 12 12
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.008 0.078 -9999 0 -0.72 6 6
GNA14 -0.008 0.09 -9999 0 -0.72 6 6
GNA15 0.014 0.02 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.015 0.014 -9999 0 -10000 0 0
GNA11 0.016 0 -9999 0 -10000 0 0
ABCC1 0.012 0.026 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.11 0.099 0.18 1 -0.34 1 2
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.014 0.02 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.014 0.02 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.1 0.14 -10000 0 -0.22 286 286
YWHAZ 0.014 0.017 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.005 0.11 -10000 0 -0.54 21 21
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.015 0.012 -10000 0 -10000 0 0
YWHAB 0.015 0.012 -10000 0 -10000 0 0
SNARE/Synip 0.001 0.01 -10000 0 -10000 0 0
YWHAG 0.016 0.01 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0.022 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.015 0.032 -10000 0 -0.72 1 1
GYS1 0.04 0.003 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.015 0.032 -10000 0 -0.72 1 1
TC10/GTP/CIP4/Exocyst -0.002 0.029 -10000 0 -0.47 2 2
AS160/14-3-3 0.049 0.047 -10000 0 -10000 0 0
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 -0.11 0.15 -10000 0 -0.24 286 286
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.033 0.002 -10000 0 -10000 0 0
SFN 0.012 0.048 -10000 0 -0.72 2 2
LNPEP 0.015 0.016 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
Syndecan-4-mediated signaling events

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
PTK2 0.027 0.01 -9999 0 -10000 0 0
Syndecan-4/Syndesmos 0.043 0.02 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.073 0.17 -9999 0 -10000 0 0
Syndecan-4/ADAM12 0.05 0.03 -9999 0 -10000 0 0
CCL5 0.006 0.08 -9999 0 -0.72 6 6
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0.007 -9999 0 -10000 0 0
ITGA5 0.016 0.007 -9999 0 -10000 0 0
SDCBP 0.015 0.032 -9999 0 -0.72 1 1
PLG 0.003 0.031 -9999 0 -0.7 1 1
ADAM12 -0.013 0.069 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.015 0.012 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.038 0.025 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.042 0.02 -9999 0 -10000 0 0
Syndecan-4/CXCL12/CXCR4 -0.07 0.18 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha3 -0.091 0.19 -9999 0 -10000 0 0
MDK 0.004 0.043 -9999 0 -10000 0 0
Syndecan-4/FZD7 -0.076 0.18 -9999 0 -10000 0 0
Syndecan-4/Midkine 0.046 0.025 -9999 0 -10000 0 0
FZD7 -0.2 0.34 -9999 0 -0.72 156 156
Syndecan-4/FGFR1/FGF -0.25 0.16 -9999 0 -0.65 13 13
THBS1 0.012 0.027 -9999 0 -10000 0 0
integrin-mediated signaling pathway 0.042 0.026 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.073 0.17 -9999 0 -10000 0 0
Syndecan-4/TACI 0.042 0.02 -9999 0 -10000 0 0
CXCR4 0.004 0.043 -9999 0 -10000 0 0
cell adhesion 0.032 0.008 -9999 0 -10000 0 0
Syndecan-4/Dynamin 0.042 0.02 -9999 0 -10000 0 0
Syndecan-4/TSP1 0.044 0.021 -9999 0 -10000 0 0
Syndecan-4/GIPC 0.043 0.02 -9999 0 -10000 0 0
Syndecan-4/RANTES 0.038 0.046 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 0.016 0.01 -9999 0 -10000 0 0
LAMA3 -0.23 0.35 -9999 0 -0.72 176 176
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.017 0.014 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin 0.042 0.02 -9999 0 -10000 0 0
TFPI -0.28 0.36 -9999 0 -0.72 207 207
F2 0.018 0.001 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0 0.003 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.079 0.19 -9999 0 -10000 0 0
ACTN1 0.016 0 -9999 0 -10000 0 0
TNC 0.01 0.042 -9999 0 -0.72 1 1
Syndecan-4/CXCL12 -0.082 0.18 -9999 0 -10000 0 0
FGF6 0.013 0.045 -9999 0 -0.72 2 2
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.21 0.34 -9999 0 -0.72 164 164
TNFRSF13B 0.016 0.01 -9999 0 -10000 0 0
FGF2 -0.55 0.31 -9999 0 -0.72 403 403
FGFR1 -0.007 0.12 -9999 0 -0.72 15 15
Syndecan-4/PI-4-5-P2 0.031 0.02 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.1 0.077 -9999 0 -10000 0 0
cell migration -0.02 0.012 -9999 0 -10000 0 0
PRKCD 0.002 0.019 -9999 0 -10000 0 0
vasculogenesis 0.043 0.021 -9999 0 -10000 0 0
SDC4 0.034 0.021 -9999 0 -10000 0 0
Syndecan-4/Tenascin C 0.043 0.027 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.02 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.042 0.027 -9999 0 -10000 0 0
MMP9 -0.057 0.081 -9999 0 -10000 0 0
Rac1/GTP 0.025 0.014 -9999 0 -10000 0 0
cytoskeleton organization 0.042 0.02 -9999 0 -10000 0 0
GIPC1 0.015 0.012 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.11 0.19 -9999 0 -10000 0 0
Syndecan-1-mediated signaling events

Figure 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
TGFB1 0.016 0.01 -9999 0 -10000 0 0
CCL5 0.006 0.08 -9999 0 -0.72 6 6
SDCBP 0.015 0.032 -9999 0 -0.72 1 1
FGFR/FGF2/Syndecan-1 -0.026 0.099 -9999 0 -0.26 47 47
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.015 0.094 -9999 0 -10000 0 0
Syndecan-1/Syntenin -0.016 0.095 -9999 0 -0.39 1 1
MAPK3 0.004 0.087 -9999 0 -10000 0 0
HGF/MET -0.054 0.16 -9999 0 -0.54 52 52
TGFB1/TGF beta receptor Type II 0.016 0.01 -9999 0 -10000 0 0
BSG 0.015 0.014 -9999 0 -10000 0 0
keratinocyte migration -0.014 0.093 -9999 0 -10000 0 0
Syndecan-1/RANTES -0.019 0.11 -9999 0 -0.55 6 6
Syndecan-1/CD147 -0.004 0.091 -9999 0 -10000 0 0
Syndecan-1/Syntenin/PIP2 -0.023 0.087 -9999 0 -0.38 1 1
LAMA5 0.015 0.014 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.023 0.086 -9999 0 -0.37 1 1
MMP7 -0.1 0.27 -9999 0 -0.72 85 85
HGF 0.016 0.01 -9999 0 -10000 0 0
Syndecan-1/CASK -0.026 0.093 -9999 0 -0.25 47 47
Syndecan-1/HGF/MET -0.044 0.16 -9999 0 -0.46 52 52
regulation of cell adhesion 0.014 0.085 -9999 0 -10000 0 0
HPSE 0.003 0.044 -9999 0 -10000 0 0
positive regulation of cell migration -0.026 0.099 -9999 0 -0.26 47 47
SDC1 -0.026 0.099 -9999 0 -0.26 47 47
Syndecan-1/Collagen -0.026 0.099 -9999 0 -0.26 47 47
PPIB 0.016 0.01 -9999 0 -10000 0 0
MET -0.057 0.22 -9999 0 -0.72 52 52
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.059 0.081 -9999 0 -10000 0 0
MAPK1 0.004 0.087 -9999 0 -10000 0 0
homophilic cell adhesion -0.026 0.098 -9999 0 -0.26 47 47
MMP1 -0.089 0.077 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.019 0.15 -9999 0 -0.72 23 23
PLK4 -0.009 0.059 -9999 0 -10000 0 0
regulation of centriole replication -0.014 0.12 -9999 0 -0.56 23 23
Noncanonical Wnt signaling pathway

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
NFATC2 0.015 0.032 -9999 0 -0.72 1 1
GNB1/GNG2 -0.042 0.15 -9999 0 -0.68 19 19
mol:DAG 0.013 0.15 -9999 0 -0.6 19 19
PLCG1 0.012 0.16 -9999 0 -0.63 19 19
YES1 -0.006 0.17 -9999 0 -0.73 18 18
FZD3 -0.019 0.16 -9999 0 -0.72 25 25
FZD6 -0.024 0.16 -9999 0 -0.72 26 26
G protein 0.011 0.16 -9999 0 -0.64 19 19
MAP3K7 0.032 0.13 -9999 0 -0.48 19 19
mol:Ca2+ 0.014 0.14 -9999 0 -0.58 19 19
mol:IP3 0.013 0.15 -9999 0 -0.6 19 19
NLK 0.031 0.016 -9999 0 -10000 0 0
GNB1 0.016 0.01 -9999 0 -10000 0 0
CAMK2A 0.023 0.14 -9999 0 -0.53 19 19
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.016 0.18 -9999 0 -0.41 72 72
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.007 0.17 -9999 0 -0.65 21 21
GO:0007205 0.013 0.15 -9999 0 -0.59 19 19
WNT6 0.012 0.048 -9999 0 -0.72 2 2
WNT4 0.005 0.05 -9999 0 -0.72 1 1
NFAT1/CK1 alpha -0.036 0.14 -9999 0 -0.64 18 18
GNG2 0.015 0.032 -9999 0 -0.72 1 1
WNT5A -0.029 0.17 -9999 0 -0.72 28 28
WNT11 -0.001 0.1 -9999 0 -0.72 10 10
CDC42 0.004 0.16 -9999 0 -0.68 18 18
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.047 0.08 -10000 0 -10000 0 0
UGCG 0.009 0.046 -10000 0 -0.75 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.017 0.17 -10000 0 -0.37 40 40
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.028 0.047 -10000 0 -0.74 1 1
mol:DAG -0.005 0.075 -10000 0 -0.99 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.087 0.15 -10000 0 -0.45 42 42
FRAP1 -0.012 0.23 -10000 0 -0.49 53 53
FOXO3 0.027 0.16 -10000 0 -0.39 35 35
AKT1 0.017 0.17 -10000 0 -0.43 35 35
GAB2 0.012 0.017 -10000 0 -10000 0 0
SMPD1 -0.001 0.018 -10000 0 -10000 0 0
SGMS1 -0.005 0.053 -10000 0 -0.66 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.025 0.14 -10000 0 -0.46 51 51
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation 0.026 0.091 -10000 0 -0.26 27 27
EIF3A 0.016 0.007 -10000 0 -10000 0 0
PI3K -0.03 0.17 -10000 0 -0.54 51 51
RPS6KB1 0.009 0.071 -10000 0 -10000 0 0
mol:sphingomyelin -0.005 0.075 -10000 0 -0.99 3 3
natural killer cell activation -0.001 0.005 -10000 0 -0.013 28 28
JAK3 0.017 0.007 -10000 0 -10000 0 0
PIK3R1 -0.056 0.22 -10000 0 -0.72 51 51
JAK1 0.013 0.046 -10000 0 -0.72 2 2
NFKB1 0.016 0 -10000 0 -10000 0 0
MYC -0.006 0.27 -10000 0 -1 29 29
MYB -0.062 0.36 -10000 0 -1.3 41 41
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.04 0.11 -10000 0 -0.32 4 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.07 -10000 0 -0.59 1 1
mol:PI-3-4-5-P3 0.04 0.11 -10000 0 -0.31 4 4
Rac1/GDP -0.015 0.13 -10000 0 -0.41 51 51
T cell proliferation 0.039 0.1 -10000 0 -0.3 4 4
SHC1 0.014 0.007 -10000 0 -10000 0 0
RAC1 0.016 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.02 -10000 0 -0.067 41 41
PRKCZ 0.038 0.1 -10000 0 -0.3 4 4
NF kappa B1 p50/RelA -0.084 0.15 -10000 0 -0.45 40 40
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.032 0.087 -10000 0 -0.27 1 1
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA 0.004 0.039 -10000 0 -10000 0 0
IL2RB 0.014 0.024 -10000 0 -10000 0 0
TERT 0.013 0.036 -10000 0 -0.72 1 1
E2F1 0.001 0.13 -10000 0 -0.44 41 41
SOS1 0.013 0.008 -10000 0 -10000 0 0
RPS6 0.015 0.032 -10000 0 -0.72 1 1
mol:cAMP -0.001 0.009 0.031 41 -10000 0 41
PTPN11 0.014 0.008 -10000 0 -10000 0 0
IL2RG 0.006 0.039 -10000 0 -10000 0 0
actin cytoskeleton organization 0.039 0.1 -10000 0 -0.3 4 4
GRB2 0.01 0.023 -10000 0 -10000 0 0
IL2 0.014 0.034 -10000 0 -0.72 1 1
PIK3CA 0.016 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.13 -10000 0 -0.39 51 51
LCK 0 0.049 -10000 0 -10000 0 0
BCL2 -0.11 0.41 -10000 0 -0.91 105 105
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.007 0.15 -9999 0 -0.53 37 37
KLHL20 -0.014 0.049 -9999 0 -0.22 8 8
CYFIP2 -0.002 0.051 -9999 0 -10000 0 0
Rac1/GDP 0.046 0.1 -9999 0 -0.31 37 37
ENAH 0.01 0.15 -9999 0 -0.53 37 37
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0.01 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.065 -9999 0 -0.72 4 4
CDC42/GTP -0.019 0.064 -9999 0 -0.45 1 1
ABI1/Sra1/Nap1 -0.011 0.032 -9999 0 -0.17 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.028 0.11 -9999 0 -0.41 37 37
RAPGEF1 0.03 0.13 -9999 0 -0.44 37 37
CTNND1 0.016 0.007 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.039 0.14 -9999 0 -0.55 37 37
CRK 0.02 0.14 -9999 0 -0.48 38 38
E-cadherin/gamma catenin/alpha catenin -0.028 0.11 -9999 0 -0.46 34 34
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.007 0.058 -9999 0 -0.42 10 10
DLG1 0.01 0.15 -9999 0 -0.53 37 37
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.029 0.064 -9999 0 -0.31 3 3
MLLT4 0.002 0.1 -9999 0 -0.72 10 10
ARF6/GTP/NME1/Tiam1 0.003 0.015 -9999 0 -10000 0 0
PI3K -0.038 0.083 -9999 0 -0.42 3 3
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.036 0.13 -9999 0 -0.54 34 34
TIAM1 0.015 0.012 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.026 0.1 -9999 0 -0.39 37 37
AKT1 -0.02 0.048 -9999 0 -0.22 3 3
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
CDH1 -0.032 0.18 -9999 0 -0.72 33 33
RhoA/GDP 0.046 0.1 -9999 0 -0.31 37 37
actin cytoskeleton organization -0.007 0.039 -9999 0 -0.16 8 8
CDC42/GDP 0.046 0.1 -9999 0 -0.31 37 37
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.01 0.083 -9999 0 -0.3 34 34
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.028 0.11 -9999 0 -0.41 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin -0.027 0.1 -9999 0 -0.4 37 37
mol:GDP 0.039 0.12 -9999 0 -0.36 37 37
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.014 0.035 -9999 0 -0.72 1 1
p120 catenin/RhoA/GDP -0.023 0.081 -9999 0 -0.41 2 2
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0.003 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.018 0.059 -9999 0 -0.22 17 17
NME1 0.011 0.029 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.009 0.15 -9999 0 -0.53 38 38
regulation of cell-cell adhesion -0.017 0.056 -9999 0 -0.38 1 1
WASF2 -0.004 0.017 -9999 0 -10000 0 0
Rap1/GTP -0.021 0.075 -9999 0 -0.42 2 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.023 0.095 -9999 0 -0.38 34 34
CCND1 0.019 0.072 -9999 0 -0.27 17 17
VAV2 0.024 0.14 -9999 0 -0.47 37 37
RAP1/GDP -0.015 0.081 -9999 0 -0.41 2 2
adherens junction assembly 0.01 0.15 -9999 0 -0.51 38 38
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0.007 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.024 0.093 -9999 0 -0.36 38 38
E-cadherin/beta catenin -0.029 0.11 -9999 0 -0.45 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.003 0.15 -9999 0 -0.53 37 37
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
Rac1/GTP -0.025 0.077 -9999 0 -0.35 11 11
E-cadherin/beta catenin/alpha catenin -0.031 0.12 -9999 0 -0.46 37 37
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.04 0.14 -9999 0 -0.56 37 37
Arf6 trafficking events

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
SLC2A4 -0.41 0.36 -10000 0 -0.72 302 302
CLTC 0.038 0.014 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.026 0.04 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.009 -10000 0 -10000 0 0
EXOC4 0.016 0 -10000 0 -10000 0 0
CD59 0.029 0.041 -10000 0 -0.27 8 8
CPE -0.065 0.19 -10000 0 -0.47 95 95
CTNNB1 0.01 0.065 -10000 0 -0.72 4 4
membrane fusion 0.025 0.043 -10000 0 -10000 0 0
CTNND1 0.039 0.013 -10000 0 -10000 0 0
DNM2 0.016 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.023 -10000 0 -10000 0 0
TSHR 0.02 0.043 -10000 0 -0.47 4 4
INS 0.024 0.008 -10000 0 -10000 0 0
BIN1 0.016 0.007 -10000 0 -10000 0 0
mol:Choline 0.025 0.043 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.015 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.008 -10000 0 -10000 0 0
JUP 0.032 0.022 -10000 0 -0.24 1 1
ASAP2/amphiphysin II 0 0.003 -10000 0 -10000 0 0
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.015 0.069 -10000 0 -0.24 33 33
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0.046 -10000 0 -0.72 2 2
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.008 0.036 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.054 0.015 -10000 0 -0.29 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.016 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.012 0.049 0.36 4 -10000 0 4
positive regulation of phagocytosis 0.024 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.002 0.029 -10000 0 -0.47 2 2
ACAP1 0.023 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.031 0.02 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.041 0.027 -10000 0 -10000 0 0
JIP4/KLC1 0 0.003 -10000 0 -10000 0 0
EXOC1 0.016 0 -10000 0 -10000 0 0
exocyst 0.054 0.015 -10000 0 -0.3 1 1
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0.003 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.039 0.013 -10000 0 -10000 0 0
NME1 0.021 0.015 -10000 0 -10000 0 0
clathrin coat assembly 0.038 0.014 -10000 0 -10000 0 0
IL2RA 0.031 0.019 -10000 0 -10000 0 0
VAMP3 0.024 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.2 0.17 -10000 0 -0.34 302 302
EXOC6 0.014 0.034 -10000 0 -0.72 1 1
PLD1 -0.013 0.062 -10000 0 -0.32 21 21
PLD2 -0.001 0.014 -10000 0 -0.32 1 1
EXOC5 0.016 0 -10000 0 -10000 0 0
PIP5K1C 0.037 0.023 -10000 0 -10000 0 0
SDC1 0.026 0.021 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.015 -10000 0 -10000 0 0
EXOC7 0.016 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.012 0.05 -10000 0 -0.37 4 4
mol:Phosphatidic acid 0.025 0.043 -10000 0 -10000 0 0
endocytosis 0 0.003 -10000 0 -10000 0 0
SCAMP2 0.016 0 -10000 0 -10000 0 0
ADRB2 -0.17 0.2 -10000 0 -0.36 284 284
EXOC3 0.016 0 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.03 0.014 -10000 0 -10000 0 0
KLC1 0.016 0 -10000 0 -10000 0 0
AVPR2 0.044 0.028 -10000 0 -0.36 2 2
RALA 0.016 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.009 0.044 -10000 0 -0.37 1 1
Caspase cascade in apoptosis

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
TOP1 0.052 0.046 0.26 2 -10000 0 2
ACTA1 -0.005 0.088 0.27 4 -0.35 1 5
NUMA1 0.052 0.048 0.26 2 -10000 0 2
SPTAN1 0.048 0.057 0.27 15 -10000 0 15
LIMK1 0.038 0.063 0.28 10 -10000 0 10
BIRC3 -0.038 0.18 -10000 0 -0.72 35 35
BIRC2 0.016 0 -10000 0 -10000 0 0
BAX 0.015 0.014 -10000 0 -10000 0 0
CASP10 0.031 0.04 -10000 0 -0.46 2 2
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.053 0.047 0.26 2 -10000 0 2
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.048 0.057 0.27 15 -10000 0 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.067 0.19 0.27 4 -0.38 126 130
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A 0.041 0.01 -10000 0 -10000 0 0
BID 0.029 0.02 -10000 0 -0.24 2 2
MAP3K1 0.026 0.05 -10000 0 -0.42 4 4
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.006 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.046 0.06 0.27 15 -0.32 1 16
CASP9 0.017 0.001 -10000 0 -10000 0 0
DNA repair -0.032 0.052 -10000 0 -0.23 33 33
neuron apoptosis 0.031 0.065 -10000 0 -0.62 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.056 0.053 0.29 2 -10000 0 2
APAF1 0.016 0.007 -10000 0 -10000 0 0
CASP6 0.057 0.025 -10000 0 -10000 0 0
TRAF2 0.015 0.012 -10000 0 -10000 0 0
ICAD/CAD 0.056 0.054 0.3 2 -10000 0 2
CASP7 0.018 0.085 0.32 35 -0.56 1 36
KRT18 0.035 0.014 -10000 0 -10000 0 0
apoptosis 0.038 0.098 0.31 10 -0.33 2 12
DFFA 0.048 0.057 0.27 15 -10000 0 15
DFFB 0.048 0.057 0.27 15 -10000 0 15
PARP1 0.032 0.052 0.23 33 -10000 0 33
actin filament polymerization 0.031 0.16 0.36 90 -0.3 2 92
TNF 0.012 0.025 -10000 0 -10000 0 0
CYCS 0.041 0.032 -10000 0 -0.2 1 1
SATB1 0.016 0.13 -10000 0 -0.46 4 4
SLK 0.047 0.06 0.27 15 -0.38 1 16
p15 BID/BAX 0.034 0.018 -10000 0 -10000 0 0
CASP2 0.05 0.056 -10000 0 -10000 0 0
JNK cascade -0.026 0.05 0.42 4 -10000 0 4
CASP3 0.041 0.062 0.29 15 -10000 0 15
LMNB2 0.063 0.026 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.005 0.09 -10000 0 -0.72 8 8
Mammalian IAPs/DIABLO -0.025 0.11 -10000 0 -0.42 35 35
negative regulation of DNA binding 0.041 0.01 -10000 0 -10000 0 0
stress fiber formation 0.047 0.06 0.27 15 -0.38 1 16
GZMB 0.021 0.046 -10000 0 -0.54 2 2
CASP1 -0.036 0.18 -10000 0 -0.49 60 60
LMNB1 0.074 0.028 -10000 0 -10000 0 0
APP 0.031 0.066 -10000 0 -0.63 5 5
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM 0.031 0.1 0.31 10 -0.32 3 13
LMNA 0.06 0.026 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.042 0.059 -10000 0 -10000 0 0
LRDD 0.016 0 -10000 0 -10000 0 0
SREBF1 0.041 0.061 0.28 14 -10000 0 14
APAF-1/Caspase 9 0.012 0.043 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.052 0.048 0.26 2 -10000 0 2
CFL2 -0.032 0.17 0.3 2 -0.37 90 92
GAS2 -0.22 0.2 0.27 4 -0.38 318 322
positive regulation of apoptosis 0.072 0.028 -10000 0 -10000 0 0
PRF1 0.012 0.025 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC2 0.014 0.017 -9999 0 -10000 0 0
GNB1/GNG2 -0.018 0.095 -9999 0 -0.46 23 23
forebrain development -0.018 0.19 -9999 0 -0.51 54 54
GNAO1 0.017 0 -9999 0 -10000 0 0
SMO/beta Arrestin2 0.006 0.11 -9999 0 -0.54 22 22
SMO -0.015 0.15 -9999 0 -0.72 22 22
ARRB2 0.018 0 -9999 0 -10000 0 0
GLI3/SPOP 0.051 0.074 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
GSK3B 0.016 0.01 -9999 0 -10000 0 0
GNAI2 0.017 0.007 -9999 0 -10000 0 0
SIN3/HDAC complex 0.001 0.009 -9999 0 -10000 0 0
GNAI1 -0.25 0.35 -9999 0 -0.72 189 189
XPO1 0.021 0.001 -9999 0 -10000 0 0
GLI1/Su(fu) -0.048 0.14 -9999 0 -0.59 17 17
SAP30 0.016 0.007 -9999 0 -10000 0 0
mol:GDP -0.015 0.15 -9999 0 -0.72 22 22
MIM/GLI2A 0.017 0.04 -9999 0 -10000 0 0
IFT88 0.015 0.032 -9999 0 -0.72 1 1
GNAI3 0.017 0 -9999 0 -10000 0 0
GLI2 0.053 0.038 -9999 0 -10000 0 0
GLI3 0.045 0.078 -9999 0 -0.27 24 24
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.015 0.032 -9999 0 -0.72 1 1
GNG2 0.015 0.032 -9999 0 -0.72 1 1
Gi family/GTP -0.066 0.16 -9999 0 -0.42 26 26
SIN3B 0.014 0.016 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.067 0.059 -9999 0 -0.39 1 1
GLI2/Su(fu) 0.066 0.059 -9999 0 -0.33 2 2
FOXA2 0.009 0.028 -9999 0 -10000 0 0
neural tube patterning -0.018 0.19 -9999 0 -0.51 54 54
SPOP 0.016 0.007 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.033 0.055 -9999 0 -0.41 1 1
GNB1 0.016 0.01 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.017 0.04 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.018 0.19 -9999 0 -0.51 54 54
SUFU 0.027 0.061 -9999 0 -0.46 1 1
LGALS3 -0.074 0.24 -9999 0 -0.72 64 64
catabolic process 0.08 0.073 -9999 0 -0.35 3 3
GLI3A/CBP -0.012 0.12 -9999 0 -0.37 54 54
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 -0.012 0.19 -9999 0 -0.53 54 54
RAB23 0.014 0.017 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.015 0.032 -9999 0 -0.72 1 1
RBBP7 0.012 0.026 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.022 0.16 -9999 0 -0.43 65 65
GNAZ 0.009 0.078 -9999 0 -0.72 6 6
RBBP4 0.016 0.007 -9999 0 -10000 0 0
CSNK1G1 0.016 0.01 -9999 0 -10000 0 0
PIAS1 0.016 0.007 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.057 0.036 -9999 0 -10000 0 0
STK36 0.019 0.032 -9999 0 -0.72 1 1
Gi family/GNB1/GNG2/GDP -0.057 0.15 -9999 0 -0.52 14 14
PTCH1 -0.004 0.17 -9999 0 -0.51 36 36
MIM/GLI1 0.001 0.19 -9999 0 -0.49 53 53
CREBBP -0.012 0.12 -9999 0 -0.37 54 54
Su(fu)/SIN3/HDAC complex 0.058 0.017 -9999 0 -10000 0 0
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 0.029 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.039 0.13 -9999 0 -0.56 16 16
NEF 0.002 0.015 -9999 0 -10000 0 0
NFKBIA 0.01 0.048 -9999 0 -0.85 1 1
BIRC3 0 0.2 -9999 0 -0.74 35 35
CYCS 0.013 0.13 -9999 0 -0.52 15 15
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.027 0.16 -9999 0 -0.72 25 25
MAP2K7 0.022 0.12 -9999 0 -0.47 13 13
protein ubiquitination 0.068 0.068 -9999 0 -0.37 1 1
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0.007 -9999 0 -10000 0 0
FAS -0.033 0.18 -9999 0 -0.72 35 35
BID 0.003 0.14 -9999 0 -0.56 15 15
NF-kappa-B/RelA/I kappa B alpha -0.023 0.083 -9999 0 -0.32 35 35
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 -0.033 0.18 -9999 0 -0.72 35 35
CFLAR 0.013 0.045 -9999 0 -0.72 2 2
FADD 0.002 0.046 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.023 0.084 -9999 0 -0.32 35 35
MAPK8 0.03 0.11 -9999 0 -0.45 13 13
APAF1 0.016 0.007 -9999 0 -10000 0 0
TRAF1 0.015 0.016 -9999 0 -10000 0 0
TRAF2 0.015 0.012 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.006 0.14 -9999 0 -0.35 64 64
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.056 0.076 -9999 0 -0.32 6 6
CHUK 0.07 0.071 -9999 0 -0.41 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.044 0.15 -9999 0 -0.42 64 64
TCRz/NEF -0.031 0.12 -9999 0 -0.55 25 25
TNF 0.012 0.025 -9999 0 -10000 0 0
FASLG -0.004 0.12 -9999 0 -0.48 25 25
NFKB1 0.012 0.03 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.004 0.019 -9999 0 -10000 0 0
CASP6 -0.03 0.096 -9999 0 -0.61 7 7
CASP7 0.028 0.2 -9999 0 -0.58 41 41
RELA 0.012 0.03 -9999 0 -10000 0 0
CASP2 0.016 0.007 -9999 0 -10000 0 0
CASP3 0.029 0.19 -9999 0 -0.58 41 41
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.003 0.014 -9999 0 -10000 0 0
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.064 0.073 -9999 0 -0.3 1 1
APAF-1/Caspase 9 -0.049 0.13 -9999 0 -0.48 40 40
BCL2 -0.036 0.18 -9999 0 -0.39 51 51
BCR signaling 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
JUN 0.002 0.13 -10000 0 -0.38 17 17
IKBKB 0.047 0.045 0.23 1 -10000 0 1
AKT1 0.032 0.082 0.26 13 -0.24 9 22
IKBKG 0.051 0.045 0.23 1 -10000 0 1
CALM1 0.028 0.074 -10000 0 -0.36 12 12
PIK3CA 0.016 0.007 -10000 0 -10000 0 0
MAP3K1 0.049 0.1 -10000 0 -0.56 13 13
MAP3K7 0.016 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.078 0.24 15 -0.39 12 27
DOK1 0.014 0.019 -10000 0 -10000 0 0
AP-1 -0.11 0.12 0.21 1 -0.26 112 113
LYN 0.016 0.01 -10000 0 -10000 0 0
BLNK 0.011 0.029 -10000 0 -10000 0 0
SHC1 0.016 0 -10000 0 -10000 0 0
BCR complex -0.018 0.086 -10000 0 -0.54 13 13
CD22 -0.019 0.11 -10000 0 -0.69 13 13
CAMK2G 0.036 0.071 -10000 0 -0.44 4 4
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.006 0.052 -10000 0 -0.37 1 1
GO:0007205 0.019 0.079 0.24 15 -0.4 12 27
SYK 0.01 0.03 -10000 0 -10000 0 0
ELK1 0.027 0.075 -10000 0 -0.37 12 12
NFATC1 0.037 0.085 -10000 0 -0.43 15 15
B-cell antigen/BCR complex -0.018 0.086 -10000 0 -0.54 13 13
PAG1/CSK -0.002 0.015 -10000 0 -10000 0 0
NFKBIB 0.033 0.019 0.12 1 -10000 0 1
HRAS 0.033 0.068 -10000 0 -0.35 12 12
NFKBIA 0.033 0.019 0.12 1 -10000 0 1
NF-kappa-B/RelA/I kappa B beta 0.036 0.018 0.13 1 -10000 0 1
RasGAP/Csk -0.007 0.088 -10000 0 -0.5 13 13
mol:GDP 0.018 0.074 0.23 15 -0.37 12 27
PTEN -0.002 0.12 -10000 0 -0.72 13 13
CD79B -0.003 0.12 -10000 0 -0.72 13 13
NF-kappa-B/RelA/I kappa B alpha 0.036 0.018 0.13 1 -10000 0 1
GRB2 0.013 0.022 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.013 0.14 -10000 0 -0.57 13 13
PIK3R1 -0.055 0.22 -10000 0 -0.72 51 51
mol:IP3 0.019 0.08 0.24 15 -0.4 12 27
CSK 0.016 0.01 -10000 0 -10000 0 0
FOS -0.24 0.19 -10000 0 -0.36 360 360
CHUK 0.05 0.049 0.23 1 -0.44 1 2
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.008 0.049 -10000 0 -0.4 4 4
PTPN6 -0.017 0.1 -10000 0 -0.64 13 13
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 0.032 0.015 -10000 0 -10000 0 0
VAV2 -0.015 0.1 -10000 0 -0.65 13 13
ubiquitin-dependent protein catabolic process 0.037 0.019 0.13 1 -10000 0 1
BTK 0.005 0.014 -10000 0 -10000 0 0
CD19 -0.023 0.11 -10000 0 -0.69 13 13
MAP4K1 0.013 0.023 -10000 0 -10000 0 0
CD72 -0.017 0.065 -10000 0 -10000 0 0
PAG1 0.012 0.026 -10000 0 -10000 0 0
MAPK14 0.056 0.09 -10000 0 -0.46 13 13
SH3BP5 -0.006 0.13 -10000 0 -0.72 16 16
PIK3AP1 0.026 0.086 0.27 13 -0.44 12 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.038 0.073 -10000 0 -0.62 4 4
RAF1 0.041 0.065 -10000 0 -0.38 5 5
RasGAP/p62DOK/SHIP -0.007 0.084 -10000 0 -0.49 13 13
CD79A 0.007 0.037 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.1 0.12 0.21 1 -0.25 112 113
RASA1 0.015 0.012 -10000 0 -10000 0 0
MAPK3 0.056 0.057 -10000 0 -0.33 4 4
MAPK1 0.056 0.057 -10000 0 -0.33 4 4
CD72/SHP1 0.042 0.11 -10000 0 -0.59 13 13
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.055 0.091 -10000 0 -0.46 13 13
actin cytoskeleton organization 0.038 0.098 -10000 0 -0.54 13 13
NF-kappa-B/RelA 0.076 0.035 0.24 1 -10000 0 1
Calcineurin -0.014 0.062 -10000 0 -0.39 4 4
PI3K -0.037 0.1 -10000 0 -0.47 14 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.003 0.089 0.27 15 -0.47 12 27
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 0.033 0.12 -10000 0 -0.72 13 13
DAPP1 -0.005 0.14 -10000 0 -0.83 13 13
cytokine secretion 0.037 0.08 -10000 0 -0.4 15 15
mol:DAG 0.019 0.08 0.24 15 -0.4 12 27
PLCG2 0 0.11 -10000 0 -0.72 11 11
MAP2K1 0.049 0.062 -10000 0 -0.37 4 4
B-cell antigen/BCR complex/FcgammaRIIB -0.012 0.099 -10000 0 -0.59 13 13
mol:PI-3-4-5-P3 -0.021 0.094 0.34 13 -0.33 13 26
ETS1 0.043 0.068 -10000 0 -0.38 5 5
B-cell antigen/BCR complex/LYN/SYK/BLNK 0 0.069 -10000 0 -0.38 13 13
B-cell antigen/BCR complex/LYN -0.016 0.12 -10000 0 -0.73 13 13
MALT1 0.016 0.007 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 0.038 0.1 -10000 0 -0.59 13 13
B-cell antigen/BCR complex/LYN/SYK -0.012 0.1 -10000 0 -0.62 13 13
CARD11 0.025 0.076 -10000 0 -0.37 12 12
FCGR2B 0.01 0.065 -10000 0 -0.72 4 4
PPP3CA 0.01 0.065 -10000 0 -0.72 4 4
BCL10 0.016 0.007 -10000 0 -10000 0 0
IKK complex 0.036 0.027 0.14 2 -0.12 1 3
PTPRC 0.006 0.057 -10000 0 -0.72 2 2
PDPK1 0.022 0.076 0.23 13 -0.25 6 19
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.006 0.085 -10000 0 -0.72 7 7
POU2F2 0.033 0.013 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR -0.1 0.27 -9999 0 -0.72 83 83
LRPAP1 0.016 0 -9999 0 -10000 0 0
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 0.003 0.1 -9999 0 -0.48 20 20
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.016 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 0.005 0.093 -9999 0 -0.43 20 20
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.016 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.023 0.11 -9999 0 -0.72 10 10
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.022 0.035 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.015 0.033 -9999 0 -0.72 1 1
CDK5R1 0.014 0.019 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.022 0 -9999 0 -10000 0 0
CDK5R2 0.016 0 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.089 0.19 -9999 0 -0.48 98 98
YWHAE 0.015 0.032 -9999 0 -0.72 1 1
NDEL1/14-3-3 E 0.043 0.079 -9999 0 -0.35 8 8
MAP1B -0.035 0.11 -9999 0 -0.36 52 52
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 0.022 0.085 -9999 0 -0.37 20 20
RELN -0.013 0.14 -9999 0 -0.72 20 20
PAFAH/LIS1 0.033 0.071 -9999 0 -0.46 10 10
LIS1/CLIP170 0.033 0.022 -9999 0 -0.46 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.009 0.045 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.012 0.14 -9999 0 -0.29 98 98
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 0.035 0.081 -9999 0 -0.34 20 20
LIS1/IQGAP1 0.034 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.029 0 -9999 0 -10000 0 0
PAFAH1B3 -0.039 0.077 -9999 0 -10000 0 0
PAFAH1B2 0.016 0.007 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.008 0.075 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.004 0.06 -9999 0 -0.33 7 7
LRP8 -0.029 0.072 -9999 0 -10000 0 0
NDEL1/Katanin 60 0.044 0.077 -9999 0 -0.35 7 7
P39/CDK5 0.023 0.084 -9999 0 -0.37 20 20
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.034 0 -9999 0 -10000 0 0
CDK5 0.014 0.089 -9999 0 -0.4 20 20
PPP2R5D 0.015 0.012 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.001 0.018 -9999 0 -0.4 1 1
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.074 0.16 -9999 0 -0.4 98 98
RELN/VLDLR -0.063 0.19 -9999 0 -0.45 98 98
CDC42 0 0 -9999 0 -10000 0 0
FoxO family 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
G6PC 0.023 0.12 -9999 0 -10000 0 0
PLK1 0.072 0.17 -9999 0 -0.57 8 8
CDKN1B 0.094 0.16 -9999 0 -0.43 16 16
FOXO3 0.069 0.18 -9999 0 -0.44 35 35
KAT2B 0.007 0.02 -9999 0 -0.043 61 61
FOXO1/SIRT1 -0.027 0.1 -9999 0 -0.28 36 36
CAT 0.009 0.37 -9999 0 -1.1 44 44
CTNNB1 0.01 0.064 -9999 0 -0.72 4 4
AKT1 0.029 0.026 -9999 0 -10000 0 0
FOXO1 0.014 0.13 -9999 0 -0.31 73 73
MAPK10 0.036 0.07 -9999 0 -0.39 12 12
mol:GTP 0.002 0.004 -9999 0 -10000 0 0
FOXO4 0.1 0.1 -9999 0 -0.36 3 3
response to oxidative stress 0.013 0.022 -9999 0 -0.038 61 61
FOXO3A/SIRT1 -0.025 0.14 -9999 0 -0.48 20 20
XPO1 0.017 0.001 -9999 0 -10000 0 0
EP300 0.02 0.002 -9999 0 -10000 0 0
BCL2L11 0.043 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 0.018 0.12 -9999 0 -0.28 73 73
mol:GDP 0.013 0.022 -9999 0 -0.038 61 61
RAN 0.017 0.004 -9999 0 -10000 0 0
GADD45A 0.086 0.18 -9999 0 -0.94 10 10
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.086 0.04 -9999 0 -10000 0 0
MST1 0.024 0.017 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.072 0.028 -9999 0 -10000 0 0
YWHAB 0.015 0.012 -9999 0 -10000 0 0
MAPK8 0.046 0.029 -9999 0 -0.38 1 1
MAPK9 0.046 0.022 -9999 0 -10000 0 0
YWHAG 0.016 0.01 -9999 0 -10000 0 0
YWHAE 0.015 0.032 -9999 0 -0.72 1 1
YWHAZ 0.014 0.017 -9999 0 -10000 0 0
SIRT1 0.006 0.011 -9999 0 -10000 0 0
SOD2 0.11 0.17 -9999 0 -0.39 22 22
RBL2 0.093 0.14 -9999 0 -0.47 5 5
RAL/GDP 0.036 0.02 -9999 0 -10000 0 0
CHUK 0.023 0.038 -9999 0 -0.75 1 1
Ran/GTP 0.016 0.006 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
RAL/GTP 0.043 0.025 -9999 0 -10000 0 0
CSNK1G1 0.016 0.01 -9999 0 -10000 0 0
FASLG 0.035 0.077 -9999 0 -1.6 1 1
SKP2 0.012 0.025 -9999 0 -10000 0 0
USP7 0.017 0.005 -9999 0 -10000 0 0
IKBKB 0.022 0.028 -9999 0 -10000 0 0
CCNB1 0.064 0.17 -9999 0 -0.58 9 9
FOXO1-3a-4/beta catenin 0.006 0.18 -9999 0 -0.4 54 54
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.12 -9999 0 -0.28 73 73
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.007 0.02 -9999 0 -0.043 61 61
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.01 -9999 0 -10000 0 0
ZFAND5 0.1 0.092 -9999 0 -10000 0 0
SFN 0.012 0.048 -9999 0 -0.72 2 2
CDK2 0.018 0.024 -9999 0 -0.14 5 5
FOXO3A/14-3-3 0.078 0.044 -9999 0 -0.34 1 1
CREBBP 0.02 0.032 -9999 0 -0.72 1 1
FBXO32 0.028 0.33 -9999 0 -1.2 29 29
BCL6 -0.014 0.41 -9999 0 -1.2 53 53
RALB 0.017 0.002 -9999 0 -10000 0 0
RALA 0.017 0.002 -9999 0 -10000 0 0
YWHAH 0.015 0.012 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.018 0.066 -9999 0 -10000 0 0
mol:Halofuginone 0.004 0.002 -9999 0 -10000 0 0
ITGA1 0.013 0.045 -9999 0 -0.72 2 2
CDKN1A -0.12 0.079 -9999 0 -0.59 2 2
PRL-3/alpha Tubulin -0.003 0.016 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.04 -9999 0 -10000 0 0
AGT -0.013 0.062 -9999 0 -10000 0 0
CCNA2 -0.32 0.17 -9999 0 -0.5 3 3
TUBA1B 0.015 0.012 -9999 0 -10000 0 0
EGR1 -0.44 0.21 -9999 0 -0.53 436 436
CDK2/Cyclin E1 -0.098 0.082 -9999 0 -0.55 2 2
MAPK3 0.025 0.02 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta -0.001 0.011 -9999 0 -10000 0 0
MAPK1 0.025 0.02 -9999 0 -10000 0 0
PTP4A1 -0.32 0.17 -9999 0 -0.49 3 3
PTP4A3 0.01 0.031 -9999 0 -10000 0 0
PTP4A2 0.013 0.022 -9999 0 -10000 0 0
ITGB1 0.025 0.02 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
RAC1 -0.12 0.072 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.29 0.16 -9999 0 -0.46 2 2
RABGGTA 0.016 0 -9999 0 -10000 0 0
BCAR1 -0.001 0.008 -9999 0 -10000 0 0
RHOC -0.12 0.072 -9999 0 -10000 0 0
RHOA -0.12 0.072 -9999 0 -10000 0 0
cell motility -0.12 0.078 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.29 0.16 -9999 0 -0.46 2 2
PRL-3/alpha1 Integrin -0.005 0.036 -9999 0 -0.54 2 2
ROCK1 -0.12 0.078 -9999 0 -10000 0 0
RABGGTB 0.016 0 -9999 0 -10000 0 0
CDK2 0.013 0.024 -9999 0 -0.14 12 12
mitosis -0.32 0.17 -9999 0 -0.49 3 3
ATF5 0.015 0.012 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.029 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.001 0.01 -10000 0 -10000 0 0
CDKN1B 0.047 0.053 -10000 0 -0.36 9 9
CDKN1A 0.052 0.026 -10000 0 -0.36 2 2
FRAP1 0.016 0 -10000 0 -10000 0 0
PRKDC 0.01 0.03 -10000 0 -10000 0 0
FOXO3 0.054 0.003 -10000 0 -10000 0 0
AKT1 0.003 0.011 -10000 0 -10000 0 0
BAD 0.016 0 -10000 0 -10000 0 0
AKT3 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.054 0.002 -10000 0 -10000 0 0
AKT1/ASK1 -0.02 0.088 -10000 0 -0.35 35 35
BAD/YWHAZ 0.001 0.009 -10000 0 -10000 0 0
RICTOR 0.016 0 -10000 0 -10000 0 0
RAF1 0.016 0.007 -10000 0 -10000 0 0
JNK cascade 0.02 0.085 0.34 35 -10000 0 35
TSC1 0.054 0.002 -10000 0 -10000 0 0
YWHAZ 0.014 0.017 -10000 0 -10000 0 0
AKT1/RAF1 0.053 0.003 -10000 0 -10000 0 0
EP300 0.016 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.011 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.054 0.002 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.012 0.095 -10000 0 -0.45 21 21
MAP3K5 -0.033 0.18 -10000 0 -0.72 35 35
MAPKAP1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.055 0.017 -10000 0 -10000 0 0
YWHAH 0.015 0.012 -10000 0 -10000 0 0
AKT1S1 0.053 0.007 -10000 0 -10000 0 0
CASP9 0.054 0.002 -10000 0 -10000 0 0
YWHAB 0.015 0.012 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.054 0.051 -10000 0 -0.33 9 9
GBL 0.016 0.007 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.001 0.007 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
SRC 0.016 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.002 0.025 -10000 0 -0.34 2 2
KIAA1303 0.016 0.01 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.048 0.001 -10000 0 -10000 0 0
CHUK 0.053 0.018 -10000 0 -0.36 1 1
BAD/BCL-XL 0.069 0.002 -10000 0 -10000 0 0
mTORC2 0 0.004 -10000 0 -10000 0 0
AKT2 0.022 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.062 0.048 -10000 0 -0.26 1 1
PDPK1 0.016 0.007 -10000 0 -10000 0 0
MDM2 0.052 0.011 -10000 0 -10000 0 0
MAPKKK cascade -0.052 0.003 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.066 0.019 -10000 0 -0.32 1 1
TSC1/TSC2 0.062 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.003 0.02 -10000 0 -0.31 1 1
glucose import -0.23 0.24 -10000 0 -0.42 310 310
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.062 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.24 0.24 -10000 0 -0.43 310 310
GSK3A 0.054 0.002 -10000 0 -10000 0 0
FOXO1 -0.002 0.14 -10000 0 -0.36 72 72
GSK3B 0.054 0.005 -10000 0 -10000 0 0
SFN 0.012 0.048 -10000 0 -0.72 2 2
G1/S transition of mitotic cell cycle 0.062 0.004 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.061 0.021 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
KPNA1 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
YWHAG 0.016 0.01 -10000 0 -10000 0 0
RHEB 0.016 0.007 -10000 0 -10000 0 0
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.015 0.15 -9999 0 -0.72 22 22
positive regulation of NF-kappaB transcription factor activity -0.022 0.11 -9999 0 -0.54 22 22
MAP2K4 0.039 0.081 -9999 0 -0.36 8 8
IKBKB 0.014 0.02 -9999 0 -10000 0 0
TNFRSF10B 0.015 0.033 -9999 0 -0.72 1 1
TNFRSF10A 0.014 0.034 -9999 0 -0.72 1 1
SMPD1 0.013 0.058 -9999 0 -0.26 23 23
IKBKG 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.024 0.11 -9999 0 -0.54 23 23
TRAIL/TRAILR3 -0.023 0.11 -9999 0 -0.54 22 22
TRAIL/TRAILR1 -0.024 0.11 -9999 0 -0.54 23 23
TRAIL/TRAILR4 -0.023 0.11 -9999 0 -0.54 22 22
TRAIL/TRAILR1/DAP3/GTP -0.018 0.087 -9999 0 -0.42 23 23
IKK complex -0.005 0.047 -9999 0 -0.77 1 1
RIPK1 0.016 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP -0.001 0.008 -9999 0 -10000 0 0
MAPK3 0.006 0.11 -9999 0 -0.54 22 22
MAP3K1 0.037 0.07 -9999 0 -0.29 22 22
TRAILR4 (trimer) 0.016 0 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.014 0.034 -9999 0 -0.72 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.032 0.069 -9999 0 -0.29 23 23
CFLAR 0.013 0.045 -9999 0 -0.72 2 2
MAPK1 0.006 0.11 -9999 0 -0.54 22 22
TRAIL/TRAILR1/FADD/TRADD/RIP -0.009 0.085 -9999 0 -0.39 23 23
mol:ceramide 0.013 0.058 -9999 0 -0.26 23 23
FADD 0.002 0.046 -9999 0 -10000 0 0
MAPK8 0.047 0.082 -9999 0 -0.37 9 9
TRAF2 0.015 0.012 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.016 0.01 -9999 0 -10000 0 0
CHUK 0.015 0.032 -9999 0 -0.72 1 1
TRAIL/TRAILR1/FADD -0.013 0.1 -9999 0 -0.47 23 23
DAP3 0.015 0.014 -9999 0 -10000 0 0
CASP10 -0.021 0.09 -9999 0 -0.45 22 22
JNK cascade -0.022 0.11 -9999 0 -0.54 22 22
TRAIL (trimer) -0.015 0.15 -9999 0 -0.72 22 22
TNFRSF10C 0.016 0.01 -9999 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD -0.01 0.086 -9999 0 -0.4 23 23
TRAIL/TRAILR2/FADD -0.013 0.098 -9999 0 -0.46 23 23
cell death 0.013 0.058 -9999 0 -0.26 23 23
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.032 0.069 -9999 0 -0.29 23 23
TRAILR2 (trimer) 0.015 0.033 -9999 0 -0.72 1 1
CASP8 0.005 0.034 -9999 0 -0.3 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.009 0.084 -9999 0 -0.38 23 23
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.001 0.03 -9999 0 -10000 0 0
MAP4K1 0.013 0.023 -9999 0 -10000 0 0
MAP3K8 -0.083 0.25 -9999 0 -0.72 70 70
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0.015 0.012 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 0.052 0.042 -9999 0 -0.36 4 4
JUN -0.046 0.17 -9999 0 -0.39 98 98
MAP3K7 0.057 0.015 -9999 0 -10000 0 0
GRAP2 0.014 0.019 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
MAP2K4 0.038 0.074 -9999 0 -0.48 3 3
LAT 0.012 0.026 -9999 0 -10000 0 0
LCP2 0.013 0.024 -9999 0 -10000 0 0
MAPK8 0.023 0.034 -9999 0 -0.57 1 1
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.05 0.015 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55 0.004 0.03 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.034 0.028 -9999 0 -0.46 1 1
SNTA1 0.015 0.032 -9999 0 -0.72 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.02 0.043 -9999 0 -0.46 1 1
MAPK12 0.016 0.09 -9999 0 -0.35 29 29
CCND1 0.01 0.093 -9999 0 -0.54 12 12
p38 gamma/SNTA1 0.022 0.086 -9999 0 -0.32 30 30
MAP2K3 0.016 0.007 -9999 0 -10000 0 0
PKN1 0.015 0.012 -9999 0 -10000 0 0
G2/M transition checkpoint 0.016 0.09 -9999 0 -0.35 29 29
MAP2K6 0.008 0.097 -9999 0 -0.39 29 29
MAPT 0.03 0.044 -9999 0 -0.34 4 4
MAPK13 0.025 0.032 -9999 0 -0.54 1 1
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.008 0.076 -9999 0 -0.41 17 17
Cellular roles of Anthrax toxin

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
ANTXR1 0.013 0.037 -10000 0 -0.72 1 1
ANTXR2 0.002 0.1 -10000 0 -0.72 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.091 11 11
monocyte activation 0.012 0.069 -10000 0 -0.45 11 11
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.002 0.011 -10000 0 -10000 0 0
MAP2K7 -0.002 0.011 -10000 0 -10000 0 0
MAP2K6 -0.011 0.065 -10000 0 -0.43 12 12
CYAA 0.01 0.061 -10000 0 -0.4 11 11
MAP2K4 -0.007 0.05 -10000 0 -0.43 7 7
IL1B 0.004 0.068 -10000 0 -0.34 15 15
Channel -0.008 0.062 -10000 0 -0.43 11 11
NLRP1 -0.006 0.047 -10000 0 -0.43 6 6
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.015 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.091 11 -10000 0 11
MAPK3 -0.002 0.011 -10000 0 -10000 0 0
MAPK1 -0.002 0.011 -10000 0 -10000 0 0
PGR -0.14 0.18 -10000 0 -0.42 160 160
PA/Cellular Receptors -0.009 0.068 -10000 0 -0.47 11 11
apoptosis -0.002 0.013 -10000 0 -0.091 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.012 0.061 -10000 0 -0.4 11 11
macrophage activation 0.023 0.012 -10000 0 -10000 0 0
TNF 0.012 0.025 -10000 0 -10000 0 0
VCAM1 0.012 0.069 -10000 0 -0.46 11 11
platelet activation -0.002 0.015 -10000 0 -10000 0 0
MAPKKK cascade -0.015 0.027 0.19 4 -10000 0 4
IL18 0.003 0.053 -10000 0 -0.34 7 7
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.091 11 11
LEF -0.002 0.013 -10000 0 -0.092 11 11
CASP1 -0.012 0.046 -10000 0 -0.27 10 10
mol:cAMP -0.002 0.015 -10000 0 -10000 0 0
necrosis -0.002 0.013 -10000 0 -0.091 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.059 -10000 0 -0.41 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.009 -10000 0 -10000 0 0
CDKN1A -0.004 0.055 -10000 0 -0.88 2 2
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.015 0.014 -10000 0 -10000 0 0
FOXO3 0 0.002 -10000 0 -10000 0 0
FOXO1 -0.085 0.25 -10000 0 -0.72 72 72
FOXO4 0.029 0.016 -10000 0 -0.33 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT 0.008 0.06 -10000 0 -0.72 3 3
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.037 -10000 0 -0.55 2 2
PPARGC1A -0.066 0.23 -10000 0 -0.72 57 57
FHL2 -0.067 0.23 -10000 0 -0.72 58 58
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.011 -10000 0 -10000 0 0
HIST2H4A 0.011 0.009 -10000 0 -10000 0 0
SIRT1/FOXO3a 0 0.01 -10000 0 -10000 0 0
SIRT1 0.001 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.011 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.005 0.018 -10000 0 -0.28 1 1
apoptosis -0.002 0.012 -10000 0 -10000 0 0
SIRT1/PGC1A -0.049 0.15 -10000 0 -0.47 57 57
p53/SIRT1 0.002 0.028 0.43 2 -10000 0 2
SIRT1/FOXO4 0.001 0.017 -10000 0 -0.28 1 1
FOXO1/FHL2/SIRT1 -0.1 0.2 -10000 0 -0.47 116 116
HIST1H1E 0.022 0.018 -10000 0 -0.33 1 1
SIRT1/p300 0.001 0.011 -10000 0 -10000 0 0
muscle cell differentiation 0.002 0.031 0.47 2 -10000 0 2
TP53 0 0.016 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.002 0.012 -10000 0 -10000 0 0
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.004 0.044 -10000 0 -0.54 3 3
ACSS2 0.026 0.009 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.002 0.032 -10000 0 -0.47 2 2
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.036 0.043 -9999 0 -0.44 4 4
VEGFR1 homodimer/NRP1 -0.004 0.04 -9999 0 -0.45 4 4
mol:DAG 0.046 0.04 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.007 0.047 -9999 0 -0.42 4 4
CaM/Ca2+ 0.053 0.037 -9999 0 -10000 0 0
HIF1A 0.019 0.066 -9999 0 -0.7 4 4
GAB1 0.014 0.034 -9999 0 -0.72 1 1
AKT1 0.03 0.13 -9999 0 -0.7 1 1
PLCG1 0.046 0.04 -9999 0 -10000 0 0
NOS3 0.064 0.056 -9999 0 -0.44 1 1
CBL 0.016 0 -9999 0 -10000 0 0
mol:NO 0.063 0.055 -9999 0 -0.42 1 1
FLT1 0.033 0.05 -9999 0 -0.52 4 4
PGF 0.016 0.01 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.01 0.05 -9999 0 -0.46 1 1
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
eNOS/Hsp90 0.071 0.053 -9999 0 -10000 0 0
endothelial cell proliferation 0.053 0.041 -9999 0 -10000 0 0
mol:Ca2+ 0.046 0.039 -9999 0 -10000 0 0
MAPK3 0.062 0.035 -9999 0 -10000 0 0
MAPK1 0.062 0.035 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
PLGF homodimer 0.016 0.01 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.52 0.33 -9999 0 -0.72 385 385
VEGFA homodimer -0.005 0.054 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.043 0.049 -9999 0 -0.46 4 4
platelet activating factor biosynthetic process 0.069 0.034 -9999 0 -10000 0 0
PI3K -0.038 0.12 -9999 0 -0.6 2 2
PRKCA 0.054 0.037 -9999 0 -10000 0 0
PRKCB 0.044 0.037 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.036 0.043 -9999 0 -0.44 4 4
VEGFA -0.005 0.054 -9999 0 -10000 0 0
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 0.046 0.04 -9999 0 -10000 0 0
RASA1 0.047 0.04 -9999 0 -0.39 4 4
NRP2 0.015 0.016 -9999 0 -10000 0 0
VEGFR1 homodimer 0.033 0.05 -9999 0 -0.52 4 4
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.21 0.18 -9999 0 -0.45 50 50
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.037 0.12 -9999 0 -0.59 2 2
mol:L-citrulline 0.063 0.055 -9999 0 -0.42 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.011 0.049 -9999 0 -0.43 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.009 0.049 -9999 0 -0.46 1 1
CD2AP 0.016 0.01 -9999 0 -10000 0 0
PI3K/GAB1 -0.036 0.11 -9999 0 -0.72 1 1
PDPK1 0.021 0.13 -9999 0 -0.7 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.009 0.049 -9999 0 -0.46 1 1
mol:NADP 0.063 0.055 -9999 0 -0.42 1 1
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.01 0.047 -9999 0 -0.42 1 1
VEGFR1 homodimer/NRP2 0.037 0.043 -9999 0 -0.44 4 4
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0 0.019 -10000 0 -0.41 1 1
HDAC3 0.016 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.001 -10000 0 -10000 0 0
GATA1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC5 0 0 -10000 0 -10000 0 0
GATA2/HDAC5 -0.004 0.018 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR -0.046 0.14 -10000 0 -0.46 53 53
HDAC9 0.014 0.017 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 -0.04 0.13 -10000 0 -0.46 46 46
HDAC4/ANKRA2 -0.003 0.041 -10000 0 -0.54 3 3
HDAC5/YWHAB 0 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.027 0.003 -10000 0 -10000 0 0
GATA2 0.007 0.037 -10000 0 -10000 0 0
HDAC4/RFXANK 0 0.003 -10000 0 -10000 0 0
BCOR 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.014 0.034 -10000 0 -0.72 1 1
HDAC5 0.016 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.001 0.024 -10000 0 -0.54 1 1
Histones 0.043 0.012 -10000 0 -10000 0 0
ADRBK1 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.003 0.041 -10000 0 -0.54 3 3
HDAC4/Ubc9 0 0 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E -0.001 0.023 -10000 0 -0.54 1 1
TUBA1B 0.015 0.012 -10000 0 -10000 0 0
HDAC6 0.016 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0 0.003 -10000 0 -10000 0 0
CAMK4 0.014 0.017 -10000 0 -10000 0 0
Tubulin/HDAC6 -0.007 0.06 -10000 0 -0.46 9 9
SUMO1 0.016 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0.012 -10000 0 -10000 0 0
GATA1 0.016 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.015 0.032 -10000 0 -0.72 1 1
NR3C1 -0.048 0.21 -10000 0 -0.72 46 46
SUMO1/HDAC4 0.038 0.002 -10000 0 -10000 0 0
SRF 0.016 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0 0.006 -10000 0 -10000 0 0
Tubulin -0.01 0.07 -10000 0 -0.54 9 9
HDAC4/14-3-3 E -0.001 0.023 -10000 0 -0.54 1 1
GNB1 0.016 0.01 -10000 0 -10000 0 0
RANGAP1 0.01 0.031 -10000 0 -10000 0 0
BCL6/BCoR -0.054 0.16 -10000 0 -0.54 53 53
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -10000 0 -10000 0 0
HDAC4/SRF 0.001 0.009 -10000 0 -10000 0 0
HDAC4/ER alpha -0.14 0.22 -10000 0 -0.54 117 117
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.043 0.012 -10000 0 -10000 0 0
cell motility -0.007 0.06 -10000 0 -0.46 9 9
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.016 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 -0.058 0.22 -10000 0 -0.72 53 53
HDAC4/CaMK II delta B 0.016 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0 0.005 -10000 0 -10000 0 0
ESR1 -0.18 0.3 -10000 0 -0.72 117 117
HDAC6/HDAC11 -0.003 0.014 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.001 0.006 -10000 0 -10000 0 0
NPC 0 0.003 -10000 0 -10000 0 0
MEF2C -0.029 0.18 -10000 0 -0.72 32 32
RAN 0.016 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.023 0.091 -10000 0 -0.38 32 32
GNG2 0.015 0.032 -10000 0 -0.72 1 1
NCOR2 0.016 0 -10000 0 -10000 0 0
TUBB2A 0.003 0.096 -10000 0 -0.72 9 9
HDAC11 0.01 0.03 -10000 0 -10000 0 0
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
RANBP2 0.016 0.007 -10000 0 -10000 0 0
ANKRA2 0.012 0.056 -10000 0 -0.72 3 3
RFXANK 0.016 0.007 -10000 0 -10000 0 0
nuclear import -0.036 0.018 0.39 1 -10000 0 1
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.026 0.16 -9999 0 -0.48 1 1
CRKL 0.036 0.055 -9999 0 -0.42 1 1
mol:DAG 0.039 0.069 -9999 0 -10000 0 0
HRAS 0.064 0.053 -9999 0 -10000 0 0
MAPK8 0.031 0.038 -9999 0 -0.42 1 1
RAP1A 0.036 0.055 -9999 0 -0.42 1 1
GAB1 0.035 0.059 -9999 0 -0.44 2 2
MAPK14 0.031 0.033 -9999 0 -10000 0 0
EPO -0.005 0.056 -9999 0 -10000 0 0
PLCG1 0.039 0.07 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.016 0.008 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.007 0.087 -9999 0 -0.48 15 15
GAB1/SHC/GRB2/SOS1 -0.001 0.034 -9999 0 -0.38 1 1
EPO/EPOR (dimer) 0.027 0.037 -9999 0 -10000 0 0
IRS2 -0.071 0.2 -9999 0 -0.4 138 138
STAT1 0.032 0.12 -9999 0 -0.45 1 1
STAT5B 0.034 0.094 -9999 0 -0.4 1 1
cell proliferation 0.038 0.037 -9999 0 -0.38 1 1
GAB1/SHIP/PIK3R1/SHP2/SHC -0.036 0.092 -9999 0 -0.37 7 7
TEC 0.036 0.055 -9999 0 -0.42 1 1
SOCS3 -0.005 0.12 -9999 0 -0.72 15 15
STAT1 (dimer) 0.032 0.12 -9999 0 -0.44 1 1
JAK2 0.014 0.034 -9999 0 -0.73 1 1
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
EPO/EPOR (dimer)/JAK2 0.05 0.068 -9999 0 -0.45 1 1
EPO/EPOR 0.027 0.037 -9999 0 -10000 0 0
LYN 0.015 0.014 -9999 0 -10000 0 0
TEC/VAV2 0.047 0.055 -9999 0 -0.4 1 1
elevation of cytosolic calcium ion concentration 0.016 0.008 -9999 0 -10000 0 0
SHC1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.041 0.039 -9999 0 -10000 0 0
mol:IP3 0.039 0.069 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.13 0.19 -9999 0 -0.45 88 88
SH2B3 0.015 0.008 -9999 0 -10000 0 0
NFKB1 0.031 0.033 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.006 0.046 -9999 0 -0.26 16 16
PTPN6 0.027 0.057 -9999 0 -0.45 1 1
TEC/VAV2/GRB2 0.054 0.054 -9999 0 -0.38 1 1
EPOR 0.016 0.008 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.001 0.035 -9999 0 -0.39 1 1
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0 0.11 -9999 0 -0.72 11 11
CRKL/CBL/C3G 0.053 0.052 -9999 0 -0.38 1 1
VAV2 0.036 0.056 -9999 0 -0.42 1 1
CBL 0.036 0.055 -9999 0 -0.42 1 1
SHC/Grb2/SOS1 -0.001 0.034 -9999 0 -0.38 1 1
STAT5A 0.032 0.097 -9999 0 -0.38 3 3
GRB2 0.013 0.022 -9999 0 -10000 0 0
STAT5 (dimer) 0.031 0.15 -9999 0 -0.55 1 1
LYN/PLCgamma2 -0.012 0.078 -9999 0 -0.54 11 11
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK 0.037 0.057 -9999 0 -0.42 1 1
BCL2 -0.1 0.42 -9999 0 -0.94 104 104
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.047 0.07 -9999 0 -0.35 13 13
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.004 0.065 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.004 0.07 -9999 0 -0.46 12 12
antigen processing and presentation of peptide antigen via MHC class I -0.033 0.096 -9999 0 -0.36 25 25
CaM/Ca2+ 0.012 0.065 -9999 0 -0.32 13 13
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.027 0.074 -9999 0 -0.33 13 13
AKT1 0.015 0.13 -9999 0 -0.46 17 17
MAP2K1 0.045 0.07 -9999 0 -0.33 5 5
MAP3K11 0.038 0.063 -9999 0 -0.33 13 13
IFNGR1 0.005 0.095 -9999 0 -0.72 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII 0.006 0.07 -9999 0 -0.54 4 4
Rap1/GTP -0.006 0.036 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.014 0.074 -9999 0 -0.37 13 13
CEBPB 0.086 0.073 -9999 0 -0.46 1 1
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.021 0.072 -9999 0 -10000 0 0
STAT1 0.031 0.075 -9999 0 -0.33 13 13
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.018 0.072 -9999 0 -0.72 1 1
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.046 0.068 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.004 0.032 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.07 -9999 0 -0.35 13 13
MAPK3 0.061 0.07 -9999 0 -10000 0 0
STAT1 (dimer) -0.038 0.14 -9999 0 -0.54 24 24
MAPK1 0.061 0.07 -9999 0 -10000 0 0
JAK2 0.015 0.033 -9999 0 -0.72 1 1
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
JAK1 0.014 0.046 -9999 0 -0.72 2 2
CAMK2D 0.01 0.065 -9999 0 -0.72 4 4
DAPK1 0.083 0.054 -9999 0 -10000 0 0
SMAD7 0.043 0.074 -9999 0 -0.21 3 3
CBL/CRKL/C3G -0.001 0.047 -9999 0 -10000 0 0
PI3K -0.025 0.13 -9999 0 -0.39 51 51
IFNG -0.018 0.072 -9999 0 -0.72 1 1
apoptosis 0.059 0.052 -9999 0 -0.25 1 1
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A 0.016 0 -9999 0 -10000 0 0
CAMK2B -0.006 0.094 -9999 0 -0.72 7 7
FRAP1 0.025 0.13 -9999 0 -0.48 10 10
PRKCD 0.016 0.14 -9999 0 -0.41 28 28
RAP1B 0.016 0.01 -9999 0 -10000 0 0
negative regulation of cell growth -0.033 0.096 -9999 0 -0.36 25 25
PTPN2 0.016 0.01 -9999 0 -10000 0 0
EP300 0.017 0 -9999 0 -10000 0 0
IRF1 0.066 0.073 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.008 0.06 -9999 0 -10000 0 0
SOCS1 0.009 0.015 -9999 0 -10000 0 0
mol:GDP -0.002 0.045 -9999 0 -10000 0 0
CASP1 0.018 0.14 -9999 0 -0.34 60 60
PTGES2 0.016 0.007 -9999 0 -10000 0 0
IRF9 0.071 0.03 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.028 0.13 -9999 0 -0.38 51 51
RAP1/GDP -0.005 0.037 -9999 0 -10000 0 0
CBL 0.037 0.063 -9999 0 -0.33 13 13
MAP3K1 0.036 0.073 -9999 0 -0.34 17 17
PIAS1 0.016 0.007 -9999 0 -10000 0 0
PIAS4 0.014 0.016 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.033 0.096 -9999 0 -0.36 25 25
PTPN11 0.026 0.066 -9999 0 -0.35 13 13
CREBBP 0.016 0.032 -9999 0 -0.72 1 1
RAPGEF1 0.016 0 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.046 0.085 -10000 0 -0.29 4 4
BAG4 0.011 0.029 -10000 0 -10000 0 0
BAD 0.037 0.029 -10000 0 -10000 0 0
NFKBIA 0.015 0.032 -10000 0 -0.72 1 1
BIRC3 -0.039 0.18 -10000 0 -0.72 35 35
BAX 0.036 0.029 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.016 0.021 -10000 0 -0.07 3 3
IKBKB 0.053 0.083 -10000 0 -0.31 3 3
MAP2K2 0.053 0.025 -10000 0 -10000 0 0
MAP2K1 0.053 0.025 -10000 0 -10000 0 0
SMPD1 0.024 0.021 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.049 0.086 -10000 0 -0.32 6 6
MAP2K4 0.036 0.062 -10000 0 -0.34 11 11
protein ubiquitination 0.055 0.084 -10000 0 -0.29 6 6
EnzymeConsortium:2.7.1.37 0.057 0.029 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAF1 0.046 0.026 -10000 0 -10000 0 0
CRADD 0.017 0 -10000 0 -10000 0 0
mol:ceramide 0.028 0.03 -10000 0 -0.12 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin -0.001 0.02 -10000 0 -0.47 1 1
MADD 0.017 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.047 -10000 0 -0.37 4 4
TRADD 0.017 0 -10000 0 -10000 0 0
RELA/p50 0.016 0 -10000 0 -10000 0 0
MAPK3 0.056 0.024 -10000 0 -10000 0 0
MAPK1 0.056 0.024 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha -0.001 0.023 -10000 0 -0.54 1 1
FADD 0.04 0.089 -10000 0 -0.32 8 8
KSR1 0.038 0.028 -10000 0 -10000 0 0
MAPK8 0.043 0.06 -10000 0 -0.31 12 12
TRAF2 0.015 0.012 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.053 0.086 -10000 0 -0.62 1 1
TNF R/SODD -0.001 0.014 -10000 0 -10000 0 0
TNF 0.013 0.025 -10000 0 -10000 0 0
CYCS 0.06 0.052 0.16 86 -10000 0 86
IKBKG 0.054 0.082 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.037 0.089 -10000 0 -0.3 35 35
RELA 0.016 0 -10000 0 -10000 0 0
RIPK1 0.016 0.001 -10000 0 -10000 0 0
AIFM1 0.06 0.052 0.16 90 -10000 0 90
TNF/TNF R/SODD 0.004 0.02 -10000 0 -10000 0 0
TNFRSF1A 0.016 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.034 0.024 -10000 0 -10000 0 0
NSMAF 0.044 0.091 -10000 0 -0.39 5 5
response to hydrogen peroxide 0.001 0 -10000 0 -10000 0 0
BCL2 -0.13 0.29 -10000 0 -0.72 104 104
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.039 0.003 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.011 0.064 -9999 0 -0.72 4 4
ITGA4 0.01 0.032 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.004 0.019 -9999 0 -10000 0 0
EPO -0.006 0.056 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.003 0.015 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
alpha4/beta1 Integrin -0.003 0.015 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.011 0.027 -9999 0 -10000 0 0
lamellipodium assembly -0.031 0.11 -9999 0 -0.35 51 51
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PI3K -0.052 0.16 -9999 0 -0.54 51 51
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 0.04 0.023 -9999 0 -0.44 1 1
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
MADCAM1 0.015 0.014 -9999 0 -10000 0 0
cell adhesion 0.004 0.018 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.03 0.067 -9999 0 -0.41 11 11
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.008 0.069 -9999 0 -0.46 11 11
p130Cas/Crk/Dock1 0.051 0.069 -9999 0 -0.34 5 5
VCAM1 -0.001 0.11 -9999 0 -0.72 11 11
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.004 0.019 -9999 0 -10000 0 0
BCAR1 0.039 0.063 -9999 0 -0.37 11 11
EPOR 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
GIT1 0.015 0.016 -9999 0 -10000 0 0
Rac1/GTP -0.033 0.11 -9999 0 -0.36 51 51
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.065 0.2 -9999 0 -0.38 147 147
PDGFB-D/PDGFRB/SLAP 0.001 0.011 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0 0 -9999 0 -10000 0 0
AKT1 0.014 0.12 -9999 0 -0.36 12 12
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.018 0.079 -9999 0 -0.49 4 4
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
FGR -0.011 0.025 -9999 0 -10000 0 0
mol:Ca2+ 0.023 0.05 -9999 0 -10000 0 0
MYC -0.002 0.22 -9999 0 -0.85 29 29
SHC1 0.016 0 -9999 0 -10000 0 0
HRAS/GDP 0 0.011 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.001 0.008 -9999 0 -10000 0 0
GRB10 0.011 0.064 -9999 0 -0.72 4 4
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0.022 0.051 -9999 0 -10000 0 0
PTEN -0.002 0.12 -9999 0 -0.72 13 13
GRB2 0.013 0.022 -9999 0 -10000 0 0
GRB7 0.001 0.048 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 -0.004 0.047 -9999 0 -0.54 4 4
cell cycle arrest 0.001 0.011 -9999 0 -10000 0 0
HRAS 0.015 0.012 -9999 0 -10000 0 0
HIF1A 0.021 0.12 -9999 0 -0.41 4 4
GAB1 0.008 0.088 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.002 0.1 -9999 0 -0.32 3 3
PDGFB-D/PDGFRB 0.005 0.02 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.034 -9999 0 -0.55 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.11 0.18 -9999 0 -0.38 146 146
positive regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
mol:IP3 0.023 0.051 -9999 0 -10000 0 0
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.015 0.01 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0 0.025 -9999 0 -10000 0 0
SHB 0.013 0.037 -9999 0 -0.72 1 1
BLK -0.006 0.029 -9999 0 -10000 0 0
PTPN2 0.015 0.011 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
VAV2 0.008 0.1 -9999 0 -0.37 10 10
CBL 0.016 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0 0.009 -9999 0 -10000 0 0
LCK -0.007 0.03 -9999 0 -10000 0 0
PDGFRB 0.013 0.009 -9999 0 -10000 0 0
ACP1 0.013 0.045 -9999 0 -0.72 2 2
HCK -0.009 0.024 -9999 0 -10000 0 0
ABL1 0.019 0.064 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/CBL 0.013 0.079 -9999 0 -10000 0 0
PTPN1 0.007 0.037 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 -0.011 0.061 -9999 0 -10000 0 0
cell proliferation 0.003 0.19 -9999 0 -0.74 29 29
SLA 0.013 0.022 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.045 0.037 -9999 0 -10000 0 0
SRC -0.01 0.023 -9999 0 -10000 0 0
PI3K -0.041 0.11 -9999 0 -0.38 25 25
PDGFB-D/PDGFRB/GRB7/SHC 0.008 0.023 -9999 0 -10000 0 0
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.018 0.08 -9999 0 -0.5 4 4
LYN -0.011 0.024 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0.007 -9999 0 -10000 0 0
STAT5A 0.013 0.045 -9999 0 -0.72 2 2
NCK1-2/p130 Cas 0.005 0.019 -9999 0 -10000 0 0
SPHK1 0.001 0.072 -9999 0 -0.73 4 4
EDG1 -0.19 0.33 -9999 0 -0.72 147 147
mol:DAG 0.023 0.051 -9999 0 -10000 0 0
PLCG1 0.023 0.052 -9999 0 -10000 0 0
NHERF/PDGFRB 0.018 0.04 -9999 0 -0.46 1 1
YES1 -0.013 0.041 -9999 0 -0.78 1 1
cell migration 0.018 0.04 -9999 0 -0.46 1 1
SHC/Grb2/SOS1 0.006 0.021 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.034 -9999 0 -0.72 1 1
SLC9A3R1 -0.022 0.069 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.009 0.08 -9999 0 -0.42 14 14
FYN -0.013 0.057 -9999 0 -0.85 2 2
DOK1 0.036 0.021 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.007 -9999 0 -10000 0 0
PDGFB 0.015 0.016 -9999 0 -10000 0 0
RAC1 0.012 0.14 -9999 0 -0.44 29 29
PRKCD 0.036 0.022 -9999 0 -10000 0 0
FER 0.036 0.022 -9999 0 -10000 0 0
MAPKKK cascade 0 0.01 -9999 0 -10000 0 0
RASA1 0.036 0.022 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
NCK2 0.016 0.01 -9999 0 -10000 0 0
p62DOK/Csk 0.016 0.026 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.001 0.025 -9999 0 -0.54 1 1
chemotaxis 0.019 0.063 -9999 0 -10000 0 0
STAT1-3-5/STAT1-3-5 0.012 0.035 -9999 0 -0.35 2 2
Bovine Papilomavirus E5/PDGFRB 0.008 0.007 -9999 0 -10000 0 0
PTPRJ 0.014 0.019 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.003 0.035 -9999 0 -0.4 4 4
RGS9BP -0.015 0.076 -9999 0 -0.72 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + 0.006 0.037 -9999 0 -0.47 2 2
mol:ADP 0.013 0.025 -9999 0 -0.55 1 1
GNAT2 0.01 0.065 -9999 0 -0.72 4 4
RGS9-1/Gbeta5/R9AP -0.018 0.13 -9999 0 -0.47 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.004 0.046 -9999 0 -0.47 5 5
GRK7 0.015 0.033 -9999 0 -0.72 1 1
CNGB3 0.008 0.034 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.022 0.037 -9999 0 -0.42 2 2
Cone PDE6 -0.011 0.11 -9999 0 -0.39 37 37
Cone Metarhodopsin II -0.001 0.019 -9999 0 -0.44 1 1
Na + (4 Units) 0.008 0.036 -9999 0 -0.42 2 2
GNAT2/GDP -0.016 0.11 -9999 0 -0.4 39 39
GNB5 0.015 0.032 -9999 0 -0.72 1 1
mol:GMP (4 units) 0.026 0.05 -9999 0 -0.43 6 6
Cone Transducin -0.003 0.037 -9999 0 -0.42 4 4
SLC24A2 0.016 0.01 -9999 0 -10000 0 0
GNB3/GNGT2 0 0.003 -9999 0 -10000 0 0
GNB3 0.016 0.007 -9999 0 -10000 0 0
GNAT2/GTP -0.005 0.048 -9999 0 -0.55 4 4
CNGA3 0.002 0.061 -9999 0 -0.72 2 2
ARR3 0.016 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.006 0.037 -9999 0 -0.47 2 2
mol:Pi -0.018 0.12 -9999 0 -0.47 35 35
Cone CNG Channel 0.004 0.055 -9999 0 -0.39 8 8
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.016 0.01 -9999 0 -10000 0 0
RGS9 -0.03 0.18 -9999 0 -0.72 32 32
PDE6C 0.014 0.034 -9999 0 -0.72 1 1
GNGT2 0.016 0 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.013 0.036 -9999 0 -0.72 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.016 0 -9999 0 -10000 0 0
NFATC1 0.059 0.026 -9999 0 -0.33 2 2
NFATC2 0.024 0.062 -9999 0 -0.21 5 5
NFATC3 0.019 0.004 -9999 0 -10000 0 0
YWHAE 0.015 0.032 -9999 0 -0.72 1 1
Calcineurin A alpha-beta B1/CABIN1 0.049 0.027 -9999 0 -10000 0 0
Exportin 1/Ran/NUP214 0 0 -9999 0 -10000 0 0
mol:DAG 0 0.002 -9999 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.001 0.018 -9999 0 -10000 0 0
BCL2/BAX -0.11 0.22 -9999 0 -0.54 104 104
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.005 -9999 0 -10000 0 0
CaM/Ca2+ 0.014 0.005 -9999 0 -10000 0 0
BAX 0.015 0.014 -9999 0 -10000 0 0
MAPK14 0.016 0.004 -9999 0 -10000 0 0
BAD 0.016 0 -9999 0 -10000 0 0
CABIN1/MEF2D 0.054 0.025 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/BCL2 -0.13 0.29 -9999 0 -0.72 104 104
FKBP8 0.016 0.007 -9999 0 -10000 0 0
activation-induced cell death of T cells -0.054 0.025 -9999 0 -10000 0 0
KPNB1 0.016 0.007 -9999 0 -10000 0 0
KPNA2 -0.029 0.072 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SFN 0.012 0.048 -9999 0 -0.72 2 2
MAP3K8 -0.083 0.25 -9999 0 -0.72 70 70
NFAT4/CK1 alpha 0 0.037 -9999 0 -0.38 4 4
MEF2D/NFAT1/Cbp/p300 -0.023 0.073 -9999 0 -0.43 6 6
CABIN1 0.049 0.027 -9999 0 -10000 0 0
CALM1 0.016 0.004 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
MAP3K1 0.005 0.071 -9999 0 -0.72 4 4
CAMK4 0.014 0.017 -9999 0 -10000 0 0
mol:Ca2+ 0.001 0.004 -9999 0 -10000 0 0
MAPK3 0.016 0 -9999 0 -10000 0 0
YWHAH 0.015 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.007 0.038 -9999 0 -0.54 2 2
YWHAB 0.015 0.012 -9999 0 -10000 0 0
MAPK8 0.015 0.032 -9999 0 -0.72 1 1
MAPK9 0.016 0.007 -9999 0 -10000 0 0
YWHAG 0.016 0.01 -9999 0 -10000 0 0
FKBP1A 0.016 0.01 -9999 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.002 0.02 -9999 0 -10000 0 0
PRKCH 0.011 0.064 -9999 0 -0.72 4 4
CABIN1/Cbp/p300 -0.001 0.023 -9999 0 -0.54 1 1
CASP3 0.016 0.004 -9999 0 -10000 0 0
PIM1 0.015 0.016 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -9999 0 -10000 0 0
apoptosis -0.032 0.065 -9999 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.054 0.018 -9999 0 -10000 0 0
PRKCB 0 0 -9999 0 -10000 0 0
PRKCE 0.016 0 -9999 0 -10000 0 0
JNK2/NFAT4 0.027 0.005 -9999 0 -10000 0 0
BAD/BCL-XL 0 0 -9999 0 -10000 0 0
PRKCD 0.014 0.019 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
PRKCZ 0 0.002 -9999 0 -10000 0 0
PRKCA 0.016 0.01 -9999 0 -10000 0 0
PRKCG 0.016 0 -9999 0 -10000 0 0
PRKCQ 0.008 0.046 -9999 0 -0.72 1 1
FKBP38/BCL2 -0.11 0.22 -9999 0 -0.54 104 104
EP300 0.017 0.003 -9999 0 -10000 0 0
PRKCB1 0.008 0.036 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
NFATc/JNK1 0.064 0.033 -9999 0 -0.31 3 3
CaM/Ca2+/FKBP38 0 0.003 -9999 0 -10000 0 0
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSNK1A1 0.025 0.006 -9999 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.001 0.008 -9999 0 -10000 0 0
NFATc/ERK1 0.066 0.025 -9999 0 -0.31 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.001 0.018 -9999 0 -10000 0 0
NR4A1 0.034 0.16 -9999 0 -0.65 27 27
GSK3B 0.016 0.011 -9999 0 -10000 0 0
positive T cell selection 0.019 0.004 -9999 0 -10000 0 0
NFAT1/CK1 alpha -0.014 0.033 -9999 0 -10000 0 0
RCH1/ KPNB1 -0.022 0.035 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0.004 -9999 0 -10000 0 0
AKAP5 0.004 0.059 -9999 0 -0.72 2 2
MEF2D 0.017 0.003 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
YWHAZ 0.014 0.017 -9999 0 -10000 0 0
NFATc/p38 alpha 0.064 0.028 -9999 0 -0.31 2 2
CREBBP 0.015 0.032 -9999 0 -0.72 1 1
BCL2 -0.13 0.29 -9999 0 -0.72 104 104
Retinoic acid receptors-mediated signaling

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
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR 0.013 0.046 -10000 0 -0.72 2 2
Cbp/p300/PCAF -0.001 0.02 -10000 0 -0.47 1 1
EP300 0.016 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.09 -10000 0 -0.41 2 2
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 -0.009 0.13 0.24 19 -0.3 79 98
RAR alpha/9cRA/Cyclin H -0.003 0.024 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.004 0.11 -10000 0 -0.49 3 3
CDC2 -0.066 0.081 -10000 0 -10000 0 0
response to UV 0.001 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.002 0.026 -10000 0 -0.57 1 1
NCOR2 0.016 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.034 -10000 0 -0.55 2 2
RXRs/RARs/NRIP1/9cRA 0.024 0.13 -10000 0 -0.51 11 11
NCOA2 0.015 0.014 -10000 0 -10000 0 0
NCOA3 0.016 0.01 -10000 0 -10000 0 0
NCOA1 0.015 0.032 -10000 0 -0.72 1 1
VDR/VDR/DNA 0.013 0.046 -10000 0 -0.72 2 2
RARG 0.017 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.017 0.002 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.016 0.032 -10000 0 -0.72 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.007 0.045 -10000 0 -10000 0 0
RARA 0.038 0.02 -10000 0 -0.27 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.005 0.1 -10000 0 -0.23 85 85
PRKCA 0.019 0.012 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.018 0.13 -10000 0 -0.57 11 11
RXRG 0.033 0.044 -10000 0 -0.39 5 5
RXRA 0.042 0.032 -10000 0 -0.24 1 1
RXRB 0.037 0.013 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.034 -10000 0 -0.55 2 2
RBP1 -0.023 0.16 -10000 0 -0.72 26 26
CRBP1/9-cic-RA -0.029 0.12 -10000 0 -0.55 26 26
RARB -0.1 0.27 -10000 0 -0.72 85 85
PRKCG 0.02 0.007 -10000 0 -10000 0 0
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.022 0.12 -10000 0 -0.45 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.029 0.11 -10000 0 -0.37 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.088 -10000 0 -0.44 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 0.018 0.13 -10000 0 -0.57 11 11
positive regulation of DNA binding -0.003 0.022 -10000 0 -10000 0 0
NRIP1 0.009 0.2 -10000 0 -1.3 10 10
RXRs/RARs 0.017 0.11 -10000 0 -0.4 12 12
RXRs/RXRs/DNA/9cRA 0.016 0.052 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0.007 -10000 0 -10000 0 0
TFIIH 0 0.004 -10000 0 -10000 0 0
RAR alpha/9cRA 0 0.008 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
RAR gamma2/9cRA 0 0.002 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0.001 0.004 -9999 0 -10000 0 0
DOCK1 0.011 0.064 -9999 0 -0.72 4 4
ITGA4 0.01 0.032 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.003 0.015 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0.032 -9999 0 -0.72 1 1
alpha4/beta1 Integrin 0.003 0.016 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.004 0.018 -9999 0 -10000 0 0
lamellipodium assembly -0.041 0.13 -9999 0 -0.42 51 51
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
PI3K -0.052 0.16 -9999 0 -0.54 51 51
ARF6 0.016 0 -9999 0 -10000 0 0
TLN1 0.016 0 -9999 0 -10000 0 0
PXN 0.029 0 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
ARF6/GTP 0.004 0.017 -9999 0 -10000 0 0
cell adhesion 0.004 0.018 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.004 0.018 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ARF6/GDP 0.001 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.003 0.059 -9999 0 -0.38 11 11
p130Cas/Crk/Dock1 -0.004 0.044 -9999 0 -0.46 5 5
VCAM1 -0.001 0.11 -9999 0 -0.72 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.004 0.019 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.005 0.021 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
mol:GDP -0.005 0.02 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GIT1 0.015 0.016 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.004 0.019 -9999 0 -10000 0 0
Rac1/GTP -0.046 0.14 -9999 0 -0.47 51 51
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.008 0.055 -10000 0 -0.36 8 8
FYN 0.068 0.08 -10000 0 -0.42 9 9
LAT/GRAP2/SLP76 -0.009 0.059 -10000 0 -0.36 8 8
IKBKB 0.014 0.02 -10000 0 -10000 0 0
AKT1 0.075 0.068 -10000 0 -0.29 9 9
B2M 0.017 0.033 -10000 0 -0.73 1 1
IKBKG -0.002 0.012 -10000 0 -10000 0 0
MAP3K8 -0.083 0.25 -10000 0 -0.72 70 70
mol:Ca2+ -0.004 0.018 -10000 0 -0.095 18 18
integrin-mediated signaling pathway 0.001 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.078 0.085 -10000 0 -0.39 9 9
TRPV6 -0.03 0.14 -10000 0 -0.74 18 18
CD28 -0.003 0.11 -10000 0 -0.72 11 11
SHC1 0.065 0.084 -10000 0 -0.43 9 9
receptor internalization 0.047 0.11 -10000 0 -0.51 12 12
PRF1 0.053 0.067 -10000 0 -10000 0 0
KRAS 0.012 0.025 -10000 0 -10000 0 0
GRB2 0.013 0.022 -10000 0 -10000 0 0
COT/AKT1 0.03 0.12 -10000 0 -0.25 75 75
LAT 0.063 0.087 -10000 0 -0.43 9 9
EntrezGene:6955 0.002 0.001 -10000 0 -10000 0 0
CD3D 0.011 0.034 -10000 0 -10000 0 0
CD3E 0.018 0.008 -10000 0 -10000 0 0
CD3G -0.009 0.11 -10000 0 -0.72 10 10
RASGRP2 0.016 0.031 -10000 0 -0.17 13 13
RASGRP1 0.084 0.07 -10000 0 -0.28 7 7
HLA-A 0.015 0.025 -10000 0 -10000 0 0
RASSF5 0.013 0.021 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.001 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.056 0.031 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.004 0.02 -10000 0 -10000 0 0
PRKCA -0.004 0.034 -10000 0 -10000 0 0
GRAP2 0.014 0.019 -10000 0 -10000 0 0
mol:IP3 0.002 0.07 0.27 18 -0.29 7 25
EntrezGene:6957 0.003 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.037 0.072 -10000 0 -0.42 7 7
ORAI1 0.018 0.07 0.37 18 -10000 0 18
CSK 0.063 0.082 -10000 0 -0.42 9 9
B7 family/CD28 -0.012 0.094 -10000 0 -0.5 13 13
CHUK 0.015 0.032 -10000 0 -0.72 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.057 0.091 -10000 0 -0.48 9 9
PTPN6 0.06 0.082 -10000 0 -0.42 9 9
VAV1 0.063 0.086 -10000 0 -0.43 9 9
Monovalent TCR/CD3 0.013 0.098 -10000 0 -0.37 28 28
CBL 0.016 0 -10000 0 -10000 0 0
LCK 0.064 0.076 -10000 0 -0.39 9 9
PAG1 0.062 0.082 -10000 0 -0.42 9 9
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.054 0.092 -10000 0 -0.49 9 9
CD80 0.006 0.041 -10000 0 -10000 0 0
CD86 0.016 0.012 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.005 0.026 -10000 0 -10000 0 0
HRAS 0.015 0.012 -10000 0 -10000 0 0
GO:0035030 0.056 0.097 -10000 0 -0.43 13 13
CD8A 0.003 0.002 -10000 0 -10000 0 0
CD8B 0.014 0.026 -10000 0 -10000 0 0
PTPRC 0.006 0.057 -10000 0 -0.73 2 2
PDK1/PKC theta 0.089 0.081 -10000 0 -0.33 9 9
CSK/PAG1 0.067 0.077 -10000 0 -0.4 7 7
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I 0.025 0.029 -10000 0 -0.55 1 1
GRAP2/SLP76 -0.01 0.066 -10000 0 -0.42 8 8
STIM1 0.01 0.036 -10000 0 -10000 0 0
RAS family/GTP 0.072 0.037 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.047 0.11 -10000 0 -0.54 12 12
mol:DAG -0.006 0.047 -10000 0 -0.26 7 7
RAP1A/GDP 0.027 0.013 -10000 0 -10000 0 0
PLCG1 0.016 0.007 -10000 0 -10000 0 0
CD247 -0.028 0.16 -10000 0 -0.72 25 25
cytotoxic T cell degranulation 0.053 0.066 -10000 0 -10000 0 0
RAP1A/GTP -0.002 0.009 -10000 0 -0.061 13 13
mol:PI-3-4-5-P3 0.076 0.077 -10000 0 -0.34 9 9
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.002 0.08 0.29 17 -0.35 7 24
NRAS 0.014 0.019 -10000 0 -10000 0 0
ZAP70 0.012 0.026 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.01 0.06 -10000 0 -0.36 7 7
MALT1 0.016 0.007 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer 0.013 0.018 -10000 0 -10000 0 0
CARD11 0.011 0.029 -10000 0 -10000 0 0
PRKCB -0.005 0.034 -10000 0 -0.19 7 7
PRKCE -0.004 0.033 -10000 0 -10000 0 0
PRKCQ 0.083 0.086 -10000 0 -0.37 9 9
LCP2 0.012 0.024 -10000 0 -10000 0 0
BCL10 0.016 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.072 0.062 -10000 0 -0.25 9 9
IKK complex 0.064 0.03 -10000 0 -0.11 1 1
RAS family/GDP 0 0.003 -10000 0 -10000 0 0
MAP3K14 0.037 0.1 -10000 0 -0.27 8 8
PDPK1 0.077 0.066 -10000 0 -0.27 9 9
TCR/CD3/MHC I/CD8/Fyn 0.05 0.086 -10000 0 -0.52 8 8
p38 MAPK 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
TRAF6/ASK1 -0.027 0.1 -9999 0 -0.4 36 36
TRAF2/ASK1 -0.031 0.12 -9999 0 -0.47 35 35
ATM 0.016 0 -9999 0 -10000 0 0
MAP2K3 0.039 0.073 -9999 0 -0.36 4 4
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.028 0.12 -9999 0 -0.37 35 35
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.014 0.019 -9999 0 -10000 0 0
TXN 0.011 0.002 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
GADD45A 0.004 0.096 -9999 0 -0.72 9 9
GADD45B 0.01 0.065 -9999 0 -0.72 4 4
MAP3K1 0.005 0.071 -9999 0 -0.72 4 4
MAP3K6 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0.01 -9999 0 -10000 0 0
MAP3K4 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.036 0.13 -9999 0 -0.54 35 35
TAK1/TAB family -0.001 0.021 -9999 0 -0.49 1 1
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.015 0.012 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.011 0.04 -9999 0 -10000 0 0
TRAF6 0.021 0.019 -9999 0 -0.41 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.006 0.094 -9999 0 -0.72 7 7
CCM2 0.016 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.001 0.057 -9999 0 -0.47 7 7
MAPK11 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.029 0.12 -9999 0 -0.43 42 42
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.021 0.007 -9999 0 -10000 0 0
TAOK2 0.022 0 -9999 0 -10000 0 0
TAOK3 0.022 0 -9999 0 -10000 0 0
MAP3K7IP1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
MAP3K7IP2 0.015 0.032 -9999 0 -0.72 1 1
MAP3K5 -0.033 0.18 -9999 0 -0.72 35 35
MAP3K10 0.012 0.047 -9999 0 -0.72 2 2
MAP3K3 0.016 0 -9999 0 -10000 0 0
TRX/ASK1 -0.012 0.12 -9999 0 -0.46 35 35
GADD45/MTK1/MTK1 -0.008 0.066 -9999 0 -0.42 12 12
HIF-2-alpha transcription factor network

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
MMP14 0.005 0.018 -10000 0 -10000 0 0
oxygen homeostasis 0.015 0.014 -10000 0 -10000 0 0
TCEB2 0.016 0.01 -10000 0 -10000 0 0
TCEB1 0.014 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.008 0.072 -10000 0 -0.38 6 6
EPO 0.19 0.18 -10000 0 -0.54 5 5
FIH (dimer) 0.031 0.014 -10000 0 -10000 0 0
APEX1 0.032 0.015 -10000 0 -10000 0 0
SERPINE1 0.19 0.18 -10000 0 -0.65 5 5
FLT1 0.005 0.046 -10000 0 -0.94 1 1
ADORA2A 0.17 0.18 -10000 0 -0.6 6 6
germ cell development 0.18 0.18 -10000 0 -0.57 7 7
SLC11A2 0.19 0.18 -10000 0 -0.64 5 5
BHLHE40 0.18 0.18 -10000 0 -0.51 12 12
HIF1AN 0.031 0.014 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.051 0.13 -10000 0 -0.41 11 11
ETS1 0.034 0.036 -10000 0 -0.72 1 1
CITED2 -0.011 0.14 -10000 0 -1.2 7 7
KDR 0.005 0.047 -10000 0 -0.94 1 1
PGK1 0.19 0.18 -10000 0 -0.61 6 6
SIRT1 0.016 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.22 0.21 -10000 0 -0.62 10 10
EPAS1 0.098 0.12 -10000 0 -0.39 16 16
SP1 0.025 0.006 -10000 0 -10000 0 0
ABCG2 0.16 0.25 -10000 0 -0.71 27 27
EFNA1 0.18 0.19 -10000 0 -0.6 7 7
FXN 0.18 0.18 -10000 0 -0.63 5 5
POU5F1 0.19 0.19 -10000 0 -0.59 7 7
neuron apoptosis -0.21 0.21 0.6 10 -10000 0 10
EP300 0.016 0 -10000 0 -10000 0 0
EGLN3 0.012 0.072 -10000 0 -0.73 1 1
EGLN2 0.031 0.02 -10000 0 -10000 0 0
EGLN1 0.029 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.004 0.017 -10000 0 -10000 0 0
VHL 0.012 0.027 -10000 0 -10000 0 0
ARNT 0.033 0.012 -10000 0 -10000 0 0
SLC2A1 0.18 0.18 -10000 0 -0.58 7 7
TWIST1 0.13 0.28 -10000 0 -0.62 56 56
ELK1 0.025 0.016 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.043 0.12 -10000 0 -0.46 9 9
VEGFA 0.18 0.19 -10000 0 -0.63 6 6
CREBBP 0.015 0.032 -10000 0 -0.72 1 1
Atypical NF-kappaB 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
BCL3/RelA -0.001 0.007 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.034 0.014 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.058 0.013 -9999 0 -10000 0 0
NFKBIA 0.035 0.015 -9999 0 -0.24 1 1
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.033 0.01 -9999 0 -10000 0 0
ARRB2 0.022 0 -9999 0 -10000 0 0
REL 0.012 0.027 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.033 0.011 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.033 0.01 -9999 0 -10000 0 0
PIK3CA 0.016 0.007 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.027 0.007 -9999 0 -10000 0 0
PIK3R1 -0.055 0.22 -9999 0 -0.72 51 51
NFKB1 0.028 0.013 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.044 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.063 0.013 -9999 0 -10000 0 0
SRC 0.016 0.007 -9999 0 -10000 0 0
PI3K -0.052 0.16 -9999 0 -0.54 51 51
NF kappa B1 p50/RelA 0.044 0.007 -9999 0 -10000 0 0
IKBKB 0.014 0.02 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.01 0.03 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.001 0.12 -9999 0 -0.38 51 51
cell death 0.06 0.012 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.034 0.014 -9999 0 -10000 0 0
LCK 0 0.049 -9999 0 -10000 0 0
BCL3 0.015 0.014 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.016 0.016 -9999 0 -10000 0 0
ELF1 0.027 0.007 -9999 0 -10000 0 0
CCNA2 -0.04 0.077 -9999 0 -10000 0 0
PIK3CA 0.017 0.007 -9999 0 -10000 0 0
JAK3 0.017 0 -9999 0 -10000 0 0
PIK3R1 -0.054 0.22 -9999 0 -0.72 51 51
JAK1 0.015 0.045 -9999 0 -0.72 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.081 0.066 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
SP1 0.02 0.051 -9999 0 -0.36 9 9
IL2RA 0.034 0.026 -9999 0 -10000 0 0
IL2RB 0.014 0.023 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
IL2RG 0.008 0.039 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.033 0.14 -9999 0 -0.76 13 13
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 0.023 0.13 -9999 0 -0.94 9 9
LCK 0.001 0.049 -9999 0 -10000 0 0
GRB2 0.014 0.022 -9999 0 -10000 0 0
IL2 0.016 0.033 -9999 0 -0.72 1 1
CDK6 0.005 0.086 -9999 0 -0.72 7 7
CCND3 0.087 0.061 -9999 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP 0.006 0.042 0.27 13 -10000 0 13
DAPP1 0.055 0.022 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK 0.084 0.024 -10000 0 -10000 0 0
mol:DAG 0.077 0.036 0.22 10 -10000 0 10
HRAS 0.016 0.012 -10000 0 -10000 0 0
RAP1A 0.017 0.002 -10000 0 -10000 0 0
ARF5/GDP 0.041 0.047 -10000 0 -0.29 1 1
PLCG2 0 0.11 -10000 0 -0.72 11 11
PLCG1 0.016 0.007 -10000 0 -10000 0 0
ARF5 0.016 0 -10000 0 -10000 0 0
mol:GTP 0.005 0.039 0.24 13 -10000 0 13
ARF1/GTP 0.005 0.038 0.24 13 -10000 0 13
RHOA 0.016 0 -10000 0 -10000 0 0
YES1 0.015 0.032 -10000 0 -0.72 1 1
RAP1A/GTP 0.005 0.037 0.24 10 -10000 0 10
ADAP1 0.005 0.036 0.23 13 -10000 0 13
ARAP3 0.005 0.038 0.24 13 -10000 0 13
INPPL1 0.015 0.012 -10000 0 -10000 0 0
PREX1 -0.027 0.091 -10000 0 -0.72 4 4
ARHGEF6 -0.013 0.14 -10000 0 -0.72 21 21
ARHGEF7 0.015 0.012 -10000 0 -10000 0 0
ARF1 0.016 0.01 -10000 0 -10000 0 0
NRAS 0.015 0.018 -10000 0 -10000 0 0
FYN 0.013 0.045 -10000 0 -0.72 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
FGR 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0.052 0.024 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.015 0.012 -10000 0 -10000 0 0
ZAP70 0.012 0.026 -10000 0 -10000 0 0
mol:IP3 0.064 0.031 -10000 0 -10000 0 0
LYN 0.016 0.01 -10000 0 -10000 0 0
ARF1/GDP 0.041 0.047 -10000 0 -0.29 1 1
RhoA/GDP 0.004 0.041 0.25 12 -10000 0 12
PDK1/Src/Hsp90 0.001 0.007 -10000 0 -10000 0 0
BLNK 0.011 0.029 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.062 0.047 -10000 0 -0.28 1 1
SRC 0.016 0.007 -10000 0 -10000 0 0
PLEKHA2 0.025 0.009 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PTEN -0.017 0.11 -10000 0 -0.7 13 13
HSP90AA1 0.016 0.01 -10000 0 -10000 0 0
ARF6/GTP 0.006 0.042 0.27 13 -10000 0 13
RhoA/GTP 0.005 0.037 0.25 10 -10000 0 10
Src family/SYK family/BLNK-LAT 0.069 0.023 -10000 0 -10000 0 0
BLK 0.002 0.045 -10000 0 -10000 0 0
PDPK1 0.016 0.007 -10000 0 -10000 0 0
CYTH1 0.005 0.036 0.23 13 -10000 0 13
HCK 0.013 0.024 -10000 0 -10000 0 0
CYTH3 0.005 0.036 0.23 13 -10000 0 13
CYTH2 0.005 0.036 0.23 13 -10000 0 13
KRAS 0.013 0.025 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.005 0.031 0.2 13 -10000 0 13
SGK1 0.005 0.032 0.21 13 -10000 0 13
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.032 0.05 -10000 0 -0.19 23 23
SOS1 0.016 0 -10000 0 -10000 0 0
SYK 0.01 0.03 -10000 0 -10000 0 0
ARF6/GDP 0.004 0.043 0.26 12 -10000 0 12
mol:PI-3-4-5-P3 0.007 0.052 0.33 13 -10000 0 13
ARAP3/RAP1A/GTP 0.005 0.037 0.24 10 -10000 0 10
VAV1 0.012 0.027 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.014 0.008 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.034 0.019 0.23 3 -10000 0 3
PLEKHA1 0.021 0.044 -10000 0 -0.47 4 4
Rac1/GDP 0.041 0.047 -10000 0 -0.29 1 1
LAT 0.012 0.026 -10000 0 -10000 0 0
Rac1/GTP 0.034 0.075 -10000 0 -0.32 20 20
ITK 0.003 0.044 0.25 10 -0.36 2 12
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.089 0.043 -10000 0 -10000 0 0
LCK 0 0.049 -10000 0 -10000 0 0
BTK 0.004 0.038 0.25 10 -10000 0 10
Aurora A signaling

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
Aurora A/GADD45A 0.015 0.067 -9999 0 -0.49 9 9
BIRC5 -0.087 0.078 -9999 0 -10000 0 0
NFKBIA 0.017 0.03 -9999 0 -0.5 1 1
CPEB1 -0.003 0.12 -9999 0 -0.72 13 13
AKT1 0.017 0.023 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.008 0.016 -9999 0 -10000 0 0
NDEL1/TACC3 0.02 0.047 -9999 0 -10000 0 0
GADD45A 0.004 0.096 -9999 0 -0.72 9 9
GSK3B 0.011 0.01 -9999 0 -10000 0 0
PAK1/Aurora A 0.023 0.035 -9999 0 -10000 0 0
MDM2 0.012 0.025 -9999 0 -10000 0 0
JUB -0.01 0.14 -9999 0 -0.72 19 19
TPX2 -0.052 0.046 -9999 0 -10000 0 0
TP53 0.026 0.011 -9999 0 -10000 0 0
DLG7 -0.046 0.053 -9999 0 -10000 0 0
AURKAIP1 0.015 0.012 -9999 0 -10000 0 0
ARHGEF7 0.015 0.012 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.021 0.05 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.008 0.016 -9999 0 -10000 0 0
AURKA 0.006 0.025 -9999 0 -10000 0 0
AURKB 0.018 0.015 -9999 0 -10000 0 0
CDC25B 0.004 0.029 -9999 0 -10000 0 0
G2/M transition checkpoint -0.006 0.083 -9999 0 -0.44 19 19
mRNA polyadenylation -0.001 0.07 -9999 0 -0.44 13 13
Aurora A/CPEB -0.001 0.07 -9999 0 -0.44 13 13
Aurora A/TACC1/TRAP/chTOG -0.001 0.1 -9999 0 -0.39 31 31
BRCA1 0.012 0.025 -9999 0 -10000 0 0
centrosome duplication 0.023 0.035 -9999 0 -10000 0 0
regulation of centrosome cycle 0.017 0.046 -9999 0 -10000 0 0
spindle assembly -0.009 0.097 -9999 0 -0.39 31 31
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.047 0.044 -9999 0 -10000 0 0
CENPA 0.025 0.021 -9999 0 -10000 0 0
Aurora A/PP2A 0.023 0.011 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.001 0.033 -9999 0 -10000 0 0
negative regulation of DNA binding 0.026 0.011 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.009 -9999 0 -10000 0 0
RASA1 0.015 0.012 -9999 0 -10000 0 0
Ajuba/Aurora A -0.006 0.084 -9999 0 -0.44 19 19
mitotic prometaphase -0.003 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.025 -9999 0 -10000 0 0
TACC1 -0.028 0.17 -9999 0 -0.72 31 31
TACC3 -0.058 0.08 -9999 0 -10000 0 0
Aurora A/Antizyme1 0.017 0.014 -9999 0 -10000 0 0
Aurora A/RasGAP 0.024 0.009 -9999 0 -10000 0 0
OAZ1 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0.002 -9999 0 -10000 0 0
GIT1 0.015 0.016 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.014 0.031 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.052 0.045 -9999 0 -10000 0 0
PPP2R5D 0.015 0.012 -9999 0 -10000 0 0
Aurora A/TPX2 -0.033 0.044 -9999 0 -10000 0 0
PAK1 -0.01 0.06 -9999 0 -10000 0 0
CKAP5 0.014 0.019 -9999 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.037 0.033 -10000 0 -10000 0 0
regulation of axonogenesis -0.021 0.061 0.27 22 -10000 0 22
myoblast fusion -0.016 0.016 -10000 0 -10000 0 0
mol:GTP -0.003 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.039 0.018 -10000 0 -10000 0 0
ARF1/GTP 0.002 0.007 -10000 0 -10000 0 0
mol:GM1 0.009 0.009 -10000 0 -10000 0 0
mol:Choline 0.013 0.095 -10000 0 -0.44 22 22
lamellipodium assembly 0.001 0.01 -10000 0 -10000 0 0
MAPK3 0.03 0.014 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.04 0.018 -10000 0 -10000 0 0
ARF1 0.016 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.017 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.028 0.015 -10000 0 -10000 0 0
ARF6 0.013 0.004 -10000 0 -10000 0 0
RAB11A 0.016 0.01 -10000 0 -10000 0 0
TIAM1 0.017 0.012 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.03 0.014 -10000 0 -10000 0 0
actin filament bundle formation -0.002 0.004 -10000 0 -10000 0 0
KALRN -0.001 0.002 -10000 0 -10000 0 0
RAB11FIP3/RAB11A -0.001 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.002 0.004 -10000 0 -10000 0 0
NME1 0.013 0.029 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.003 0.005 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.001 0.01 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
liver development -0.003 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.003 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.003 0.004 -10000 0 -10000 0 0
mol:GDP -0.001 0.009 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.006 0.011 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.002 0.1 -10000 0 -0.5 21 21
RAB11FIP3 0.015 0.012 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.01 -10000 0 -10000 0 0
ruffle organization 0.021 0.061 -10000 0 -0.27 22 22
regulation of epithelial cell migration -0.003 0.005 -10000 0 -10000 0 0
PLD2 0.022 0.024 -10000 0 -0.5 1 1
PIP5K1A 0.021 0.061 -10000 0 -0.27 22 22
mol:Phosphatidic acid 0.013 0.095 -10000 0 -0.44 22 22
Rac1/GTP 0.001 0.01 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.002 0.015 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.001 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.016 -9999 0 -10000 0 0
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.016 0.007 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.027 0.003 -9999 0 -10000 0 0
FKBP3 0.016 0.007 -9999 0 -10000 0 0
Histones 0.002 0.012 -9999 0 -10000 0 0
YY1/LSF 0.03 0.038 -9999 0 -0.4 4 4
SMG5 0.014 0.02 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.043 0.016 -9999 0 -0.32 1 1
I kappa B alpha/HDAC1 0.04 0.02 -9999 0 -0.41 1 1
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.048 0.013 -9999 0 -0.23 1 1
HDAC1/Smad7 0 0.004 -9999 0 -10000 0 0
RANGAP1 0.01 0.031 -9999 0 -10000 0 0
HDAC3/TR2 0.04 0.02 -9999 0 -0.41 1 1
NuRD/MBD3 Complex 0.06 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.051 0.012 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.007 0.037 -9999 0 -10000 0 0
GATA1 0.016 0 -9999 0 -10000 0 0
Mad/Max 0 0.003 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.074 0.004 -9999 0 -10000 0 0
RBBP7 0.012 0.026 -9999 0 -10000 0 0
NPC 0 0.003 -9999 0 -10000 0 0
RBBP4 0.016 0.007 -9999 0 -10000 0 0
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA 0.035 0.022 -9999 0 -0.46 1 1
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.055 0.003 -9999 0 -10000 0 0
SIN3 complex 0.001 0.009 -9999 0 -10000 0 0
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.015 0.012 -9999 0 -10000 0 0
SAP30 0.016 0.007 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.015 0.032 -9999 0 -0.72 1 1
YY1/HDAC3 0.049 0.012 -9999 0 -10000 0 0
YY1/HDAC2 0.033 0.015 -9999 0 -0.28 1 1
YY1/HDAC1 0.032 0.013 -9999 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.06 0.003 -9999 0 -10000 0 0
PPARG -0.24 0.15 -9999 0 -0.33 388 388
HDAC8/hEST1B 0.001 0.01 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.041 0.003 -9999 0 -10000 0 0
MBD3L2 0.015 0.032 -9999 0 -0.72 1 1
ubiquitin-dependent protein catabolic process 0 0.003 -9999 0 -10000 0 0
CREBBP 0.015 0.032 -9999 0 -0.72 1 1
NuRD/MBD3/MBD3L2 Complex 0.07 0.011 -9999 0 -10000 0 0
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 0.036 0.004 -9999 0 -10000 0 0
HDAC2 0.014 0.017 -9999 0 -10000 0 0
YY1 0.029 0.016 -9999 0 -0.33 1 1
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.016 0.007 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.016 0.007 -9999 0 -10000 0 0
STAT3 0.032 0.019 -9999 0 -0.39 1 1
NFKB1 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0.007 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.003 0.032 -9999 0 -0.4 3 3
YY1/SAP30/HDAC1 0 0.011 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.032 0.019 -9999 0 -0.39 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.022 -9999 0 -0.46 1 1
histone deacetylation 0.06 0.003 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.052 0.014 -9999 0 -10000 0 0
nuclear export -0.001 0.01 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.012 0.026 -9999 0 -10000 0 0
GATA2/HDAC3 0.044 0.012 -9999 0 -10000 0 0
GATA1/HDAC1 0 0 -9999 0 -10000 0 0
GATA1/HDAC3 0.041 0.003 -9999 0 -10000 0 0
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.002 0.012 -9999 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.061 0.003 -9999 0 -10000 0 0
NuRD Complex 0.071 0.003 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.002 0.011 -9999 0 -10000 0 0
SIN3B 0.015 0.016 -9999 0 -10000 0 0
MTA2 0.016 0.007 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.038 0.002 -9999 0 -10000 0 0
HDAC complex 0.003 0.017 -9999 0 -10000 0 0
GATA1/Fog1 0 0.003 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.001 0.009 -9999 0 -10000 0 0
TNF 0.012 0.025 -9999 0 -10000 0 0
negative regulation of cell growth 0.061 0.003 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.06 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.001 0.006 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0 0.014 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.058 0.011 -9999 0 -10000 0 0
TFCP2 0.012 0.056 -9999 0 -0.72 3 3
NR2C1 0.015 0.032 -9999 0 -0.72 1 1
MBD3 0.016 0 -9999 0 -10000 0 0
MBD2 0.016 0.01 -9999 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.021 0.048 -9999 0 -0.47 5 5
ADCY5 0.023 0.024 -9999 0 -0.47 1 1
ADCY6 0.025 0 -9999 0 -10000 0 0
ADCY7 0.023 0.014 -9999 0 -10000 0 0
ADCY1 0.025 0.007 -9999 0 -10000 0 0
ADCY2 0.017 0.058 -9999 0 -0.47 7 7
ADCY3 0.025 0.005 -9999 0 -10000 0 0
ADCY8 0.024 0.013 -9999 0 -10000 0 0
PRKCE 0.015 0 -9999 0 -10000 0 0
ADCY9 0.024 0.012 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.042 0.03 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.004 0.019 -9999 0 -10000 0 0
KIRREL 0.018 0.003 -9999 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.004 0.019 -9999 0 -10000 0 0
PLCG1 0.016 0.007 -9999 0 -10000 0 0
ARRB2 0.016 0 -9999 0 -10000 0 0
WASL 0.015 0.032 -9999 0 -0.72 1 1
Nephrin/NEPH1/podocin/CD2AP 0.005 0.021 -9999 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.048 0.015 -9999 0 -10000 0 0
FYN 0.031 0.025 -9999 0 -0.34 2 2
mol:Ca2+ 0.004 0.02 -9999 0 -10000 0 0
mol:DAG 0.004 0.02 -9999 0 -10000 0 0
NPHS2 0.018 0.003 -9999 0 -10000 0 0
mol:IP3 0.004 0.02 -9999 0 -10000 0 0
regulation of endocytosis 0.003 0.027 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/Cholesterol 0.004 0.018 -9999 0 -10000 0 0
establishment of cell polarity 0.004 0.019 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.005 0.022 -9999 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.045 0.024 -9999 0 -0.31 2 2
NPHS1 0.011 0.032 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin 0.003 0.028 -9999 0 -0.33 2 2
TJP1 0.013 0.045 -9999 0 -0.72 2 2
NCK1 0.016 0 -9999 0 -10000 0 0
NCK2 0.016 0.01 -9999 0 -10000 0 0
heterophilic cell adhesion 0 0 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.004 0.021 -9999 0 -10000 0 0
CD2AP 0.016 0.01 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.006 0.023 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
TRPC6 0.015 0.099 -9999 0 -0.42 26 26
cytoskeleton organization 0.057 0.016 -9999 0 -10000 0 0
Nephrin/NEPH1 0.003 0.016 -9999 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.002 0.036 -9999 0 -0.49 2 2
Ephrin A reverse signaling

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
MAPKKK cascade 0 0.021 -9999 0 -0.47 1 1
EFNA5 0.014 0.034 -9999 0 -0.72 1 1
FYN 0.03 0.035 -9999 0 -0.42 3 3
neuron projection morphogenesis 0 0.021 -9999 0 -0.47 1 1
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0 0.021 -9999 0 -0.47 1 1
EPHA5 0.016 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.012 0.017 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.005 0.02 -9999 0 -10000 0 0
STXBP1 0.016 0 -9999 0 -10000 0 0
ACh/CHRNA1 0.019 0.012 -9999 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.006 0.021 -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 0.006 0.039 -9999 0 -10000 0 0
mol:ACh 0.01 0.016 -9999 0 -0.14 5 5
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.003 0.025 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.019 0.012 -9999 0 -10000 0 0
UNC13B 0.015 0.014 -9999 0 -10000 0 0
CHRNA1 0.015 0.012 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 0.024 0.075 -9999 0 -0.41 11 11
SNAP25 0.005 0.036 -9999 0 -0.35 5 5
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.046 0.11 -9999 0 -0.72 8 8
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.021 0.014 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.003 0.025 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.013 0.045 -9999 0 -0.72 2 2
SMAD2 0.018 0.022 -9999 0 -0.28 2 2
SMAD3 0.052 0.021 -9999 0 -10000 0 0
SMAD3/SMAD4 0.063 0.022 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.029 -9999 0 -0.46 2 2
SMAD2/SMAD2/SMAD4 0.023 0.048 -9999 0 -0.34 2 2
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.025 0.033 -9999 0 -0.41 2 2
MAP3K1 0.005 0.071 -9999 0 -0.72 4 4
TRAP-1/SMAD4 -0.002 0.033 -9999 0 -0.54 2 2
MAPK3 0.016 0 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.013 0.045 -9999 0 -0.72 2 2
KPNB1 0.016 0.007 -9999 0 -10000 0 0
TGFBRAP1 0.016 0.007 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.015 0.012 -9999 0 -10000 0 0
KPNA2 -0.029 0.072 -9999 0 -10000 0 0
PIAS4 0.015 0.016 -9999 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.02 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.021 -9999 0 -10000 0 0
ERC1 0.013 0.022 -9999 0 -10000 0 0
RIP2/NOD2 -0.018 0.035 -9999 0 -10000 0 0
NFKBIA 0.058 0.034 -9999 0 -0.73 1 1
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.014 0.02 -9999 0 -10000 0 0
RIPK2 0.014 0.02 -9999 0 -10000 0 0
IKBKG 0.009 0.017 -9999 0 -10000 0 0
IKK complex/A20 0.005 0.023 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.014 0.02 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM 0.062 0.007 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.003 0.022 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0.005 -9999 0 -10000 0 0
NOD2 -0.018 0.066 -9999 0 -10000 0 0
NFKB1 0.02 0.005 -9999 0 -10000 0 0
RELA 0.02 0.005 -9999 0 -10000 0 0
MALT1 0.016 0.007 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.016 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.002 0.012 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.016 0.01 -9999 0 -10000 0 0
CHUK 0.015 0.032 -9999 0 -0.72 1 1
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF 0.012 0.025 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.001 0.014 -9999 0 -0.31 1 1
BCL10 0.016 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.034 -9999 0 -0.72 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex 0.013 0.03 -9999 0 -10000 0 0
CYLD 0.016 0.007 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.002 0.021 -9999 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.003 0.014 -9999 0 -10000 0 0
ATM 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
PRKDC 0.01 0.03 -9999 0 -10000 0 0
ATR 0.016 0 -9999 0 -10000 0 0
UBE2L3 0.016 0 -9999 0 -10000 0 0
FANCD2 0.033 0.002 -9999 0 -10000 0 0
protein ubiquitination 0.022 0.039 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
M/R/N Complex 0 0.004 -9999 0 -10000 0 0
MRE11A 0.016 0 -9999 0 -10000 0 0
DNA-PK 0.003 0.015 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.016 0.031 -9999 0 -0.41 1 1
FANCF 0.015 0.032 -9999 0 -0.72 1 1
BRCA1 0.012 0.025 -9999 0 -10000 0 0
CCNE1 -0.018 0.066 -9999 0 -10000 0 0
CDK2/Cyclin E1 -0.019 0.038 -9999 0 -10000 0 0
FANCG 0.014 0.017 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.016 -9999 0 -10000 0 0
FANCE 0.015 0.033 -9999 0 -0.72 1 1
FANCC 0.014 0.017 -9999 0 -10000 0 0
NBN 0.016 0.007 -9999 0 -10000 0 0
FANCA -0.024 0.07 -9999 0 -10000 0 0
DNA repair 0.046 0.05 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin -0.004 0.016 -9999 0 -10000 0 0
BARD1/DNA-PK 0.005 0.021 -9999 0 -10000 0 0
FANCL 0.016 0 -9999 0 -10000 0 0
mRNA polyadenylation 0.003 0.014 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.05 0.02 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.004 0.018 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0.004 0.019 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.005 0.019 -9999 0 -10000 0 0
BRCA1/BACH1 0.012 0.025 -9999 0 -10000 0 0
BARD1 0.013 0.024 -9999 0 -10000 0 0
PCNA 0.01 0.031 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.004 0.017 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.004 0.017 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.052 0.051 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0.006 0.022 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.004 0.016 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0.001 0.041 -9999 0 -0.41 4 4
FA complex 0.048 0.02 -9999 0 -0.28 1 1
BARD1/EWS -0.002 0.012 -9999 0 -10000 0 0
RBBP8 0.025 0.05 -9999 0 -0.54 4 4
TP53 0.016 0.01 -9999 0 -10000 0 0
TOPBP1 0.015 0.012 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.004 0.019 -9999 0 -10000 0 0
BRCA1/BARD1 0.024 0.042 -9999 0 -10000 0 0
CSTF1 0.015 0.016 -9999 0 -10000 0 0
BARD1/EWS-Fli1 -0.002 0.014 -9999 0 -10000 0 0
CDK2 0.013 0.024 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 -0.078 0.08 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.016 -9999 0 -10000 0 0
EWSR1 0.016 0 -9999 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.044 0.051 -9999 0 -10000 0 0
CLOCK 0.02 0.002 -9999 0 -10000 0 0
TIMELESS/CRY2 0.051 0.016 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.024 -9999 0 -0.53 1 1
ATR 0.016 0 -9999 0 -10000 0 0
NR1D1 0.052 0.012 -9999 0 -10000 0 0
ARNTL 0.019 0.032 -9999 0 -0.72 1 1
TIMELESS 0.049 0.021 -9999 0 -10000 0 0
NPAS2 0.017 0.022 -9999 0 -10000 0 0
CRY2 0.016 0 -9999 0 -10000 0 0
mol:CO -0.016 0.006 -9999 0 -10000 0 0
CHEK1 -0.053 0.08 -9999 0 -10000 0 0
mol:HEME 0.016 0.006 -9999 0 -10000 0 0
PER1 0.002 0.1 -9999 0 -0.72 10 10
BMAL/CLOCK/NPAS2 0.05 0.028 -9999 0 -0.44 1 1
BMAL1/CLOCK 0.065 0.032 -9999 0 -0.44 1 1
S phase of mitotic cell cycle 0.044 0.051 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.044 0.052 -9999 0 -10000 0 0
mol:NADPH 0.016 0.006 -9999 0 -10000 0 0
PER1/TIMELESS 0.043 0.063 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.015 0.012 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.016 0 -9999 0 -9999 0 0
ITGB7 0.016 0 -9999 0 -9999 0 0
ITGA4 0.01 0.032 -9999 0 -9999 0 0
alpha4/beta7 Integrin -0.003 0.015 -9999 0 -9999 0 0
alpha4/beta1 Integrin -0.003 0.015 -9999 0 -9999 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.002 0.046 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.021 0.038 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.002 0.028 -9999 0 -0.64 1 1
AURKB -0.014 0.063 -9999 0 -10000 0 0
AURKC 0.013 0.022 -9999 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.005 0.011 -9999 0 -10000 0 0
BUB1B 0.005 0.023 -9999 0 -10000 0 0
PLK1 0.017 0.011 -9999 0 -10000 0 0
PLK1S1 0.008 0.007 -9999 0 -10000 0 0
KIF2A 0.026 0.01 -9999 0 -10000 0 0
regulation of mitotic centrosome separation 0.017 0.011 -9999 0 -10000 0 0
GOLGA2 0.016 0.01 -9999 0 -10000 0 0
Hec1/SPC24 0.031 0.042 -9999 0 -10000 0 0
WEE1 0.019 0.052 -9999 0 -0.55 4 4
cytokinesis 0.016 0.023 -9999 0 -10000 0 0
PP2A-alpha B56 0.067 0.027 -9999 0 -10000 0 0
AURKA 0.02 0.005 -9999 0 -10000 0 0
PICH/PLK1 -0.032 0.088 -9999 0 -0.32 3 3
CENPE -0.011 0.045 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.026 0.01 -9999 0 -10000 0 0
PPP2CA 0.016 0 -9999 0 -10000 0 0
FZR1 0.016 0.007 -9999 0 -10000 0 0
TPX2 0.019 0.006 -9999 0 -10000 0 0
PAK1 -0.011 0.058 -9999 0 -10000 0 0
SPC24 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
CLSPN 0.018 0.006 -9999 0 -10000 0 0
GORASP1 0.016 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 0.008 0.007 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.001 -9999 0 -10000 0 0
STAG2 0.016 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.015 0.013 -9999 0 -10000 0 0
spindle elongation 0.017 0.011 -9999 0 -10000 0 0
ODF2 0.013 0.015 -9999 0 -10000 0 0
BUB1 0.057 0.027 -9999 0 -10000 0 0
TPT1 0.015 0.007 -9999 0 -10000 0 0
CDC25C 0.025 0.005 -9999 0 -10000 0 0
CDC25B 0.005 0.045 -9999 0 -10000 0 0
SGOL1 0.005 0.011 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.065 0.071 -9999 0 -0.34 2 2
CDC14B 0 0.089 -9999 0 -0.56 13 13
CDC20 -0.04 0.077 -9999 0 -10000 0 0
PLK1/PBIP1 -0.024 0.027 -9999 0 -10000 0 0
mitosis -0.004 0.005 -9999 0 -10000 0 0
FBXO5 0.017 0.017 -9999 0 -10000 0 0
CDC2 -0.064 0.08 -9999 0 -10000 0 0
NDC80 -0.077 0.08 -9999 0 -10000 0 0
metaphase plate congression 0.016 0.007 -9999 0 -10000 0 0
ERCC6L -0.027 0.069 -9999 0 -0.37 3 3
NLP/gamma Tubulin 0.013 0.007 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.015 0.007 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0.016 0 -9999 0 -10000 0 0
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 0.061 0.075 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.002 0.008 -9999 0 -10000 0 0
RAB1A 0.016 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.018 0.012 -9999 0 -10000 0 0
mitotic prometaphase 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.04 -9999 0 -10000 0 0
microtubule-based process 0.046 0.042 -9999 0 -10000 0 0
Golgi organization 0.017 0.011 -9999 0 -10000 0 0
Cohesin/SA2 0 0.002 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0.001 -9999 0 -10000 0 0
KIF20A -0.09 0.077 -9999 0 -10000 0 0
APC/C/CDC20 0.032 0.036 -9999 0 -10000 0 0
PPP2R1A 0.016 0.007 -9999 0 -10000 0 0
chromosome segregation -0.024 0.026 -9999 0 -10000 0 0
PRC1 -0.065 0.081 -9999 0 -10000 0 0
ECT2 0.003 0.041 -9999 0 -10000 0 0
C13orf34 0.02 0.011 -9999 0 -10000 0 0
NUDC 0.016 0.007 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.005 0.023 -9999 0 -10000 0 0
spindle assembly 0.016 0.01 -9999 0 -10000 0 0
spindle stabilization 0.008 0.007 -9999 0 -10000 0 0
APC/C/HCDH1 0.01 0.077 -9999 0 -0.47 13 13
MKLP2/PLK1 0.047 0.042 -9999 0 -10000 0 0
CCNB1 -0.046 0.078 -9999 0 -10000 0 0
PPP1CB 0.016 0 -9999 0 -10000 0 0
BTRC 0.013 0.023 -9999 0 -10000 0 0
ROCK2 0.026 0.024 -9999 0 -0.49 1 1
TUBG1 0.015 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.018 0.034 -9999 0 -0.33 2 2
MLF1IP -0.041 0.055 -9999 0 -10000 0 0
INCENP 0.002 0.046 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.004 0.04 -9999 0 -9999 0 0
TP53 -0.003 0.013 -9999 0 -9999 0 0
Senescence -0.003 0.013 -9999 0 -9999 0 0
Apoptosis -0.003 0.013 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.007 0.026 -9999 0 -9999 0 0
MDM4 0.015 0.016 -9999 0 -9999 0 0
Glypican 2 network

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
MDK 0.004 0.043 -9999 0 -9999 0 0
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine -0.007 0.025 -9999 0 -9999 0 0
neuron projection morphogenesis -0.007 0.025 -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 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.001 -9999 0 -9999 0 0
MDM2/SUMO1 0.039 0.008 -9999 0 -9999 0 0
HDAC4 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.001 -9999 0 -9999 0 0
SUMO1 0.016 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.022 0.002 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.036 0.003 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.016 0.007 -9999 0 -9999 0 0
SUMO1/HDAC4 0.038 0.002 -9999 0 -9999 0 0
SUMO1/HDAC1 0.038 0.002 -9999 0 -9999 0 0
RANGAP1 0.01 0.031 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.002 0.014 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.027 0.003 -9999 0 -9999 0 0
Ran/GTP 0.001 0.004 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.012 0.025 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.001 0.006 -9999 0 -9999 0 0
NPC 0 0.003 -9999 0 -9999 0 0
PIAS2 0.016 0 -9999 0 -9999 0 0
PIAS1 0.016 0.007 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.016 0 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.016 0.01 -9999 0 -10000 0 0
TCEB1 0.014 0.019 -9999 0 -10000 0 0
HIF1A/p53 0.041 0.029 -9999 0 -10000 0 0
HIF1A 0.032 0.03 -9999 0 -0.29 2 2
COPS5 0.016 0.007 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.004 0.019 -9999 0 -10000 0 0
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.011 0.061 -9999 0 -10000 0 0
ARNT/IPAS 0 0 -9999 0 -10000 0 0
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.016 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.041 0.029 -9999 0 -10000 0 0
CUL2 0.016 0.007 -9999 0 -10000 0 0
OS9 0.016 0.01 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.001 0.01 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.041 0.029 -9999 0 -10000 0 0
PHD1-3/OS9 0.018 0.041 -9999 0 -0.41 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.001 0.024 -9999 0 -10000 0 0
VHL 0.012 0.027 -9999 0 -10000 0 0
HSP90AA1 0.016 0.01 -9999 0 -10000 0 0
HIF1A/JAB1 0.041 0.029 -9999 0 -10000 0 0
EGLN3 -0.017 0.071 -9999 0 -0.72 1 1
EGLN2 0.014 0.017 -9999 0 -10000 0 0
EGLN1 0.015 0.016 -9999 0 -10000 0 0
TP53 0.016 0.01 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.05 0.009 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0.015 0.012 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF 0.048 0.035 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.003 0.035 -10000 0 -0.4 4 4
MAPK9 0.011 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.013 0.015 -10000 0 -10000 0 0
GNB1/GNG2 -0.001 0.021 -10000 0 -0.47 1 1
GNB1 0.016 0.01 -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 0.011 0 -10000 0 -10000 0 0
Gs family/GTP -0.003 0.033 -10000 0 -0.44 3 3
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.001 0.008 0.1 3 -10000 0 3
GNAL 0.012 0.056 -10000 0 -0.72 3 3
GNG2 0.015 0.032 -10000 0 -0.72 1 1
CRH 0.013 0.022 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.01 0.019 -10000 0 -0.42 1 1
MAPK11 0.011 0 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.001 0.005 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0.006 -9999 0 -10000 0 0
AP2 -0.001 0.01 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.008 -9999 0 -10000 0 0
CLTB 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.032 0.001 -9999 0 -10000 0 0
CD4 0.016 0 -9999 0 -10000 0 0
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.001 0.002 -9999 0 -10000 0 0
ARFGAP1 0.013 0.012 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.011 -9999 0 -0.23 1 1
ARF1/GTP -0.001 0.009 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.034 0.006 -9999 0 -10000 0 0
mol:Choline 0 0.011 -9999 0 -0.24 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.015 0.01 -9999 0 -10000 0 0
DDEF1 0 0.011 -9999 0 -0.24 1 1
ARF1/GDP 0 0.007 -9999 0 -10000 0 0
AP2M1 0.016 0.01 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.004 -9999 0 -10000 0 0
Rac/GTP 0 0.002 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.009 -9999 0 -10000 0 0
ARFIP2 0.013 0.017 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.03 0.004 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.004 -9999 0 -10000 0 0
GGA3 0.016 0.007 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.005 -9999 0 -10000 0 0
AP2A1 0.015 0.014 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.034 0.004 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.006 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP -0.001 0.007 -9999 0 -10000 0 0
CYTH2 0.001 0.002 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.001 0.006 -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 0.045 0.002 -9999 0 -10000 0 0
PLD2 0 0.011 -9999 0 -0.24 1 1
ARF-GAP1/v-SNARE 0.013 0.012 -9999 0 -10000 0 0
PIP5K1A 0 0.011 -9999 0 -0.23 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.007 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0.011 -9999 0 -0.24 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.013 0.012 -9999 0 -10000 0 0
GOSR2 0 0.005 -9999 0 -10000 0 0
USO1 0 0.005 -9999 0 -10000 0 0
GBF1 0 0.005 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.01 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0.009 -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 -0.001 0.023 -9999 0 -0.54 1 1
FBXW11 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
CHUK 0.015 0.032 -9999 0 -0.72 1 1
NF kappa B2 p100/RelB 0.002 0.022 -9999 0 -0.38 1 1
NFKB1 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.002 0.012 -9999 0 -10000 0 0
RELB 0.013 0.024 -9999 0 -10000 0 0
NFKB2 0.015 0.012 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.001 0.013 -9999 0 -10000 0 0
regulation of B cell activation 0.001 0.012 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 526 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.E2.A1BD TCGA.E2.A1BC TCGA.E2.A1B6 TCGA.E2.A1B5
109_MAP3K5 0.07 0.07 0.073 0.073
47_PPARGC1A 0.016 0.016 0.016 -0.15
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 0.016 0.016 0.016 0.016
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR 0 0 -0.41 0.087
30_TGFB1/TGF beta receptor Type II 0.016 0.015 0.015 0.016
84_STAT5B -0.25 -0.045 -0.037 -0.25
84_STAT5A -0.25 -0.045 -0.037 -0.25
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/2841012/2.GDAC_MergeDataFiles.Finished/BRCA-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = 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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