Head and Neck Squamous Cell Carcinoma: PARADIGM pathway analysis of mRNASeq expression data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 38 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
TCGA08_retinoblastoma 120
Syndecan-1-mediated signaling events 113
Syndecan-4-mediated signaling events 94
IL4-mediated signaling events 84
HIF-1-alpha transcription factor network 72
Osteopontin-mediated events 58
amb2 Integrin signaling 49
IL23-mediated signaling events 44
Glypican 2 network 43
Syndecan-2-mediated signaling events 42
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
TCGA08_retinoblastoma 120 967 8 -0.31 0.14 1000 -1000 -0.026 -1000
Syndecan-1-mediated signaling events 113 3855 34 -0.72 0.013 1000 -1000 -0.076 -1000
Syndecan-4-mediated signaling events 94 6321 67 -0.74 0.099 1000 -1000 -0.11 -1000
IL4-mediated signaling events 84 7724 91 -1.4 1.3 1000 -1000 -0.22 -1000
HIF-1-alpha transcription factor network 72 5547 76 -1 0.022 1000 -1000 -0.2 -1000
Osteopontin-mediated events 58 2223 38 -0.45 0.013 1000 -1000 -0.14 -1000
amb2 Integrin signaling 49 4058 82 -0.61 0.013 1000 -1000 -0.12 -1000
IL23-mediated signaling events 44 2671 60 -0.7 0.013 1000 -1000 -0.2 -1000
Glypican 2 network 43 173 4 -0.12 -0.12 1000 -1000 -0.057 -1000
Syndecan-2-mediated signaling events 42 2923 69 -0.44 0.027 1000 -1000 -0.065 -1000
Endothelins 40 3848 96 -0.55 0.014 1000 -1000 -0.1 -1000
TCGA08_p53 36 257 7 -0.24 0.12 1000 -1000 -0.019 -1000
p75(NTR)-mediated signaling 30 3755 125 -0.55 0.013 1000 -1000 -0.13 -1000
Visual signal transduction: Cones 28 1082 38 -0.31 0.013 1000 -1000 -0.098 -1000
Visual signal transduction: Rods 25 1313 52 -0.46 0.013 1000 -1000 -0.11 -1000
ErbB4 signaling events 24 1658 69 -0.38 0.091 1000 -1000 -0.1 -1000
FOXA2 and FOXA3 transcription factor networks 24 1114 46 -0.54 0.021 1000 -1000 -0.13 -1000
Effects of Botulinum toxin 24 636 26 -0.23 0.013 1000 -1000 -0.087 -1000
BMP receptor signaling 23 1931 81 -0.41 0.047 1000 -1000 -0.13 -1000
Calcium signaling in the CD4+ TCR pathway 23 720 31 -0.48 0.014 1000 -1000 -0.11 -1000
Signaling events regulated by Ret tyrosine kinase 22 1848 82 -0.18 0.013 1000 -1000 -0.11 -1000
Glypican 1 network 21 1055 48 -0.4 0.035 1000 -1000 -0.067 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 21 1463 68 -0.52 0.025 1000 -1000 -0.16 -1000
PDGFR-beta signaling pathway 21 2095 97 -0.21 0.014 1000 -1000 -0.12 -1000
Ephrin B reverse signaling 20 1006 48 -0.17 0.15 1000 -1000 -0.087 -1000
Neurotrophic factor-mediated Trk receptor signaling 20 2489 120 -0.28 0.12 1000 -1000 -0.092 -1000
IL12-mediated signaling events 19 1657 87 -0.26 0.098 1000 -1000 -0.17 -1000
TCR signaling in naïve CD8+ T cells 19 1813 93 -0.33 0.17 1000 -1000 -0.097 -1000
Coregulation of Androgen receptor activity 17 1364 76 -0.52 0.042 1000 -1000 -0.076 -1000
Thromboxane A2 receptor signaling 17 1864 105 -0.14 0.022 1000 -1000 -0.088 -1000
Glucocorticoid receptor regulatory network 17 1977 114 -0.64 0.24 1000 -1000 -0.1 -1000
LPA4-mediated signaling events 16 196 12 -0.11 0.022 1000 -1000 -0.036 -1000
Caspase cascade in apoptosis 16 1223 74 -0.14 0.049 1000 -1000 -0.063 -1000
Signaling mediated by p38-gamma and p38-delta 16 247 15 -0.14 0.024 1000 -1000 -0.042 -1000
Canonical Wnt signaling pathway 16 849 51 -0.34 0.12 1000 -1000 -0.092 -1000
EPHB forward signaling 16 1405 85 -0.3 0.12 1000 -1000 -0.12 -1000
Nongenotropic Androgen signaling 16 867 52 -0.11 0.044 1000 -1000 -0.082 -1000
BCR signaling pathway 16 1679 99 -0.17 0.031 1000 -1000 -0.13 -1000
Reelin signaling pathway 15 882 56 -0.25 0.013 1000 -1000 -0.099 -1000
IL1-mediated signaling events 15 940 62 -0.24 0.073 1000 -1000 -0.12 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 15 1203 78 -0.11 0.035 1000 -1000 -0.11 -1000
Signaling events mediated by the Hedgehog family 14 735 52 -0.43 0.071 1000 -1000 -0.11 -1000
Presenilin action in Notch and Wnt signaling 14 868 61 -0.34 0.038 1000 -1000 -0.097 -1000
Regulation of nuclear SMAD2/3 signaling 13 1876 136 -0.38 0.37 1000 -1000 -0.11 -1000
Nephrin/Neph1 signaling in the kidney podocyte 13 458 34 -0.063 0.013 1000 -1000 -0.08 -1000
Signaling events mediated by PTP1B 13 1000 76 -0.22 0.041 1000 -1000 -0.11 -1000
Syndecan-3-mediated signaling events 13 459 35 -0.23 0.013 1000 -1000 -0.097 -1000
Integrins in angiogenesis 13 1131 84 -0.45 0.019 1000 -1000 -0.13 -1000
LPA receptor mediated events 13 1390 102 -0.61 0.016 1000 -1000 -0.12 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 13 444 33 -0.31 0.037 1000 -1000 -0.088 -1000
IL27-mediated signaling events 12 617 51 -0.16 0.025 1000 -1000 -0.11 -1000
EGFR-dependent Endothelin signaling events 12 259 21 -0.14 0.013 1000 -1000 -0.095 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 11 629 54 -0.34 0.028 1000 -1000 -0.12 -1000
Angiopoietin receptor Tie2-mediated signaling 11 982 88 -0.44 0.077 1000 -1000 -0.15 -1000
Regulation of Androgen receptor activity 11 795 70 -0.54 0.034 1000 -1000 -0.09 -1000
Ephrin A reverse signaling 10 70 7 -0.02 0.003 1000 -1000 -0.04 -1000
Arf6 signaling events 10 672 62 -0.16 0.044 1000 -1000 -0.081 -1000
PDGFR-alpha signaling pathway 10 477 44 -0.17 0.03 1000 -1000 -0.086 -1000
IFN-gamma pathway 10 697 68 -0.18 0.041 1000 -1000 -0.12 -1000
Wnt signaling 10 74 7 -0.074 0.013 1000 -1000 -0.053 -1000
ErbB2/ErbB3 signaling events 9 587 65 -0.38 0.026 1000 -1000 -0.093 -1000
Fc-epsilon receptor I signaling in mast cells 9 885 97 -0.22 0.036 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 9 342 37 -0.078 0.013 1000 -1000 -0.1 -1000
TRAIL signaling pathway 9 459 48 -0.084 0.017 1000 -1000 -0.087 -1000
Cellular roles of Anthrax toxin 8 338 39 -0.049 0.019 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class III 8 356 40 -0.21 0.091 1000 -1000 -0.061 -1000
S1P1 pathway 8 318 36 -0.22 0.014 1000 -1000 -0.078 -1000
Signaling mediated by p38-alpha and p38-beta 8 379 44 -0.17 0.013 1000 -1000 -0.074 -1000
Regulation of Telomerase 8 890 102 -0.18 0.046 1000 -1000 -0.14 -1000
Nectin adhesion pathway 7 461 63 -0.22 0.046 1000 -1000 -0.091 -1000
Plasma membrane estrogen receptor signaling 7 664 86 -0.3 0.039 1000 -1000 -0.12 -1000
S1P3 pathway 7 294 42 -0.22 0.041 1000 -1000 -0.076 -1000
Signaling events mediated by PRL 7 264 34 -0.14 0.032 1000 -1000 -0.065 -1000
Class IB PI3K non-lipid kinase events 7 21 3 -0.004 -1000 1000 -1000 -0.025 -1000
JNK signaling in the CD4+ TCR pathway 6 110 17 -0.042 0.036 1000 -1000 -0.089 -1000
a4b1 and a4b7 Integrin signaling 6 34 5 -0.022 0.011 1000 -1000 -0.047 -1000
RXR and RAR heterodimerization with other nuclear receptor 6 333 52 -0.24 0.03 1000 -1000 -0.08 -1000
FAS signaling pathway (CD95) 6 292 47 -0.084 0.014 1000 -1000 -0.064 -1000
Retinoic acid receptors-mediated signaling 6 390 58 -0.15 0.018 1000 -1000 -0.11 -1000
IL2 signaling events mediated by PI3K 6 370 58 -0.16 0.056 1000 -1000 -0.11 -1000
Stabilization and expansion of the E-cadherin adherens junction 6 497 74 -0.37 0.084 1000 -1000 -0.11 -1000
Ras signaling in the CD4+ TCR pathway 6 116 17 -0.029 0.025 1000 -1000 -0.057 -1000
Noncanonical Wnt signaling pathway 5 152 26 -0.074 0.013 1000 -1000 -0.12 -1000
Ceramide signaling pathway 5 450 76 -0.14 0.043 1000 -1000 -0.083 -1000
Paxillin-dependent events mediated by a4b1 5 190 36 -0.078 0.025 1000 -1000 -0.098 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 5 234 45 -0.084 0.041 1000 -1000 -0.12 -1000
IL6-mediated signaling events 5 442 75 -0.1 0.067 1000 -1000 -0.13 -1000
Rapid glucocorticoid signaling 5 107 20 -0.06 0.013 1000 -1000 -0.051 -1000
FOXM1 transcription factor network 5 261 51 -0.32 0.14 1000 -1000 -0.22 -1000
p38 MAPK signaling pathway 5 252 44 -0.16 0.021 1000 -1000 -0.08 -1000
EPO signaling pathway 4 226 55 -0.054 0.04 1000 -1000 -0.12 -1000
Class I PI3K signaling events mediated by Akt 4 273 68 -0.14 0.064 1000 -1000 -0.085 -1000
IL2 signaling events mediated by STAT5 4 107 22 -0.056 0.045 1000 -1000 -0.067 -1000
IGF1 pathway 4 254 57 -0.054 0.038 1000 -1000 -0.12 -1000
Insulin Pathway 4 350 74 -0.29 0.042 1000 -1000 -0.11 -1000
Sphingosine 1-phosphate (S1P) pathway 3 109 28 -0.095 0.019 1000 -1000 -0.086 -1000
Circadian rhythm pathway 3 80 22 -0.092 0.047 1000 -1000 -0.071 -1000
Aurora A signaling 3 190 60 -0.075 0.033 1000 -1000 -0.079 -1000
Arf6 downstream pathway 3 143 43 -0.03 0.025 1000 -1000 -0.052 -1000
HIF-2-alpha transcription factor network 3 139 43 -0.24 0.025 1000 -1000 -0.12 -1000
Regulation of p38-alpha and p38-beta 3 165 54 -0.12 0.032 1000 -1000 -0.081 -1000
VEGFR1 specific signals 3 189 56 -0.12 0.044 1000 -1000 -0.11 -1000
S1P4 pathway 3 89 25 -0.035 0.029 1000 -1000 -0.073 -1000
Aurora B signaling 3 243 67 -0.3 0.046 1000 -1000 -0.089 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 2 251 85 -0.092 0.066 1000 -1000 -0.099 -1000
Hedgehog signaling events mediated by Gli proteins 2 139 65 -0.089 0.068 1000 -1000 -0.09 -1000
ceramide signaling pathway 2 104 49 -0.024 0.048 1000 -1000 -0.065 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 2 169 83 -0.069 0.067 1000 -1000 -0.1 -1000
TCGA08_rtk_signaling 2 52 26 -0.031 0.048 1000 -1000 -0.029 -1000
Class I PI3K signaling events 2 180 73 -0.12 0.042 1000 -1000 -0.1 -1000
Arf6 trafficking events 2 168 71 -0.27 0.047 1000 -1000 -0.1 -1000
E-cadherin signaling events 2 10 5 -0.005 0.011 1000 -1000 -0.059 -1000
Canonical NF-kappaB pathway 1 43 39 -0.028 0.09 1000 -1000 -0.12 -1000
Signaling events mediated by HDAC Class II 1 107 75 -0.04 0.032 1000 -1000 -0.091 -1000
PLK1 signaling events 1 148 85 -0.013 0.034 1000 -1000 -0.07 -1000
S1P5 pathway 1 20 17 -0.007 0.029 1000 -1000 -0.071 -1000
Signaling events mediated by VEGFR1 and VEGFR2 1 238 125 -0.088 0.099 1000 -1000 -0.13 -1000
E-cadherin signaling in the nascent adherens junction 1 82 76 -0.016 0.06 1000 -1000 -0.11 -1000
E-cadherin signaling in keratinocytes 1 67 43 -0.016 0.052 1000 -1000 -0.088 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 10 23 -0.006 0.05 1000 -1000 -0.097 -1000
BARD1 signaling events 0 53 57 -0.007 0.074 1000 -1000 -0.082 -1000
PLK2 and PLK4 events 0 0 3 0.013 0.025 1000 -1000 -0.025 -1000
Aurora C signaling 0 5 7 -0.004 0.011 1000 -1000 -0.058 -1000
Insulin-mediated glucose transport 0 27 32 -0.081 0.05 1000 -1000 -0.083 -1000
mTOR signaling pathway 0 0 53 0 0.037 1000 -1000 -0.077 -1000
Signaling events mediated by HDAC Class I 0 59 104 -0.14 0.063 1000 -1000 -0.088 -1000
FoxO family signaling 0 47 64 -0.016 0.16 1000 -1000 -0.1 -1000
Atypical NF-kappaB pathway 0 18 31 -0.014 0.048 1000 -1000 -0.089 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 0 0.031 1000 -1000 -0.085 -1000
Arf1 pathway 0 7 54 -0.005 0.036 1000 -1000 -0.059 -1000
Alternative NF-kappaB pathway 0 10 13 -0.004 0.013 1000 -1000 -0.085 -1000
Total 1862 109590 7203 -29 -990 131000 -131000 -12 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.1 0.24 -10000 0 -0.6 57 57
CDKN2C 0.009 0.15 -10000 0 -0.73 11 11
CDKN2A -0.31 0.38 -10000 0 -0.77 124 124
CCND2 0.12 0.14 0.24 155 -0.15 1 156
RB1 -0.13 0.15 -10000 0 -0.26 154 154
CDK4 0.14 0.16 0.27 157 -10000 0 157
CDK6 0.14 0.16 0.27 154 -10000 0 154
G1/S progression 0.12 0.16 0.26 154 -10000 0 154
Syndecan-1-mediated signaling events

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
TGFB1 0.011 0.047 -9999 0 -0.8 1 1
CCL5 -0.097 0.28 -9999 0 -0.8 41 41
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.45 0.17 -9999 0 -0.54 221 221
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 -0.42 0.17 -9999 0 -0.51 221 221
Syndecan-1/Syntenin -0.42 0.17 -9999 0 -0.51 221 221
MAPK3 -0.38 0.16 -9999 0 -0.62 43 43
HGF/MET -0.019 0.098 -9999 0 -0.52 11 11
TGFB1/TGF beta receptor Type II 0.011 0.047 -9999 0 -0.8 1 1
BSG 0.013 0 -9999 0 -10000 0 0
keratinocyte migration -0.42 0.16 -9999 0 -0.5 221 221
Syndecan-1/RANTES -0.48 0.23 -9999 0 -0.58 231 231
Syndecan-1/CD147 -0.4 0.16 -9999 0 -0.49 216 216
Syndecan-1/Syntenin/PIP2 -0.41 0.16 -9999 0 -0.5 221 221
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.4 0.15 -9999 0 -0.48 221 221
MMP7 -0.13 0.3 -9999 0 -0.76 55 55
HGF -0.008 0.12 -9999 0 -0.7 9 9
Syndecan-1/CASK -0.43 0.17 -9999 0 -0.52 221 221
Syndecan-1/HGF/MET -0.42 0.17 -9999 0 -0.5 225 225
regulation of cell adhesion -0.36 0.15 -9999 0 -0.59 43 43
HPSE 0.009 0.053 -9999 0 -0.64 2 2
positive regulation of cell migration -0.45 0.17 -9999 0 -0.54 221 221
SDC1 -0.46 0.18 -9999 0 -0.55 221 221
Syndecan-1/Collagen -0.45 0.17 -9999 0 -0.54 221 221
PPIB 0.013 0 -9999 0 -10000 0 0
MET 0.009 0.06 -9999 0 -0.72 2 2
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.61 0.35 -9999 0 -0.8 230 230
MAPK1 -0.38 0.16 -9999 0 -0.62 43 43
homophilic cell adhesion -0.45 0.17 -9999 0 -0.54 221 221
MMP1 -0.72 0.25 -9999 0 -0.8 271 271
Syndecan-4-mediated 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
PTK2 -0.26 0.23 -9999 0 -0.46 170 170
Syndecan-4/Syndesmos -0.42 0.25 -9999 0 -0.61 168 168
positive regulation of JNK cascade -0.42 0.22 -9999 0 -0.57 184 184
Syndecan-4/ADAM12 -0.74 0.33 -9999 0 -0.94 212 212
CCL5 -0.097 0.28 -9999 0 -0.8 41 41
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 -0.27 0.39 -9999 0 -0.8 105 105
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG 0.007 0.013 -9999 0 -10000 0 0
ADAM12 -0.63 0.33 -9999 0 -0.8 239 239
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.12 0.061 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.61 0.34 -9999 0 -0.8 203 203
Syndecan-4/CXCL12/CXCR4 -0.44 0.24 -9999 0 -0.61 184 184
Syndecan-4/Laminin alpha3 -0.53 0.33 -9999 0 -0.74 189 189
MDK -0.01 0.14 -9999 0 -0.78 9 9
Syndecan-4/FZD7 -0.42 0.26 -9999 0 -0.61 169 169
Syndecan-4/Midkine -0.43 0.26 -9999 0 -0.62 172 172
FZD7 0 0.1 -9999 0 -0.77 5 5
Syndecan-4/FGFR1/FGF -0.4 0.23 -9999 0 -0.57 176 176
THBS1 -0.02 0.16 -9999 0 -0.77 13 13
integrin-mediated signaling pathway -0.47 0.3 -9999 0 -0.68 177 177
positive regulation of MAPKKK cascade -0.42 0.22 -9999 0 -0.57 184 184
Syndecan-4/TACI -0.47 0.28 -9999 0 -0.66 185 185
CXCR4 -0.019 0.16 -9999 0 -0.8 12 12
cell adhesion -0.22 0.2 -9999 0 -0.47 90 90
Syndecan-4/Dynamin -0.42 0.25 -9999 0 -0.61 168 168
Syndecan-4/TSP1 -0.43 0.27 -9999 0 -0.64 168 168
Syndecan-4/GIPC -0.42 0.25 -9999 0 -0.61 168 168
Syndecan-4/RANTES -0.47 0.29 -9999 0 -0.67 183 183
ITGB1 0.011 0.047 -9999 0 -0.8 1 1
LAMA1 -0.37 0.41 -9999 0 -0.8 143 143
LAMA3 -0.22 0.37 -9999 0 -0.8 87 87
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.099 0.072 -9999 0 -0.77 1 1
Syndecan-4/alpha-Actinin -0.42 0.25 -9999 0 -0.61 168 168
TFPI 0.009 0.06 -9999 0 -0.72 2 2
F2 -0.07 0.23 -9999 0 -0.81 26 26
alpha5/beta1 Integrin -0.22 0.29 -9999 0 -0.61 106 106
positive regulation of cell adhesion -0.68 0.36 -9999 0 -0.87 214 214
ACTN1 0.011 0.047 -9999 0 -0.8 1 1
TNC -0.15 0.33 -9999 0 -0.8 61 61
Syndecan-4/CXCL12 -0.45 0.25 -9999 0 -0.62 181 181
FGF6 0.003 0.005 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.048 0.19 -9999 0 -0.65 28 28
TNFRSF13B -0.093 0.27 -9999 0 -0.8 39 39
FGF2 -0.012 0.13 -9999 0 -0.68 11 11
FGFR1 0.008 0.066 -9999 0 -0.8 2 2
Syndecan-4/PI-4-5-P2 -0.42 0.25 -9999 0 -0.62 168 168
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.44 0.41 -9999 0 -0.8 170 170
cell migration -0.041 0.02 -9999 0 -10000 0 0
PRKCD 0.026 0.012 -9999 0 -10000 0 0
vasculogenesis -0.41 0.26 -9999 0 -0.61 168 168
SDC4 -0.45 0.27 -9999 0 -0.65 168 168
Syndecan-4/Tenascin C -0.5 0.32 -9999 0 -0.72 177 177
Syndecan-4/PI-4-5-P2/PKC alpha -0.097 0.048 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.42 0.25 -9999 0 -0.61 168 168
MMP9 -0.6 0.35 -9999 0 -0.8 230 230
Rac1/GTP -0.23 0.21 -9999 0 -0.48 90 90
cytoskeleton organization -0.4 0.24 -9999 0 -0.58 168 168
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.42 0.25 -9999 0 -0.61 169 169
IL4-mediated signaling events

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
BCL2L1 -1.1 0.48 -10000 0 -1.4 195 195
STAT6 (cleaved dimer) -1.2 0.51 -10000 0 -1.4 220 220
IGHG1 -0.33 0.12 -10000 0 -0.47 47 47
IGHG3 -1.1 0.46 -10000 0 -1.3 212 212
AKT1 -0.42 0.18 -10000 0 -0.83 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.31 0.17 -10000 0 -0.8 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.44 0.18 -10000 0 -0.84 14 14
THY1 -1.2 0.54 -10000 0 -1.5 202 202
MYB -0.054 0.2 -10000 0 -0.65 31 31
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.55 0.24 -10000 0 -0.95 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.44 0.18 -10000 0 -0.84 14 14
SP1 0.011 0.011 -10000 0 -10000 0 0
INPP5D 0.011 0.038 -10000 0 -0.64 1 1
SOCS5 0.036 0.01 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -1.2 0.49 -10000 0 -1.4 219 219
SOCS1 -0.68 0.25 -10000 0 -0.86 149 149
SOCS3 -0.45 0.2 -10000 0 -0.99 11 11
FCER2 -0.79 0.35 -10000 0 -1 140 140
PARP14 0.008 0.066 -10000 0 -0.8 2 2
CCL17 -1.1 0.49 -10000 0 -1.4 200 200
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.35 0.15 -10000 0 -0.8 11 11
T cell proliferation -1.2 0.52 -10000 0 -1.5 203 203
IL4R/JAK1 -1.1 0.49 -10000 0 -1.4 200 200
EGR2 -1.1 0.49 -10000 0 -1.4 199 199
JAK2 -0.031 0.019 -10000 0 -10000 0 0
JAK3 -0.023 0.18 -10000 0 -0.8 16 16
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.001 0.005 -10000 0 -10000 0 0
COL1A2 -0.59 0.36 -10000 0 -0.93 155 155
CCL26 -1.2 0.5 -10000 0 -1.5 203 203
IL4R -1.2 0.54 -10000 0 -1.6 198 198
PTPN6 0.035 0.007 -10000 0 -10000 0 0
IL13RA2 -1.2 0.51 -10000 0 -1.5 199 199
IL13RA1 -0.031 0.019 -10000 0 -10000 0 0
IRF4 -0.3 0.35 -10000 0 -0.95 59 59
ARG1 -0.49 0.53 -10000 0 -1.3 76 76
CBL -0.51 0.22 -10000 0 -0.9 36 36
GTF3A 0.005 0.016 -10000 0 -10000 0 0
PIK3CA 0.013 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.043 0.023 -10000 0 -10000 0 0
IRF4/BCL6 -0.28 0.32 -10000 0 -0.88 59 59
CD40LG -0.069 0.23 -10000 0 -0.66 39 39
MAPK14 -0.51 0.22 -10000 0 -0.91 34 34
mitosis -0.41 0.17 -10000 0 -0.77 17 17
STAT6 -1.4 0.71 -10000 0 -1.8 210 210
SPI1 -0.009 0.059 -10000 0 -0.7 1 1
RPS6KB1 -0.39 0.17 -10000 0 -0.76 14 14
STAT6 (dimer) -1.4 0.71 -10000 0 -1.8 210 210
STAT6 (dimer)/PARP14 -1.3 0.58 -10000 0 -1.6 209 209
mast cell activation 0.022 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.42 0.19 -10000 0 -0.87 19 19
FRAP1 -0.42 0.18 -10000 0 -0.83 17 17
LTA -1.2 0.5 -10000 0 -1.4 206 206
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 1.3 0.62 1.7 210 -10000 0 210
CCL11 -1.2 0.47 -10000 0 -1.5 226 226
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.42 0.19 -10000 0 -0.87 18 18
IL2RG -0.008 0.15 -10000 0 -0.78 11 11
IL10 -1.1 0.49 -10000 0 -1.4 194 194
IRS1 0.013 0 -10000 0 -10000 0 0
IRS2 0.009 0.053 -10000 0 -0.64 2 2
IL4 -0.21 0.069 -10000 0 -10000 0 0
IL5 -1.1 0.49 -10000 0 -1.5 191 191
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.81 0.29 -10000 0 -0.99 193 193
COL1A1 -0.73 0.35 -10000 0 -0.96 206 206
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -1.2 0.53 -10000 0 -1.5 189 189
IL2R gamma/JAK3 -0.031 0.2 -10000 0 -0.73 22 22
TFF3 -1.3 0.58 -10000 0 -1.6 217 217
ALOX15 -1.2 0.52 -10000 0 -1.5 207 207
MYBL1 0 0.1 -10000 0 -0.8 5 5
T-helper 2 cell differentiation -0.84 0.31 -10000 0 -1 198 198
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB -0.006 0.044 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.42 0.17 -10000 0 -0.8 16 16
mol:PI-3-4-5-P3 -0.42 0.18 -10000 0 -0.83 17 17
PI3K -0.44 0.2 -10000 0 -0.89 18 18
DOK2 0.011 0.038 -10000 0 -0.64 1 1
ETS1 0.03 0.068 -10000 0 -0.8 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.33 0.15 -10000 0 -0.73 14 14
ITGB3 -1.1 0.49 -10000 0 -1.5 194 194
PIGR -1.4 0.59 -10000 0 -1.7 232 232
IGHE 0.056 0.043 0.27 3 -10000 0 3
MAPKKK cascade -0.32 0.14 -10000 0 -0.74 12 12
BCL6 0.013 0.002 -10000 0 -10000 0 0
OPRM1 -1.1 0.48 -10000 0 -1.4 196 196
RETNLB -1.1 0.49 -10000 0 -1.5 199 199
SELP -1.2 0.52 -10000 0 -1.5 206 206
AICDA -1.1 0.47 -10000 0 -1.4 208 208
HIF-1-alpha transcription factor network

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
PKM2 -0.72 0.5 -9999 0 -1.2 117 117
HDAC7 0.014 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.48 0.32 -9999 0 -0.85 63 63
SMAD4 0.013 0.037 -9999 0 -0.64 1 1
ID2 -0.72 0.5 -9999 0 -1.2 105 105
AP1 -0.076 0.17 -9999 0 -0.47 49 49
ABCG2 -0.73 0.5 -9999 0 -1.3 107 107
HIF1A -0.083 0.056 -9999 0 -10000 0 0
TFF3 -0.86 0.57 -9999 0 -1.3 151 151
GATA2 0.01 0.066 -9999 0 -0.8 2 2
AKT1 -0.086 0.065 -9999 0 -10000 0 0
response to hypoxia -0.11 0.068 -9999 0 -10000 0 0
MCL1 -0.72 0.5 -9999 0 -1.2 117 117
NDRG1 -0.72 0.5 -9999 0 -1.2 119 119
SERPINE1 -0.94 0.56 -9999 0 -1.4 166 166
FECH -0.72 0.5 -9999 0 -1.3 96 96
FURIN -0.72 0.5 -9999 0 -1.2 105 105
NCOA2 0.005 0.075 -9999 0 -0.64 4 4
EP300 -0.091 0.093 -9999 0 -0.33 4 4
HMOX1 -0.72 0.5 -9999 0 -1.2 105 105
BHLHE40 -0.72 0.5 -9999 0 -1.2 117 117
BHLHE41 -0.73 0.51 -9999 0 -1.3 107 107
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.068 0.061 -9999 0 -0.48 2 2
ENG -0.044 0.077 -9999 0 -10000 0 0
JUN 0.014 0.001 -9999 0 -10000 0 0
RORA -0.72 0.5 -9999 0 -1.2 117 117
ABCB1 -0.2 0.32 -9999 0 -1.4 18 18
TFRC -0.74 0.5 -9999 0 -1.3 109 109
CXCR4 -0.74 0.51 -9999 0 -1.3 111 111
TF -0.93 0.56 -9999 0 -1.3 185 185
CITED2 -0.72 0.5 -9999 0 -1.2 117 117
HIF1A/ARNT -0.84 0.64 -9999 0 -1.4 146 146
LDHA -0.069 0.046 -9999 0 -10000 0 0
ETS1 -0.72 0.5 -9999 0 -1.3 96 96
PGK1 -0.72 0.5 -9999 0 -1.2 105 105
NOS2 -0.78 0.52 -9999 0 -1.3 120 120
ITGB2 -0.74 0.5 -9999 0 -1.3 108 108
ALDOA -0.72 0.5 -9999 0 -1.2 117 117
Cbp/p300/CITED2 -0.7 0.51 -9999 0 -1.3 92 92
FOS -0.091 0.24 -9999 0 -0.64 49 49
HK2 -0.72 0.5 -9999 0 -1.2 104 104
SP1 0.022 0.006 -9999 0 -10000 0 0
GCK -0.18 0.22 -9999 0 -0.79 24 24
HK1 -0.72 0.5 -9999 0 -1.3 96 96
NPM1 -0.72 0.5 -9999 0 -1.2 117 117
EGLN1 -0.72 0.5 -9999 0 -1.2 117 117
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.72 0.5 -9999 0 -1.2 104 104
SMAD3 0.013 0.037 -9999 0 -0.64 1 1
EDN1 -0.1 0.18 -9999 0 -1.3 3 3
IGFBP1 -0.75 0.51 -9999 0 -1.2 123 123
VEGFA -0.4 0.3 -9999 0 -0.89 14 14
HIF1A/JAB1 -0.042 0.029 -9999 0 -10000 0 0
CP -0.85 0.57 -9999 0 -1.3 157 157
CXCL12 -0.74 0.52 -9999 0 -1.3 107 107
COPS5 0.013 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.003 0.038 -9999 0 -0.47 2 2
BNIP3 -0.72 0.5 -9999 0 -1.2 109 109
EGLN3 -0.74 0.52 -9999 0 -1.3 109 109
CA9 -1 0.51 -9999 0 -1.4 196 196
TERT -0.8 0.54 -9999 0 -1.3 128 128
ENO1 -0.72 0.5 -9999 0 -1.2 104 104
PFKL -0.72 0.5 -9999 0 -1.2 104 104
NCOA1 0.013 0.003 -9999 0 -10000 0 0
ADM -0.72 0.5 -9999 0 -1.3 105 105
ARNT -0.083 0.055 -9999 0 -10000 0 0
HNF4A -0.071 0.24 -9999 0 -0.8 30 30
ADFP -0.73 0.5 -9999 0 -1.2 139 139
SLC2A1 -0.41 0.31 -9999 0 -1 16 16
LEP -0.77 0.54 -9999 0 -1.3 117 117
HIF1A/ARNT/Cbp/p300 -0.5 0.34 -9999 0 -0.86 88 88
EPO -0.37 0.27 -9999 0 -0.97 20 20
CREBBP -0.091 0.093 -9999 0 -0.37 1 1
HIF1A/ARNT/Cbp/p300/HDAC7 -0.48 0.33 -9999 0 -0.88 55 55
PFKFB3 -0.72 0.5 -9999 0 -1.2 105 105
NT5E -0.78 0.55 -9999 0 -1.3 125 125
Osteopontin-mediated 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
IKK alpha homodimer -0.28 0.27 -9999 0 -0.57 91 91
NF kappa B1 p50/RelA/I kappa B alpha -0.28 0.23 -9999 0 -0.57 81 81
alphaV/beta3 Integrin/Osteopontin/Src -0.36 0.32 -9999 0 -0.63 172 172
AP1 -0.38 0.31 -9999 0 -0.83 72 72
ILK -0.29 0.28 -9999 0 -0.56 105 105
bone resorption -0.24 0.22 -9999 0 -0.78 9 9
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.27 0.24 -9999 0 -0.88 8 8
ITGAV 0.004 0.077 -9999 0 -0.76 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.002 0.027 -9999 0 -0.47 1 1
alphaV/beta3 Integrin/Osteopontin -0.34 0.29 -9999 0 -0.57 176 176
MAP3K1 -0.3 0.28 -9999 0 -0.52 176 176
JUN 0.012 0.002 -9999 0 -10000 0 0
MAPK3 -0.3 0.29 -9999 0 -0.63 91 91
MAPK1 -0.3 0.29 -9999 0 -0.63 91 91
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.28 0.28 -9999 0 -0.56 103 103
ITGB3 -0.02 0.15 -9999 0 -0.77 12 12
NFKBIA -0.3 0.28 -9999 0 -0.63 91 91
FOS -0.094 0.24 -9999 0 -0.64 49 49
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.44 0.4 -9999 0 -0.95 91 91
NF kappa B1 p50/RelA -0.3 0.24 -9999 0 -0.66 33 33
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.03 0.13 -9999 0 -0.63 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.29 0.28 -9999 0 -0.52 176 176
VAV3 -0.29 0.28 -9999 0 -0.57 105 105
MAP3K14 -0.31 0.29 -9999 0 -0.54 176 176
ROCK2 0.011 0.038 -9999 0 -0.64 1 1
SPP1 -0.45 0.41 -9999 0 -0.81 171 171
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.28 0.24 -9999 0 -0.6 49 49
MMP2 -0.34 0.34 -9999 0 -0.81 76 76
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.18 0.31 -9999 0 -0.63 82 82
alphaM/beta2 Integrin/GPIbA -0.089 0.24 -9999 0 -0.7 37 37
alphaM/beta2 Integrin/proMMP-9 -0.46 0.32 -9999 0 -0.61 231 231
PLAUR -0.022 0.16 -9999 0 -0.8 13 13
HMGB1 0.01 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.073 0.22 -9999 0 -0.69 30 30
AGER 0.005 0.067 -9999 0 -0.8 2 2
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG 0.013 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.086 0.2 -9999 0 -0.62 31 31
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.61 0.35 -9999 0 -0.8 230 230
CYR61 0.009 0.06 -9999 0 -0.72 2 2
TLN1 0.011 0.047 -9999 0 -0.8 1 1
Rap1/GTP -0.19 0.16 -9999 0 -0.51 37 37
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.1 0.25 -9999 0 -0.64 54 54
MYH2 -0.42 0.26 -9999 0 -0.62 165 165
MST1R 0 0.091 -9999 0 -0.64 6 6
leukocyte activation during inflammatory response -0.087 0.22 -9999 0 -0.57 44 44
APOB -0.01 0.13 -9999 0 -0.78 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.15 0.33 -9999 0 -0.8 61 61
JAM3 0.011 0.047 -9999 0 -0.8 1 1
GP1BA -0.017 0.15 -9999 0 -0.79 11 11
alphaM/beta2 Integrin/CTGF -0.074 0.22 -9999 0 -0.68 31 31
alphaM/beta2 Integrin -0.22 0.2 -9999 0 -0.44 108 108
JAM3 homodimer 0.011 0.047 -9999 0 -0.8 1 1
ICAM2 0.009 0.053 -9999 0 -0.64 2 2
ICAM1 -0.032 0.19 -9999 0 -0.8 17 17
phagocytosis triggered by activation of immune response cell surface activating receptor -0.22 0.2 -9999 0 -0.44 108 108
cell adhesion -0.089 0.24 -9999 0 -0.69 37 37
NFKB1 -0.044 0.24 -9999 0 -0.82 15 15
THY1 -0.26 0.38 -9999 0 -0.8 101 101
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.032 0.13 -9999 0 -0.53 18 18
alphaM/beta2 Integrin/LRP/tPA -0.076 0.21 -9999 0 -0.62 36 36
IL6 -0.072 0.31 -9999 0 -0.79 39 39
ITGB2 -0.024 0.16 -9999 0 -0.79 13 13
elevation of cytosolic calcium ion concentration -0.29 0.33 -9999 0 -0.57 153 153
alphaM/beta2 Integrin/JAM2/JAM3 -0.075 0.21 -9999 0 -0.65 30 30
JAM2 -0.004 0.1 -9999 0 -0.64 8 8
alphaM/beta2 Integrin/ICAM1 -0.094 0.24 -9999 0 -0.66 39 39
alphaM/beta2 Integrin/uPA/Plg -0.28 0.31 -9999 0 -0.55 151 151
RhoA/GTP -0.27 0.22 -9999 0 -0.54 95 95
positive regulation of phagocytosis -0.17 0.19 -9999 0 -0.59 36 36
Ron/MSP -0.014 0.083 -9999 0 -0.49 9 9
alphaM/beta2 Integrin/uPAR/uPA -0.29 0.34 -9999 0 -0.57 153 153
alphaM/beta2 Integrin/uPAR -0.092 0.25 -9999 0 -0.7 38 38
PLAU -0.34 0.4 -9999 0 -0.8 133 133
PLAT -0.008 0.13 -9999 0 -0.8 8 8
actin filament polymerization -0.4 0.24 -9999 0 -0.58 165 165
MST1 0.006 0.071 -9999 0 -0.7 3 3
alphaM/beta2 Integrin/lipoprotein(a) -0.089 0.22 -9999 0 -0.58 44 44
TNF -0.048 0.26 -9999 0 -0.77 25 25
RAP1B 0.011 0.047 -9999 0 -0.8 1 1
alphaM/beta2 Integrin/uPA -0.3 0.33 -9999 0 -0.6 151 151
fibrinolysis -0.27 0.3 -9999 0 -0.55 151 151
HCK 0.004 0.084 -9999 0 -0.72 4 4
dendritic cell antigen processing and presentation -0.22 0.2 -9999 0 -0.44 108 108
VTN -0.059 0.23 -9999 0 -0.8 27 27
alphaM/beta2 Integrin/CYR61 -0.074 0.22 -9999 0 -0.68 31 31
LPA -0.019 0.14 -9999 0 -0.8 10 10
LRP1 0.013 0 -9999 0 -10000 0 0
cell migration -0.52 0.38 -9999 0 -0.66 236 236
FN1 -0.44 0.4 -9999 0 -0.8 170 170
alphaM/beta2 Integrin/Thy1 -0.24 0.35 -9999 0 -0.65 112 112
MPO -0.01 0.12 -9999 0 -0.67 10 10
KNG1 -0.005 0.093 -9999 0 -0.8 4 4
RAP1/GDP -0.002 0.031 -9999 0 -0.54 1 1
ROCK1 -0.24 0.21 -9999 0 -0.5 92 92
ELA2 0 0 -9999 0 -10000 0 0
PLG 0.002 0.005 -9999 0 -10000 0 0
CTGF 0.009 0.053 -9999 0 -0.64 2 2
alphaM/beta2 Integrin/Hck -0.077 0.22 -9999 0 -0.69 31 31
ITGAM -0.061 0.23 -9999 0 -0.79 27 27
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.13 0.23 -9999 0 -0.66 30 30
HP -0.24 0.32 -9999 0 -0.65 116 116
leukocyte adhesion -0.2 0.27 -9999 0 -0.85 28 28
SELP -0.1 0.25 -9999 0 -0.64 54 54
IL23-mediated 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
CCL2 -0.55 0.44 -10000 0 -1.2 70 70
IL23A -0.53 0.42 -10000 0 -1.2 51 51
NF kappa B1 p50/RelA/I kappa B alpha -0.53 0.4 -10000 0 -1.1 72 72
positive regulation of T cell mediated cytotoxicity -0.59 0.47 -10000 0 -1.2 82 82
ITGA3 -0.53 0.42 -10000 0 -1.1 68 68
IL17F -0.36 0.27 -10000 0 -0.76 38 38
IL12B -0.094 0.26 -10000 0 -0.84 33 33
STAT1 (dimer) -0.59 0.47 -10000 0 -1.2 83 83
CD4 -0.52 0.4 -10000 0 -1.1 57 57
IL23 -0.55 0.42 -10000 0 -1.1 64 64
IL23R -0.084 0.11 -10000 0 -0.7 6 6
IL1B -0.56 0.44 -10000 0 -1.2 69 69
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.7 0.44 -10000 0 -1.1 122 122
TYK2 -0.001 0.012 -10000 0 -10000 0 0
STAT4 -0.002 0.11 -10000 0 -0.78 6 6
STAT3 0.013 0.001 -10000 0 -10000 0 0
IL18RAP -0.007 0.12 -10000 0 -0.71 8 8
IL12RB1 -0.088 0.26 -10000 0 -0.83 32 32
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.073 0.2 -10000 0 -0.65 32 32
IL23R/JAK2 -0.099 0.11 -10000 0 -0.74 4 4
positive regulation of chronic inflammatory response -0.59 0.47 -10000 0 -1.2 82 82
natural killer cell activation 0.008 0.009 0.059 6 -10000 0 6
JAK2 0.003 0.014 -10000 0 -10000 0 0
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
NFKB1 0.01 0.003 -10000 0 -10000 0 0
RELA 0.01 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.52 0.4 -10000 0 -1.1 64 64
ALOX12B -0.62 0.46 -10000 0 -1.2 93 93
CXCL1 -0.56 0.44 -10000 0 -1.2 73 73
T cell proliferation -0.59 0.47 -10000 0 -1.2 82 82
NFKBIA 0.01 0.003 -10000 0 -10000 0 0
IL17A -0.28 0.22 -10000 0 -0.62 17 17
PI3K -0.54 0.41 -10000 0 -1.1 74 74
IFNG -0.03 0.047 0.13 5 -0.11 57 62
STAT3 (dimer) -0.51 0.39 -10000 0 -1.1 73 73
IL18R1 0.008 0.061 -10000 0 -0.73 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.33 0.26 -10000 0 -0.77 38 38
IL18/IL18R -0.004 0.12 -10000 0 -0.45 19 19
macrophage activation -0.027 0.015 -10000 0 -0.045 34 34
TNF -0.55 0.44 -10000 0 -1.2 64 64
STAT3/STAT4 -0.55 0.41 -10000 0 -1.1 84 84
STAT4 (dimer) -0.57 0.45 -10000 0 -1.2 75 75
IL18 -0.009 0.12 -10000 0 -0.64 10 10
IL19 -0.66 0.52 -10000 0 -1.3 106 106
STAT5A (dimer) -0.56 0.45 -10000 0 -1.2 74 74
STAT1 -0.048 0.22 -10000 0 -0.8 23 23
SOCS3 0.011 0.038 -10000 0 -0.64 1 1
CXCL9 -0.65 0.47 -10000 0 -1.1 113 113
MPO -0.54 0.42 -10000 0 -1.2 55 55
positive regulation of humoral immune response -0.59 0.47 -10000 0 -1.2 82 82
IL23/IL23R/JAK2/TYK2 -0.61 0.51 -10000 0 -1.3 78 78
IL6 -0.56 0.46 -10000 0 -1.2 71 71
STAT5A 0.013 0 -10000 0 -10000 0 0
IL2 0.005 0.047 -10000 0 -0.79 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.009 0.059 6 -10000 0 6
CD3E -0.52 0.41 -10000 0 -1.1 63 63
keratinocyte proliferation -0.59 0.47 -10000 0 -1.2 82 82
NOS2 -0.57 0.43 -10000 0 -1.2 67 67
Glypican 2 network

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
MDK -0.01 0.14 -9999 0 -0.78 9 9
GPC2 -0.12 0.3 -9999 0 -0.8 50 50
GPC2/Midkine -0.12 0.25 -9999 0 -0.63 57 57
neuron projection morphogenesis -0.12 0.25 -9999 0 -0.63 57 57
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.31 0.31 -9999 0 -0.56 171 171
EPHB2 -0.17 0.34 -9999 0 -0.8 67 67
Syndecan-2/TACI -0.072 0.21 -9999 0 -0.54 51 51
LAMA1 -0.37 0.41 -9999 0 -0.8 143 143
Syndecan-2/alpha2 ITGB1 -0.15 0.22 -9999 0 -0.46 97 97
HRAS 0.013 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.023 0.11 -9999 0 -0.54 13 13
ITGA5 -0.27 0.39 -9999 0 -0.8 105 105
BAX 0.02 0.11 -9999 0 -0.79 1 1
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.021 0.098 -9999 0 -0.48 13 13
LAMA3 -0.22 0.37 -9999 0 -0.8 87 87
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.009 0.06 -9999 0 -0.72 2 2
Syndecan-2/MMP2 -0.11 0.26 -9999 0 -0.59 66 66
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.002 0.035 -9999 0 -0.61 1 1
dendrite morphogenesis -0.12 0.25 -9999 0 -0.55 77 77
Syndecan-2/GM-CSF -0.28 0.3 -9999 0 -0.55 162 162
determination of left/right symmetry -0.005 0.13 -9999 0 -0.61 13 13
Syndecan-2/PKC delta 0.003 0.11 -9999 0 -0.53 13 13
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.25 0.28 -9999 0 -0.5 162 162
MAPK1 -0.25 0.28 -9999 0 -0.5 162 162
Syndecan-2/RACK1 -0.019 0.092 -9999 0 -0.45 13 13
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.005 0.13 -9999 0 -0.61 13 13
ITGA2 0.013 0 -9999 0 -10000 0 0
MAPK8 0.011 0.12 -9999 0 -0.54 14 14
Syndecan-2/alpha2/beta1 Integrin -0.23 0.25 -9999 0 -0.48 144 144
Syndecan-2/Kininogen -0.019 0.13 -9999 0 -0.56 16 16
ITGB1 0.011 0.047 -9999 0 -0.8 1 1
SRC 0.02 0.094 -9999 0 -0.42 13 13
Syndecan-2/CASK/Protein 4.1 -0.021 0.098 -9999 0 -0.49 13 13
extracellular matrix organization 0.001 0.12 -9999 0 -0.56 13 13
actin cytoskeleton reorganization -0.3 0.3 -9999 0 -0.56 171 171
Syndecan-2/Caveolin-2/Ras -0.023 0.1 -9999 0 -0.47 15 15
Syndecan-2/Laminin alpha3 -0.16 0.27 -9999 0 -0.55 96 96
Syndecan-2/RasGAP -0.018 0.087 -9999 0 -0.43 13 13
alpha5/beta1 Integrin -0.22 0.29 -9999 0 -0.61 106 106
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.12 0.25 -9999 0 -0.55 77 77
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.092 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.093 0.27 -9999 0 -0.8 39 39
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.002 0.035 -9999 0 -0.61 1 1
Syndecan-2/Synbindin 0.003 0.11 -9999 0 -0.53 13 13
TGFB1 0.011 0.047 -9999 0 -0.8 1 1
CASP3 0.014 0.1 -9999 0 -0.48 13 13
FN1 -0.44 0.4 -9999 0 -0.8 170 170
Syndecan-2/IL8 -0.12 0.26 -9999 0 -0.56 73 73
SDC2 -0.005 0.13 -9999 0 -0.61 13 13
KNG1 -0.005 0.093 -9999 0 -0.8 4 4
Syndecan-2/Neurofibromin 0.003 0.11 -9999 0 -0.53 13 13
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.41 0.41 -9999 0 -0.8 157 157
Syndecan-2/TGFB1 0.001 0.12 -9999 0 -0.56 13 13
Syndecan-2/Syntenin/PI-4-5-P2 -0.021 0.098 -9999 0 -0.49 13 13
Syndecan-2/Ezrin -0.02 0.097 -9999 0 -0.48 13 13
PRKACA 0.014 0.1 -9999 0 -0.48 13 13
angiogenesis -0.11 0.26 -9999 0 -0.56 73 73
MMP2 -0.15 0.33 -9999 0 -0.8 61 61
IL8 -0.16 0.33 -9999 0 -0.8 65 65
calcineurin-NFAT signaling pathway -0.071 0.21 -9999 0 -0.54 51 51
Endothelins

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
AKT1 -0.23 0.3 -10000 0 -0.7 46 46
PTK2B 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.091 0.22 -10000 0 -0.65 25 25
EDN1 -0.14 0.2 -10000 0 -0.4 42 42
EDN3 -0.31 0.32 -10000 0 -0.64 147 147
EDN2 -0.09 0.26 -10000 0 -0.71 43 43
HRAS/GDP -0.086 0.18 -10000 0 -0.55 9 9
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.083 0.14 -10000 0 -0.39 20 20
ADCY4 -0.23 0.25 -10000 0 -0.61 60 60
ADCY5 -0.31 0.26 -10000 0 -0.64 91 91
ADCY6 -0.24 0.25 -10000 0 -0.63 62 62
ADCY7 -0.23 0.25 -10000 0 -0.61 60 60
ADCY1 -0.25 0.26 -10000 0 -0.64 67 67
ADCY2 -0.34 0.26 -10000 0 -0.64 104 104
ADCY3 -0.23 0.25 -10000 0 -0.61 60 60
ADCY8 -0.25 0.26 -10000 0 -0.63 68 68
ADCY9 -0.23 0.25 -10000 0 -0.61 60 60
arachidonic acid secretion -0.12 0.23 -10000 0 -0.55 41 41
ETB receptor/Endothelin-1/Gq/GTP -0.08 0.14 -10000 0 -0.42 20 20
GNAO1 0.009 0.06 -10000 0 -0.72 2 2
HRAS 0.012 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.16 0.34 0.34 63 -0.67 44 107
ETA receptor/Endothelin-1/Gs/GTP -0.2 0.33 0.32 53 -0.64 61 114
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.51 0.48 -10000 0 -0.86 190 190
EDNRB -0.026 0.072 -10000 0 -0.64 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.3 0.4 -10000 0 -0.96 58 58
CYSLTR1 -0.27 0.33 -10000 0 -0.75 60 60
SLC9A1 -0.095 0.16 -10000 0 -0.33 15 15
mol:GDP -0.098 0.18 -10000 0 -0.49 22 22
SLC9A3 -0.27 0.35 -10000 0 -0.74 86 86
RAF1 -0.12 0.2 -10000 0 -0.51 37 37
JUN -0.069 0.17 -10000 0 -0.66 1 1
JAK2 -0.23 0.3 -10000 0 -0.71 44 44
mol:IP3 -0.1 0.16 -10000 0 -0.5 20 20
ETA receptor/Endothelin-1 -0.22 0.41 0.4 67 -0.77 50 117
PLCB1 0.009 0.038 -10000 0 -0.64 1 1
PLCB2 0.01 0.038 -10000 0 -0.64 1 1
ETA receptor/Endothelin-3 -0.3 0.27 -10000 0 -0.55 147 147
FOS -0.18 0.37 -10000 0 -0.97 49 49
Gai/GDP 0.009 0.07 -10000 0 -0.6 2 2
CRK 0.013 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.25 0.28 -10000 0 -0.66 59 59
BCAR1 0.014 0 -10000 0 -10000 0 0
PRKCB1 -0.1 0.16 -10000 0 -0.47 22 22
GNAQ 0.013 0.007 -10000 0 -10000 0 0
GNAZ -0.004 0.11 -10000 0 -0.73 7 7
GNAL -0.06 0.21 -10000 0 -0.64 34 34
Gs family/GDP -0.15 0.16 -10000 0 -0.5 33 33
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.17 -10000 0 -0.42 30 30
MAPK14 -0.048 0.12 -10000 0 -0.6 3 3
TRPC6 -0.095 0.22 -10000 0 -0.68 25 25
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.011 0.038 -10000 0 -0.64 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.06 0.12 -10000 0 -0.38 17 17
ETB receptor/Endothelin-2 -0.091 0.19 -10000 0 -0.54 46 46
ETB receptor/Endothelin-3 -0.25 0.24 -10000 0 -0.49 149 149
ETB receptor/Endothelin-1 -0.12 0.18 -10000 0 -0.58 6 6
MAPK3 -0.16 0.32 -10000 0 -0.82 50 50
MAPK1 -0.16 0.32 -10000 0 -0.82 50 50
Rac1/GDP -0.085 0.17 -10000 0 -0.54 10 10
cAMP biosynthetic process -0.27 0.23 -10000 0 -0.59 72 72
MAPK8 -0.088 0.19 -10000 0 -0.56 15 15
SRC 0.013 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.028 0.089 -10000 0 -0.46 1 1
p130Cas/CRK/Src/PYK2 -0.092 0.19 -10000 0 -0.57 14 14
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.088 0.18 -10000 0 -0.55 10 10
COL1A2 -0.41 0.47 -10000 0 -0.85 155 155
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.14 0.23 -10000 0 -0.61 43 43
mol:DAG -0.1 0.16 -10000 0 -0.5 20 20
MAP2K2 -0.13 0.25 -10000 0 -0.63 44 44
MAP2K1 -0.13 0.25 -10000 0 -0.63 44 44
EDNRA -0.12 0.18 -10000 0 -0.61 1 1
positive regulation of muscle contraction -0.19 0.26 -10000 0 -0.63 43 43
Gq family/GDP -0.11 0.17 -10000 0 -0.52 24 24
HRAS/GTP -0.11 0.18 -10000 0 -0.48 28 28
PRKCH -0.094 0.16 -10000 0 -0.48 19 19
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.096 0.16 -10000 0 -0.48 19 19
PRKCB -0.1 0.17 -10000 0 -0.51 26 26
PRKCE -0.094 0.16 -10000 0 -0.47 20 20
PRKCD -0.095 0.16 -10000 0 -0.48 19 19
PRKCG -0.14 0.21 -10000 0 -0.55 41 41
regulation of vascular smooth muscle contraction -0.2 0.43 -10000 0 -1.1 50 50
PRKCQ -0.1 0.17 -10000 0 -0.5 25 25
PLA2G4A -0.13 0.24 -10000 0 -0.6 41 41
GNA14 -0.095 0.24 -10000 0 -0.64 50 50
GNA15 0.012 0.006 -10000 0 -10000 0 0
GNA12 0.008 0.066 -10000 0 -0.8 2 2
GNA11 0.012 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.16 0.34 0.34 64 -0.66 44 108
MMP1 -0.55 0.23 -10000 0 -0.63 271 271
TCGA08_p53

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
CDKN2A -0.24 0.3 -10000 0 -0.59 124 124
TP53 -0.071 0.088 -10000 0 -0.41 3 3
Senescence -0.071 0.088 -10000 0 -0.41 3 3
Apoptosis -0.071 0.088 -10000 0 -0.41 3 3
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.12 0.15 0.3 124 -10000 0 124
MDM4 0.013 0 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.014 0.08 -9999 0 -0.47 9 9
Necdin/E2F1 -0.041 0.15 -9999 0 -0.59 21 21
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.13 0.2 -9999 0 -0.45 73 73
NGF (dimer)/p75(NTR)/BEX1 -0.16 0.25 -9999 0 -0.53 94 94
NT-4/5 (dimer)/p75(NTR) -0.027 0.12 -9999 0 -0.55 15 15
IKBKB 0.013 0 -9999 0 -10000 0 0
AKT1 -0.083 0.21 -9999 0 -0.44 72 72
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.042 0.2 -9999 0 -0.72 23 23
MGDIs/NGR/p75(NTR)/LINGO1 -0.073 0.2 -9999 0 -0.61 33 33
FURIN 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.069 0.17 -9999 0 -0.47 45 45
LINGO1 -0.046 0.21 -9999 0 -0.8 22 22
Sortilin/TRAF6/NRIF -0.009 0.051 -9999 0 -10000 0 0
proBDNF (dimer) -0.042 0.2 -9999 0 -0.72 23 23
NTRK1 -0.062 0.24 -9999 0 -0.8 28 28
RTN4R -0.005 0.12 -9999 0 -0.8 7 7
neuron apoptosis -0.065 0.18 -9999 0 -0.59 12 12
IRAK1 0.013 0 -9999 0 -10000 0 0
SHC1 -0.12 0.24 -9999 0 -0.51 81 81
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.026 -9999 0 -0.45 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.14 0.22 -9999 0 -0.49 73 73
MAGEH1 0.011 0.047 -9999 0 -0.8 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.14 0.22 -9999 0 -0.5 74 74
Mammalian IAPs/DIABLO -0.031 0.14 -9999 0 -0.6 16 16
proNGF (dimer) -0.16 0.33 -9999 0 -0.8 66 66
MAGED1 0.011 0.038 -9999 0 -0.64 1 1
APP 0.013 0 -9999 0 -10000 0 0
NT-4/5 (dimer) 0.013 0.001 -9999 0 -10000 0 0
ZNF274 0.013 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.12 0.19 -9999 0 -0.45 72 72
NGF -0.16 0.34 -9999 0 -0.8 66 66
cell cycle arrest -0.12 0.22 -9999 0 -0.49 72 72
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.038 0.13 -9999 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.023 0.1 -9999 0 -0.47 15 15
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.14 0.23 -9999 0 -0.51 81 81
PSENEN 0.011 0.047 -9999 0 -0.8 1 1
mol:ceramide -0.11 0.22 -9999 0 -0.48 72 72
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.017 0.11 -9999 0 -0.6 1 1
p75(NTR)/beta APP -0.027 0.12 -9999 0 -0.55 15 15
BEX1 -0.03 0.18 -9999 0 -0.8 15 15
mol:GDP -0.12 0.24 -9999 0 -0.52 81 81
NGF (dimer) -0.19 0.26 -9999 0 -0.54 96 96
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.066 0.18 -9999 0 -0.56 33 33
PIK3R1 0.013 0 -9999 0 -10000 0 0
RAC1/GTP -0.12 0.2 -9999 0 -0.45 81 81
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.14 0.23 -9999 0 -0.51 81 81
RHOB 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.034 0.14 -9999 0 -0.61 17 17
NT3 (dimer) -0.18 0.3 -9999 0 -0.64 90 90
TP53 -0.015 0.16 -9999 0 -0.63 3 3
PRDM4 -0.11 0.23 -9999 0 -0.48 72 72
BDNF (dimer) -0.44 0.3 -9999 0 -0.59 222 222
PIK3CA 0.013 0 -9999 0 -10000 0 0
SORT1 -0.006 0.11 -9999 0 -0.64 9 9
activation of caspase activity -0.12 0.2 -9999 0 -0.45 73 73
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.14 0.21 -9999 0 -0.48 72 72
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 -0.07 0.19 -9999 0 -0.52 13 13
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 -0.11 0.23 -9999 0 -0.48 72 72
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.15 0.23 -9999 0 -0.51 89 89
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.17 0.24 -9999 0 -0.49 102 102
MAPK8 -0.06 0.19 -9999 0 -0.52 10 10
MAPK9 -0.058 0.19 -9999 0 -0.52 9 9
APAF1 0.013 0 -9999 0 -10000 0 0
NTF3 -0.18 0.3 -9999 0 -0.64 90 90
NTF4 0.013 0.001 -9999 0 -10000 0 0
NDN 0.005 0.075 -9999 0 -0.64 4 4
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.11 0.18 -9999 0 -10000 0 0
p75 CTF/Sortilin/TRAF6/NRIF -0.01 0.06 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.14 0.23 -9999 0 -0.51 81 81
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.058 0.14 -9999 0 -0.47 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.063 0.15 -9999 0 -0.5 21 21
PRKACB 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.041 0.14 -9999 0 -0.54 23 23
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.024 0.17 -9999 0 -0.8 14 14
BIRC2 -0.003 0.11 -9999 0 -0.8 6 6
neuron projection morphogenesis -0.11 0.21 -9999 0 -0.44 73 73
BAD -0.053 0.18 -9999 0 -0.49 9 9
RIPK2 0.013 0 -9999 0 -10000 0 0
NGFR -0.023 0.16 -9999 0 -0.73 15 15
CYCS -0.095 0.22 -9999 0 -0.45 72 72
ADAM17 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.12 0.21 -9999 0 -0.48 72 72
BCL2L11 -0.053 0.18 -9999 0 -0.49 9 9
BDNF (dimer)/p75(NTR) -0.068 0.18 -9999 0 -0.54 38 38
PI3K -0.12 0.21 -9999 0 -0.48 72 72
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.14 0.21 -9999 0 -0.48 72 72
NDNL2 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.16 0.26 -9999 0 -0.6 81 81
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.14 0.21 -9999 0 -0.48 72 72
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.038 -9999 0 -0.64 1 1
PLG 0.002 0.005 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.11 0.22 -9999 0 -0.6 17 17
SQSTM1 0.013 0 -9999 0 -10000 0 0
NGFRAP1 0.011 0.047 -9999 0 -0.8 1 1
CASP3 -0.046 0.17 -9999 0 -0.45 9 9
E2F1 -0.032 0.19 -9999 0 -0.8 17 17
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.12 0.18 -9999 0 -0.7 7 7
NGF (dimer)/TRKA -0.19 0.3 -9999 0 -0.64 88 88
MMP7 -0.13 0.3 -9999 0 -0.76 55 55
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.12 0.2 -9999 0 -0.45 72 72
MMP3 -0.55 0.38 -9999 0 -0.8 210 210
APAF-1/Caspase 9 -0.11 0.17 -9999 0 -0.69 8 8
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.008 0.06 -9999 0 -0.44 5 5
RGS9BP -0.013 0.13 -9999 0 -0.64 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.003 0.006 -9999 0 -10000 0 0
mol:Na + -0.2 0.26 -9999 0 -0.54 112 112
mol:ADP -0.059 0.2 -9999 0 -0.62 35 35
GNAT2 0.012 0.004 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.019 0.085 -9999 0 -0.53 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 -0.081 0.26 -9999 0 -0.8 35 35
CNGB3 -0.29 0.39 -9999 0 -0.8 112 112
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.3 0.33 -9999 0 -0.58 162 162
Cone PDE6 -0.016 0.073 -9999 0 -10000 0 0
Cone Metarhodopsin II -0.058 0.16 -9999 0 -0.5 35 35
Na + (4 Units) -0.31 0.32 -9999 0 -0.58 162 162
GNAT2/GDP -0.016 0.072 -9999 0 -0.45 1 1
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.005 -9999 0 -10000 0 0
Cone Transducin -0.009 0.063 -9999 0 -0.46 5 5
SLC24A2 -0.21 0.36 -9999 0 -0.8 83 83
GNB3/GNGT2 -0.011 0.079 -9999 0 -0.56 6 6
GNB3 0.001 0.096 -9999 0 -0.74 5 5
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0.01 0.006 -9999 0 -10000 0 0
ARR3 0.001 0.004 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.2 0.26 -9999 0 -0.54 112 112
mol:Pi -0.019 0.085 -9999 0 -0.53 1 1
Cone CNG Channel -0.16 0.22 -9999 0 -0.45 112 112
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.21 0.36 -9999 0 -0.8 83 83
RGS9 0.009 0.06 -9999 0 -0.72 2 2
PDE6C 0.002 0.005 -9999 0 -10000 0 0
GNGT2 0.011 0.047 -9999 0 -0.8 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.004 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.005 0.054 -9999 0 -0.55 3 3
PDE6G/GNAT1/GTP -0.021 0.11 -9999 0 -0.54 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.007 0.007 -9999 0 -10000 0 0
GRK1 0.003 0.006 -9999 0 -10000 0 0
CNG Channel -0.46 0.3 -9999 0 -0.78 123 123
mol:Na + -0.32 0.26 -9999 0 -0.79 38 38
mol:ADP 0.003 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.019 0.085 -9999 0 -0.53 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.33 0.27 -9999 0 -0.83 38 38
CNGB1 -0.45 0.4 -9999 0 -0.8 172 172
RDH5 0.011 0.038 -9999 0 -0.64 1 1
SAG 0.002 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.29 0.26 -9999 0 -0.76 38 38
Na + (4 Units) -0.3 0.24 -9999 0 -0.73 38 38
RGS9 0.009 0.06 -9999 0 -0.72 2 2
GNB1/GNGT1 -0.1 0.23 -9999 0 -0.61 51 51
GNAT1/GDP -0.016 0.072 -9999 0 -0.45 1 1
GUCY2D -0.027 0.18 -9999 0 -0.8 15 15
GNGT1 -0.12 0.3 -9999 0 -0.8 51 51
GUCY2F 0 0.047 -9999 0 -0.8 1 1
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.21 0.23 -9999 0 -0.63 34 34
mol:11-cis-retinal 0.011 0.037 -9999 0 -0.64 1 1
mol:cGMP -0.082 0.18 -9999 0 -0.49 48 48
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.008 0.066 -9999 0 -0.58 4 4
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 -0.038 0.18 -9999 0 -0.64 24 24
Metarhodopsin II -0.005 0.049 -9999 0 -0.5 3 3
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.085 0.19 -9999 0 -0.52 47 47
RGS9BP -0.013 0.13 -9999 0 -0.64 12 12
Metarhodopsin II/Transducin -0.034 0.11 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.062 0.16 -9999 0 -0.49 38 38
PDE6A/B -0.28 0.27 -9999 0 -0.51 166 166
mol:Pi -0.019 0.085 -9999 0 -0.53 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.083 0.18 -9999 0 -0.49 51 51
PDE6B -0.046 0.2 -9999 0 -0.71 25 25
PDE6A -0.32 0.33 -9999 0 -0.64 155 155
PDE6G -0.019 0.16 -9999 0 -0.8 12 12
RHO -0.004 0.08 -9999 0 -0.8 3 3
PDE6 -0.22 0.22 -9999 0 -0.68 30 30
GUCA1A -0.079 0.26 -9999 0 -0.8 34 34
GC2/GCAP Family -0.063 0.17 -9999 0 -0.5 35 35
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.003 0.083 -9999 0 -0.64 5 5
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.017 0.082 -10000 0 -10000 0 0
epithelial cell differentiation -0.087 0.14 -10000 0 -0.56 3 3
ITCH 0.028 0.02 -10000 0 -10000 0 0
WWP1 -0.012 0.076 -10000 0 -10000 0 0
FYN 0.011 0.047 -10000 0 -0.8 1 1
EGFR -0.014 0.15 -10000 0 -0.8 10 10
PRL -0.003 0.08 -10000 0 -0.8 3 3
neuron projection morphogenesis -0.046 0.18 -10000 0 -10000 0 0
PTPRZ1 0.003 0.083 -10000 0 -0.64 5 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.1 0.17 -10000 0 -0.51 24 24
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.1 0.22 -10000 0 -0.52 61 61
ADAM17 0.028 0.02 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.027 0.098 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.051 0.12 -10000 0 -0.43 17 17
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.12 0.19 -10000 0 -0.49 61 61
GRIN2B -0.088 0.2 -10000 0 -0.46 64 64
ErbB4/ErbB2/betacellulin -0.13 0.17 -10000 0 -0.45 37 37
STAT1 -0.048 0.22 -10000 0 -0.8 23 23
HBEGF 0.013 0 -10000 0 -10000 0 0
PRLR -0.13 0.27 -10000 0 -0.65 64 64
E4ICDs/ETO2 -0.017 0.082 -10000 0 -10000 0 0
axon guidance -0.026 0.091 -10000 0 -0.38 4 4
NEDD4 0.028 0.02 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.11 0.21 -10000 0 -0.49 66 66
CBFA2T3 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF -0.028 0.053 -10000 0 -0.5 2 2
MAPK3 -0.056 0.18 -10000 0 -10000 0 0
STAT1 (dimer) -0.056 0.16 -10000 0 -0.56 23 23
MAPK1 -0.056 0.18 -10000 0 -10000 0 0
JAK2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.11 0.2 -10000 0 -0.49 62 62
NRG1 -0.096 0.26 -10000 0 -0.61 61 61
NRG3 -0.029 0.15 -10000 0 -0.64 17 17
NRG2 -0.38 0.32 -10000 0 -0.64 184 184
NRG4 -0.07 0.22 -10000 0 -0.64 38 38
heart development -0.026 0.091 -10000 0 -0.38 4 4
neural crest cell migration -0.11 0.2 -10000 0 -0.48 62 62
ERBB2 0.03 0.054 -10000 0 -0.62 2 2
WWOX/E4ICDs -0.017 0.082 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.097 0.16 -10000 0 -0.49 31 31
apoptosis 0.091 0.14 0.53 17 -10000 0 17
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.26 0.21 -10000 0 -0.42 184 184
ErbB4/ErbB2/epiregulin -0.12 0.16 -10000 0 -0.46 30 30
ErbB4/ErbB4/betacellulin/betacellulin -0.14 0.2 -10000 0 -0.42 94 94
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.1 0.15 -10000 0 -0.65 3 3
MDM2 -0.013 0.084 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.11 0.19 -10000 0 -0.49 60 60
STAT5A -0.016 0.086 -10000 0 -0.38 2 2
ErbB4/EGFR/neuregulin 1 beta -0.13 0.21 -10000 0 -0.5 68 68
DLG4 0.011 0.038 -10000 0 -0.64 1 1
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.04 0.058 -10000 0 -10000 0 0
STAT5A (dimer) -0.092 0.14 -10000 0 -0.61 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.017 0.085 -10000 0 -0.38 2 2
LRIG1 0 0.091 -10000 0 -0.64 6 6
EREG -0.17 0.3 -10000 0 -0.64 84 84
BTC -0.19 0.3 -10000 0 -0.64 94 94
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.026 0.092 -10000 0 -0.38 4 4
ERBB4 -0.027 0.098 -10000 0 -10000 0 0
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.02 0.053 -10000 0 -0.37 6 6
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.071 0.13 -10000 0 -0.44 23 23
glial cell differentiation 0.04 0.057 -10000 0 -10000 0 0
WWOX 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.17 0.25 -10000 0 -0.61 48 48
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.22 0.36 -9999 0 -1.1 24 24
PCK1 -0.54 0.64 -9999 0 -1.3 112 112
HNF4A -0.27 0.43 -9999 0 -1.2 29 29
KCNJ11 -0.32 0.49 -9999 0 -1.2 56 56
AKT1 -0.076 0.14 -9999 0 -10000 0 0
response to starvation -0.003 0.023 -9999 0 -10000 0 0
DLK1 -0.45 0.58 -9999 0 -1.2 103 103
NKX2-1 -0.076 0.33 -9999 0 -0.84 27 27
ACADM -0.22 0.36 -9999 0 -1.1 26 26
TAT -0.15 0.23 -9999 0 -0.77 13 13
CEBPB 0.015 0.002 -9999 0 -10000 0 0
CEBPA 0.01 0.053 -9999 0 -0.64 2 2
TTR -0.29 0.3 -9999 0 -0.87 36 36
PKLR -0.26 0.41 -9999 0 -1.1 42 42
APOA1 -0.26 0.41 -9999 0 -1.3 19 19
CPT1C -0.22 0.36 -9999 0 -1.1 26 26
ALAS1 -0.082 0.16 -9999 0 -10000 0 0
TFRC -0.22 0.31 -9999 0 -0.94 24 24
FOXF1 0.014 0.11 -9999 0 -0.7 5 5
NF1 0.021 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.001 0.12 -9999 0 -0.8 6 6
CPT1A -0.22 0.36 -9999 0 -1.1 25 25
HMGCS1 -0.22 0.36 -9999 0 -1.1 25 25
NR3C1 0.016 0.032 -9999 0 -10000 0 0
CPT1B -0.22 0.38 -9999 0 -1.1 26 26
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.026 -9999 0 -10000 0 0
GCK -0.25 0.38 -9999 0 -1.1 33 33
CREB1 -0.041 0.086 -9999 0 -10000 0 0
IGFBP1 -0.11 0.22 -9999 0 -0.82 16 16
PDX1 -0.11 0.22 -9999 0 -0.88 8 8
UCP2 -0.22 0.37 -9999 0 -1.1 25 25
ALDOB -0.25 0.4 -9999 0 -1.1 30 30
AFP -0.21 0.24 -9999 0 -0.65 40 40
BDH1 -0.22 0.36 -9999 0 -1.1 22 22
HADH -0.23 0.38 -9999 0 -1.1 23 23
F2 -0.28 0.43 -9999 0 -1.3 24 24
HNF1A -0.001 0.12 -9999 0 -0.8 6 6
G6PC -0.064 0.14 -9999 0 -10000 0 0
SLC2A2 -0.13 0.22 -9999 0 -1.1 1 1
INS -0.005 0.035 -9999 0 -10000 0 0
FOXA1 -0.23 0.33 -9999 0 -0.65 113 113
FOXA3 -0.15 0.3 -9999 0 -0.9 34 34
FOXA2 -0.27 0.44 -9999 0 -1.2 31 31
ABCC8 -0.24 0.39 -9999 0 -1.1 28 28
ALB -0.25 0.3 -9999 0 -0.78 54 54
Effects of Botulinum toxin

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
STX1A 0 0.089 -9999 0 -0.62 6 6
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.066 0.16 -9999 0 -0.47 42 42
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.16 0.25 -9999 0 -0.51 98 98
RAB3GAP2/RIMS1/UNC13B -0.055 0.14 -9999 0 -0.4 42 42
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 -0.08 0.22 -9999 0 -0.64 41 41
mol:ACh 0.002 0.032 -9999 0 -0.12 20 20
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.052 0.11 -9999 0 -0.44 1 1
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.16 0.25 -9999 0 -0.51 98 98
UNC13B 0.011 0.038 -9999 0 -0.64 1 1
CHRNA1 -0.23 0.35 -9999 0 -0.73 98 98
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.15 0.26 -9999 0 -0.56 84 84
SNAP25 -0.006 0.064 -9999 0 -0.3 14 14
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.21 0.36 -9999 0 -0.79 84 84
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.008 0.077 -9999 0 -0.54 6 6
STX1A/SNAP25 fragment 1/VAMP2 -0.052 0.11 -9999 0 -0.44 1 1
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.24 0.28 -9999 0 -0.84 29 29
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.062 0.22 -9999 0 -0.71 31 31
SMAD9 -0.07 0.16 -9999 0 -0.71 15 15
SMAD4 0.011 0.038 -9999 0 -0.64 1 1
SMAD5 -0.053 0.16 -9999 0 -0.52 18 18
BMP7/USAG1 -0.17 0.27 -9999 0 -0.55 94 94
SMAD5/SKI -0.043 0.15 -9999 0 -0.51 14 14
SMAD1 0.041 0.029 -9999 0 -10000 0 0
BMP2 -0.016 0.15 -9999 0 -0.79 11 11
SMAD1/SMAD1/SMAD4 -0.001 0.017 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.077 0.25 -9999 0 -0.77 35 35
BMPR1A-1B/BAMBI -0.074 0.18 -9999 0 -0.5 45 45
AHSG -0.041 0.2 -9999 0 -0.8 19 19
CER1 -0.007 0.092 -9999 0 -0.8 4 4
BMP2-4/CER1 -0.033 0.12 -9999 0 -0.49 20 20
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.095 0.21 -9999 0 -0.58 31 31
BMP2-4 (homodimer) -0.03 0.13 -9999 0 -0.56 16 16
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.057 0.15 -9999 0 -0.48 30 30
RGMA -0.071 0.22 -9999 0 -0.64 39 39
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.094 0.2 -9999 0 -0.54 31 31
BMP2-4/USAG1 -0.14 0.22 -9999 0 -0.45 97 97
SMAD6/SMURF1/SMAD5 -0.043 0.15 -9999 0 -0.51 14 14
SOSTDC1 -0.18 0.31 -9999 0 -0.67 85 85
BMP7/BMPR2/BMPR1A-1B -0.078 0.17 -9999 0 -0.5 30 30
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.006 0.076 -9999 0 -0.75 3 3
HFE2 -0.17 0.29 -9999 0 -0.64 81 81
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.042 0.14 -9999 0 -0.51 25 25
SMAD5/SMAD5/SMAD4 -0.044 0.15 -9999 0 -0.52 15 15
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.097 0.15 -9999 0 -0.57 15 15
BMP7 (homodimer) -0.035 0.17 -9999 0 -0.65 22 22
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.044 0.16 -9999 0 -0.61 22 22
SMAD1/SKI 0.047 0.028 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.058 0.17 -9999 0 -0.52 34 34
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.41 0.41 -9999 0 -0.8 158 158
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.068 0.19 -9999 0 -0.58 35 35
CHRDL1 -0.3 0.33 -9999 0 -0.64 143 143
ENDOFIN/SMAD1 0.047 0.028 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.001 0.004 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.012 0.13 -9999 0 -0.7 11 11
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.21 0.23 -9999 0 -0.43 147 147
BMP2-4/GREM1 -0.3 0.29 -9999 0 -0.55 164 164
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.04 0.16 -9999 0 -0.68 15 15
SMAD1/SMAD6 0.047 0.028 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.035 0.17 -9999 0 -0.65 22 22
BMP6 0.006 0.076 -9999 0 -0.75 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.075 0.17 -9999 0 -0.47 30 30
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.047 0.028 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.18 0.25 -9999 0 -0.56 69 69
CHRD -0.013 0.14 -9999 0 -0.79 10 10
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.1 0.2 -9999 0 -0.57 31 31
BMP4 0.003 0.083 -9999 0 -0.64 5 5
FST -0.29 0.4 -9999 0 -0.8 113 113
BMP2-4/NOG -0.071 0.17 -9999 0 -0.46 47 47
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.073 0.16 -9999 0 -0.73 2 2
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.013 0.036 -9999 0 -10000 0 0
NFATC2 -0.042 0.11 -9999 0 -0.46 19 19
NFATC3 -0.013 0.036 -9999 0 -10000 0 0
CD40LG -0.33 0.36 -9999 0 -0.88 66 66
PTGS2 -0.34 0.37 -9999 0 -0.87 75 75
JUNB 0.013 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.016 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.016 0.015 -9999 0 -10000 0 0
CALM1 0.004 0.011 -9999 0 -10000 0 0
JUN 0.005 0.011 -9999 0 -10000 0 0
mol:Ca2+ -0.017 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.004 -9999 0 -10000 0 0
FOSL1 0.005 0.081 -9999 0 -0.8 3 3
CREM 0.013 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.14 0.15 -9999 0 -0.62 11 11
FOS -0.1 0.24 -9999 0 -0.66 49 49
IFNG -0.36 0.38 -9999 0 -0.86 86 86
AP-1/NFAT1-c-4 -0.39 0.37 -9999 0 -1.1 51 51
FASLG -0.31 0.34 -9999 0 -0.87 56 56
NFAT1-c-4/ICER1 -0.085 0.11 -9999 0 -0.54 8 8
IL2RA -0.33 0.37 -9999 0 -0.89 66 66
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.48 0.42 -9999 0 -0.81 166 166
JunB/Fra1/NFAT1-c-4 -0.081 0.11 -9999 0 -0.51 11 11
IL4 -0.3 0.31 -9999 0 -0.82 49 49
IL2 -0.012 0.042 -9999 0 -0.67 1 1
IL3 -0.028 0.023 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 0.005 0.081 -9999 0 -0.8 3 3
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.014 0.002 -9999 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.041 0.058 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.1 0.14 -9999 0 -0.46 20 20
JUN -0.059 0.16 -9999 0 -0.47 21 21
HRAS 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.26 -9999 0 -0.62 56 56
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.005 0.081 -9999 0 -0.8 3 3
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.26 -9999 0 -0.61 55 55
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.12 0.21 -9999 0 -0.44 83 83
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.23 -9999 0 -0.55 55 55
GRB7 0.003 0.089 -9999 0 -0.76 4 4
RET51/GFRalpha1/GDNF -0.17 0.26 -9999 0 -0.61 55 55
MAPKKK cascade -0.13 0.19 -9999 0 -0.64 20 20
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.21 -9999 0 -0.44 81 81
lamellipodium assembly -0.093 0.14 -9999 0 -0.42 20 20
RET51/GFRalpha1/GDNF/SHC -0.17 0.26 -9999 0 -0.61 55 55
PIK3CA 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.12 0.21 -9999 0 -0.44 81 81
RET9/GFRalpha1/GDNF/Shank3 -0.12 0.21 -9999 0 -0.44 81 81
MAPK3 -0.11 0.24 -9999 0 -0.72 20 20
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.001 0.1 -9999 0 -0.72 6 6
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.095 0.22 -9999 0 -0.66 20 20
DOK5 -0.008 0.12 -9999 0 -0.7 9 9
GFRA1 -0.12 0.27 -9999 0 -0.64 64 64
MAPK8 -0.071 0.17 -9999 0 -0.5 21 21
HRAS/GTP -0.15 0.22 -9999 0 -0.74 20 20
tube development -0.11 0.2 -9999 0 -0.57 26 26
MAPK1 -0.11 0.24 -9999 0 -0.72 20 20
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.059 0.16 -9999 0 -0.54 9 9
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PDLIM7 0.008 0.066 -9999 0 -0.8 2 2
RET51/GFRalpha1/GDNF/Dok6 -0.17 0.25 -9999 0 -0.58 59 59
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.26 -9999 0 -0.61 55 55
RET51/GFRalpha1/GDNF/Dok5 -0.18 0.26 -9999 0 -0.61 62 62
PRKCA 0.011 0.047 -9999 0 -0.8 1 1
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.072 0.17 -9999 0 -0.5 20 20
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.056 0.15 -9999 0 -0.54 9 9
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.26 -9999 0 -0.62 59 59
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.079 0.26 -9999 0 -0.79 35 35
DOK4 0.013 0 -9999 0 -10000 0 0
JNK cascade -0.057 0.16 -9999 0 -0.46 21 21
RET9/GFRalpha1/GDNF/FRS2 -0.12 0.21 -9999 0 -0.44 84 84
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.056 0.15 -9999 0 -0.55 9 9
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.085 0.18 -9999 0 -0.53 21 21
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.082 0.18 -9999 0 -0.53 20 20
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.085 0.19 -9999 0 -0.58 20 20
PI3K -0.095 0.24 -9999 0 -0.69 20 20
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.11 0.2 -9999 0 -0.57 26 26
GRB10 0.011 0.047 -9999 0 -0.8 1 1
activation of MAPKK activity -0.08 0.18 -9999 0 -0.52 21 21
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.26 -9999 0 -0.62 57 57
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 0.013 0 -9999 0 -10000 0 0
IRS2 0.009 0.053 -9999 0 -0.64 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.085 0.19 -9999 0 -0.58 20 20
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.26 -9999 0 -0.61 56 56
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.058 0.23 -9999 0 -0.8 26 26
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.26 -9999 0 -0.61 55 55
Rac1/GTP -0.11 0.16 -9999 0 -0.52 20 20
RET9/GFRalpha1/GDNF -0.13 0.23 -9999 0 -0.49 81 81
GFRalpha1/GDNF -0.15 0.26 -9999 0 -0.56 81 81
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.021 0.096 -10000 0 -0.53 6 6
fibroblast growth factor receptor signaling pathway -0.021 0.096 -10000 0 -0.53 6 6
LAMA1 -0.37 0.41 -10000 0 -0.8 143 143
PRNP 0.011 0.047 -10000 0 -0.8 1 1
GPC1/SLIT2 -0.035 0.13 -10000 0 -0.48 22 22
SMAD2 0.035 0.029 -10000 0 -0.48 1 1
GPC1/PrPc/Cu2+ -0.004 0.043 -10000 0 -0.54 2 2
GPC1/Laminin alpha1 -0.29 0.31 -10000 0 -0.61 143 143
TDGF1 0 0.081 -10000 0 -0.8 3 3
CRIPTO/GPC1 -0.008 0.07 -10000 0 -0.61 4 4
APP/GPC1 -0.002 0.035 -10000 0 -0.61 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.019 0.063 -10000 0 -0.53 4 4
FLT1 0.013 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.002 0.03 -10000 0 -0.53 1 1
SERPINC1 0.007 0.066 -10000 0 -0.8 2 2
FYN 0.017 0.071 -10000 0 -0.53 5 5
FGR 0.017 0.071 -10000 0 -0.53 5 5
positive regulation of MAPKKK cascade 0.001 0.12 -10000 0 -0.56 2 2
SLIT2 -0.033 0.17 -10000 0 -0.65 21 21
GPC1/NRG -0.12 0.25 -10000 0 -0.61 62 62
NRG1 -0.15 0.32 -10000 0 -0.8 61 61
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.043 -10000 0 -0.53 2 2
LYN 0.019 0.063 -10000 0 -0.53 4 4
mol:Spermine 0.01 0.036 -10000 0 -0.62 1 1
cell growth -0.021 0.096 -10000 0 -0.53 6 6
BMP signaling pathway -0.011 0.047 0.8 1 -10000 0 1
SRC 0.019 0.063 -10000 0 -0.53 4 4
TGFBR1 0.013 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.4 0.32 -10000 0 -0.64 193 193
GPC1 0.011 0.047 -10000 0 -0.8 1 1
TGFBR1 (dimer) 0.013 0 -10000 0 -10000 0 0
VEGFA 0.011 0.047 -10000 0 -0.8 1 1
BLK -0.075 0.21 -10000 0 -0.52 52 52
HCK 0.013 0.093 -10000 0 -0.56 7 7
FGF2 -0.012 0.13 -10000 0 -0.68 11 11
FGFR1 0.008 0.066 -10000 0 -0.8 2 2
VEGFR1 homodimer 0.013 0 -10000 0 -10000 0 0
TGFBR2 0.013 0 -10000 0 -10000 0 0
cell death -0.002 0.035 -10000 0 -0.61 1 1
ATIII/GPC1 -0.006 0.061 -10000 0 -0.61 3 3
PLA2G2A/GPC1 -0.3 0.23 -10000 0 -0.47 194 194
LCK 0.001 0.12 -10000 0 -0.53 14 14
neuron differentiation -0.12 0.24 -10000 0 -0.61 62 62
PrPc/Cu2+ -0.002 0.036 -10000 0 -0.62 1 1
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.013 0 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.14 0.35 -10000 0 -0.92 50 50
NFATC2 -0.011 0.21 -10000 0 -0.83 13 13
NFATC3 -0.011 0.06 -10000 0 -10000 0 0
CD40LG -0.36 0.44 -10000 0 -1.1 48 48
ITCH 0.015 0.098 -10000 0 -10000 0 0
CBLB 0.015 0.098 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.33 0.46 -10000 0 -1.2 59 59
JUNB 0.013 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.039 0.1 -10000 0 -10000 0 0
T cell anergy -0.004 0.16 -10000 0 -0.44 18 18
TLE4 0.011 0.17 -10000 0 -0.79 8 8
Jun/NFAT1-c-4/p21SNFT -0.15 0.24 -10000 0 -1 12 12
AP-1/NFAT1-c-4 -0.38 0.44 -10000 0 -1.2 51 51
IKZF1 -0.001 0.21 -10000 0 -0.89 12 12
T-helper 2 cell differentiation -0.04 0.21 -10000 0 -0.85 12 12
AP-1/NFAT1 -0.14 0.2 -10000 0 -0.64 25 25
CALM1 0.005 0.063 -10000 0 -10000 0 0
EGR2 -0.048 0.32 -10000 0 -1.5 10 10
EGR3 -0.03 0.25 -10000 0 -1.2 7 7
NFAT1/FOXP3 -0.14 0.36 -10000 0 -0.81 58 58
EGR1 -0.01 0.12 -10000 0 -0.64 11 11
JUN -0.018 0.035 -10000 0 -10000 0 0
EGR4 -0.08 0.26 -10000 0 -0.79 35 35
mol:Ca2+ -0.01 0.068 -10000 0 -10000 0 0
GBP3 -0.016 0.23 -10000 0 -0.8 20 20
FOSL1 0.005 0.081 -10000 0 -0.8 3 3
NFAT1-c-4/MAF/IRF4 -0.12 0.27 -10000 0 -1 13 13
DGKA 0.012 0.16 -10000 0 -0.74 8 8
CREM 0.013 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.22 0.3 -10000 0 -1.1 17 17
CTLA4 -0.16 0.42 -10000 0 -1 50 50
NFAT1-c-4 (dimer)/EGR1 -0.097 0.25 -10000 0 -0.98 15 15
NFAT1-c-4 (dimer)/EGR4 -0.14 0.28 -10000 0 -0.94 19 19
FOS -0.13 0.24 -10000 0 -0.67 49 49
IFNG -0.19 0.32 -10000 0 -0.76 61 61
T cell activation -0.094 0.21 -10000 0 -0.79 8 8
MAF 0.009 0.053 -10000 0 -0.64 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.025 0.16 0.7 8 -10000 0 8
TNF -0.11 0.31 -10000 0 -0.96 21 21
FASLG -0.096 0.37 -10000 0 -1.3 18 18
TBX21 -0.042 0.19 -10000 0 -0.8 17 17
BATF3 0.005 0.081 -10000 0 -0.8 3 3
PRKCQ -0.001 0.1 -10000 0 -0.72 6 6
PTPN1 0.012 0.16 -10000 0 -0.74 8 8
NFAT1-c-4/ICER1 -0.084 0.23 -10000 0 -0.96 13 13
GATA3 -0.012 0.14 -10000 0 -0.77 10 10
T-helper 1 cell differentiation -0.18 0.33 -10000 0 -0.74 61 61
IL2RA -0.3 0.4 -10000 0 -1 58 58
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.012 0.16 -10000 0 -0.74 8 8
E2F1 -0.025 0.19 -10000 0 -0.8 17 17
PPARG -0.24 0.32 -10000 0 -0.64 116 116
SLC3A2 0.012 0.16 -10000 0 -0.74 8 8
IRF4 -0.059 0.23 -10000 0 -0.77 28 28
PTGS2 -0.37 0.46 -10000 0 -1.1 56 56
CSF2 -0.52 0.51 -10000 0 -1.1 110 110
JunB/Fra1/NFAT1-c-4 -0.078 0.22 -10000 0 -0.93 12 12
IL4 -0.043 0.22 -10000 0 -0.94 10 10
IL5 -0.33 0.39 -10000 0 -1.1 39 39
IL2 -0.096 0.21 -10000 0 -0.83 7 7
IL3 -0.062 0.051 -10000 0 -10000 0 0
RNF128 -0.048 0.26 -10000 0 -0.7 40 40
NFATC1 -0.025 0.16 -10000 0 -0.71 8 8
CDK4 0.008 0.15 0.72 1 -10000 0 1
PTPRK 0.012 0.16 -10000 0 -0.74 8 8
IL8 -0.4 0.47 -10000 0 -1.1 78 78
POU2F1 0.014 0.002 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.086 0.14 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SLAP -0.17 0.27 -9999 0 -0.6 86 86
PDGFB-D/PDGFRB/APS/CBL -0.15 0.23 -9999 0 -0.52 86 86
AKT1 -0.047 0.18 -9999 0 -0.62 2 2
mol:PI-4-5-P2 -0.001 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.061 0.16 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
FGR -0.11 0.18 -9999 0 -0.41 2 2
mol:Ca2+ -0.064 0.16 -9999 0 -10000 0 0
MYC -0.023 0.12 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.12 0.19 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB -0.16 0.24 -9999 0 -0.53 89 89
GRB10 0.011 0.047 -9999 0 -0.8 1 1
PTPN11 0.013 0 -9999 0 -10000 0 0
GO:0007205 -0.066 0.16 -9999 0 -10000 0 0
PTEN 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 0.003 0.089 -9999 0 -0.76 4 4
PDGFB-D/PDGFRB/SHP2 -0.17 0.27 -9999 0 -0.6 85 85
PDGFB-D/PDGFRB/GRB10 -0.17 0.27 -9999 0 -0.6 86 86
cell cycle arrest -0.17 0.27 -9999 0 -0.6 86 86
HRAS 0.013 0 -9999 0 -10000 0 0
HIF1A -0.031 0.16 -9999 0 -0.53 2 2
GAB1 -0.066 0.16 -9999 0 -0.45 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.059 0.16 -9999 0 -0.43 1 1
PDGFB-D/PDGFRB -0.14 0.24 -9999 0 -0.52 85 85
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.17 0.27 -9999 0 -0.6 85 85
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.089 0.14 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.17 0.27 -9999 0 -0.6 85 85
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.066 0.16 -9999 0 -10000 0 0
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.18 0.28 -9999 0 -0.61 87 87
SHB 0.009 0.053 -9999 0 -0.64 2 2
BLK -0.17 0.21 -9999 0 -0.61 20 20
PTPN2 0.012 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.17 0.27 -9999 0 -0.6 85 85
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 -0.062 0.16 -9999 0 -0.44 1 1
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.17 0.27 -9999 0 -0.6 85 85
LCK -0.12 0.18 -9999 0 -0.45 12 12
PDGFRB -0.21 0.36 -9999 0 -0.8 85 85
ACP1 0.013 0 -9999 0 -10000 0 0
HCK -0.11 0.18 -9999 0 -0.5 3 3
ABL1 -0.076 0.17 -9999 0 -0.4 12 12
PDGFB-D/PDGFRB/CBL -0.064 0.16 -9999 0 -0.44 1 1
PTPN1 0.012 0.003 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 -0.048 0.22 -9999 0 -0.8 23 23
cell proliferation -0.02 0.12 -9999 0 -10000 0 0
SLA 0.011 0.047 -9999 0 -0.8 1 1
actin cytoskeleton reorganization -0.1 0.18 -9999 0 -10000 0 0
SRC -0.11 0.18 -9999 0 -10000 0 0
PI3K -0.1 0.17 -9999 0 -0.71 2 2
PDGFB-D/PDGFRB/GRB7/SHC -0.15 0.24 -9999 0 -0.53 87 87
SH2B2 0.011 0.047 -9999 0 -0.8 1 1
PLCgamma1/SPHK1 -0.063 0.16 -9999 0 -10000 0 0
LYN -0.11 0.18 -9999 0 -10000 0 0
LRP1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.11 0.18 -9999 0 -10000 0 0
SPHK1 0.002 0.08 -9999 0 -0.8 3 3
EDG1 -0.001 0.004 -9999 0 -10000 0 0
mol:DAG -0.066 0.16 -9999 0 -10000 0 0
PLCG1 -0.068 0.16 -9999 0 -10000 0 0
NHERF/PDGFRB -0.15 0.24 -9999 0 -0.52 86 86
YES1 -0.11 0.18 -9999 0 -0.41 1 1
cell migration -0.15 0.24 -9999 0 -0.52 86 86
SHC/Grb2/SOS1 -0.11 0.18 -9999 0 -10000 0 0
SLC9A3R2 0.011 0.047 -9999 0 -0.8 1 1
SLC9A3R1 0.009 0.053 -9999 0 -0.64 2 2
NHERF1-2/PDGFRB/PTEN -0.14 0.22 -9999 0 -0.48 85 85
FYN -0.11 0.18 -9999 0 -0.54 2 2
DOK1 -0.1 0.23 -9999 0 -0.46 85 85
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB -0.003 0.11 -9999 0 -0.8 6 6
RAC1 -0.045 0.15 -9999 0 -10000 0 0
PRKCD -0.1 0.23 -9999 0 -0.47 85 85
FER -0.1 0.23 -9999 0 -0.47 85 85
MAPKKK cascade -0.11 0.18 -9999 0 -10000 0 0
RASA1 -0.1 0.23 -9999 0 -0.47 85 85
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk -0.11 0.2 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.17 0.27 -9999 0 -0.6 87 87
chemotaxis -0.074 0.17 -9999 0 -0.39 12 12
STAT1-3-5/STAT1-3-5 -0.14 0.2 -9999 0 -0.82 6 6
Bovine Papilomavirus E5/PDGFRB -0.17 0.28 -9999 0 -0.61 85 85
PTPRJ 0.013 0 -9999 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 -0.17 0.34 -10000 0 -0.8 67 67
EFNB1 -0.021 0.16 -10000 0 -0.62 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.15 0.22 -10000 0 -0.82 10 10
Ephrin B2/EPHB1-2 -0.14 0.22 -10000 0 -0.48 87 87
neuron projection morphogenesis -0.14 0.21 -10000 0 -0.78 10 10
Ephrin B1/EPHB1-2/Tiam1 -0.15 0.24 -10000 0 -0.49 92 92
DNM1 -0.044 0.21 -10000 0 -0.8 21 21
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.014 0.065 -10000 0 -0.62 3 3
YES1 -0.007 0.086 -10000 0 -0.86 3 3
Ephrin B1/EPHB1-2/NCK2 -0.15 0.24 -10000 0 -0.49 91 91
PI3K 0.014 0.065 -10000 0 -0.63 3 3
mol:GDP -0.16 0.24 -10000 0 -0.48 92 92
ITGA2B -0.04 0.2 -10000 0 -0.8 20 20
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.007 0.086 -10000 0 -0.86 3 3
MAP3K7 -0.006 0.066 -10000 0 -0.66 3 3
FGR -0.007 0.085 -10000 0 -0.85 3 3
TIAM1 0.007 0.065 -10000 0 -0.64 3 3
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.017 0.15 -10000 0 -0.64 4 4
LYN -0.007 0.086 -10000 0 -0.86 3 3
Ephrin B1/EPHB1-2/Src Family Kinases -0.01 0.08 -10000 0 -0.8 3 3
Ephrin B1/EPHB1-2 -0.012 0.071 -10000 0 -0.72 3 3
SRC -0.007 0.085 -10000 0 -0.85 3 3
ITGB3 -0.017 0.15 -10000 0 -0.76 12 12
EPHB1 -0.038 0.19 -10000 0 -0.75 20 20
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.063 0.19 -10000 0 -0.62 31 31
BLK -0.027 0.095 -10000 0 -0.86 3 3
HCK -0.008 0.087 -10000 0 -0.86 3 3
regulation of stress fiber formation 0.15 0.24 0.49 91 -10000 0 91
MAPK8 0.02 0.068 -10000 0 -0.58 3 3
Ephrin B1/EPHB1-2/RGS3 -0.15 0.24 -10000 0 -0.49 91 91
endothelial cell migration -0.001 0.057 -10000 0 -0.56 3 3
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.004 0.076 -10000 0 -0.75 3 3
regulation of focal adhesion formation 0.15 0.24 0.49 91 -10000 0 91
chemotaxis 0.15 0.24 0.49 91 -10000 0 91
PIK3CA 0.013 0 -10000 0 -10000 0 0
Rac1/GTP -0.14 0.22 -10000 0 -0.81 10 10
angiogenesis -0.012 0.071 -10000 0 -0.72 3 3
LCK -0.01 0.086 -10000 0 -0.85 3 3
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.011 0.047 -10000 0 -0.8 1 1
RAS family/GTP/Tiam1 -0.092 0.11 -10000 0 -0.46 2 2
NT3 (dimer)/TRKC -0.25 0.3 -10000 0 -0.56 133 133
NT3 (dimer)/TRKB -0.25 0.3 -10000 0 -0.53 141 141
SHC/Grb2/SOS1/GAB1/PI3K 0.04 0 -10000 0 -10000 0 0
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.042 0.2 -10000 0 -0.72 23 23
PIK3CA 0.013 0 -10000 0 -10000 0 0
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.062 0.24 -10000 0 -0.8 28 28
NTRK2 -0.17 0.31 -10000 0 -0.68 80 80
NTRK3 -0.14 0.28 -10000 0 -0.64 73 73
NT-4/5 (dimer)/TRKB -0.14 0.22 -10000 0 -0.45 90 90
neuron apoptosis 0.12 0.13 0.46 10 -10000 0 10
SHC 2-3/Grb2 -0.12 0.14 -10000 0 -0.51 10 10
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.11 0.13 0.22 1 -0.4 32 33
SHC3 -0.12 0.14 -10000 0 -0.41 36 36
STAT3 (dimer) 0.014 0.054 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.19 0.25 -10000 0 -0.47 121 121
RIN/GDP -0.053 0.11 -10000 0 -0.29 2 2
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.088 0.13 0.26 1 -0.47 6 7
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.014 0.12 -10000 0 -0.8 7 7
MAGED1 0.011 0.038 -10000 0 -0.64 1 1
PTPN11 0.013 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.013 0.001 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.18 0.27 -10000 0 -0.57 92 92
TRKA/NEDD4-2 -0.057 0.18 -10000 0 -0.61 28 28
ELMO1 0.013 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.16 0.34 -10000 0 -0.8 66 66
HRAS 0.013 0 -10000 0 -10000 0 0
DOCK1 0.013 0 -10000 0 -10000 0 0
GAB2 0.009 0.053 -10000 0 -0.64 2 2
RIT2 0.001 0.003 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.005 0.081 -10000 0 -0.8 3 3
DNM1 -0.043 0.21 -10000 0 -0.8 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.085 0.13 0.25 1 -0.46 6 7
mol:GDP -0.079 0.15 -10000 0 -0.42 9 9
NGF (dimer) -0.16 0.33 -10000 0 -0.8 66 66
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.047 0.11 -10000 0 -0.28 3 3
TIAM1 0.007 0.065 -10000 0 -0.64 3 3
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.15 0.22 -10000 0 -0.45 99 99
KIDINS220/CRKL/C3G -0.002 0.035 -10000 0 -0.61 1 1
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.005 0.052 -10000 0 -0.53 3 3
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.18 0.3 -10000 0 -0.64 90 90
RAP1/GDP -0.06 0.072 -10000 0 -0.37 1 1
KIDINS220/CRKL 0.011 0.047 -10000 0 -0.8 1 1
BDNF (dimer) -0.042 0.2 -10000 0 -0.72 23 23
ubiquitin-dependent protein catabolic process -0.16 0.26 -10000 0 -0.56 86 86
Schwann cell development -0.051 0.038 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.005 0.047 -10000 0 -0.48 3 3
FRS2 family/SHP2/CRK family/C3G/GAB2 0.039 0.035 -10000 0 -10000 0 0
RAP1B 0.011 0.047 -10000 0 -0.8 1 1
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.28 0.3 -10000 0 -0.7 85 85
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.05 0.077 -10000 0 -0.57 1 1
STAT3 0.014 0.054 -10000 0 -10000 0 0
axon guidance -0.26 0.28 -10000 0 -0.66 85 85
MAPK3 -0.13 0.26 -10000 0 -0.52 92 92
MAPK1 -0.13 0.26 -10000 0 -0.52 92 92
CDC42/GDP -0.047 0.11 -10000 0 -0.29 1 1
NTF3 -0.18 0.3 -10000 0 -0.64 90 90
NTF4 0.013 0.001 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM -0.16 0.26 -10000 0 -0.56 86 86
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.19 0.23 0.26 1 -0.54 70 71
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.21 0.3 -10000 0 -0.51 135 135
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.007 0.087 -10000 0 -10000 0 0
Rac1/GDP -0.047 0.11 -10000 0 -0.29 2 2
NGF (dimer)/TRKA/GRIT -0.16 0.27 -10000 0 -0.57 88 88
neuron projection morphogenesis -0.051 0.13 -10000 0 -0.54 1 1
NGF (dimer)/TRKA/NEDD4-2 -0.16 0.26 -10000 0 -0.56 86 86
MAP2K1 0.043 0 -10000 0 -10000 0 0
NGFR -0.023 0.16 -10000 0 -0.73 15 15
NGF (dimer)/TRKA/GIPC/GAIP -0.07 0.16 -10000 0 -0.55 9 9
RAS family/GTP/PI3K 0.034 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.004 0.044 -10000 0 -0.45 3 3
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.038 -10000 0 -0.64 1 1
MAPKKK cascade -0.09 0.14 -10000 0 -0.44 11 11
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.057 0.18 -10000 0 -0.61 28 28
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.13 0.2 -10000 0 -0.52 31 31
NGF (dimer)/TRKA/p62/Atypical PKCs -0.14 0.22 -10000 0 -0.9 6 6
MATK -0.008 0.13 -10000 0 -0.8 8 8
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.056 0.067 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.095 0.14 0.28 1 -0.39 21 22
Rac1/GTP -0.13 0.13 -10000 0 -0.38 34 34
FRS2 family/SHP2/CRK family -0.006 0.051 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.099 0.24 -10000 0 -0.6 38 38
TBX21 -0.13 0.45 -10000 0 -1.2 30 30
B2M 0.011 0.01 -10000 0 -10000 0 0
TYK2 0.018 0.02 -10000 0 -10000 0 0
IL12RB1 -0.068 0.26 -10000 0 -0.82 32 32
GADD45B -0.047 0.29 -10000 0 -0.85 12 12
IL12RB2 -0.15 0.33 -10000 0 -0.79 63 63
GADD45G -0.063 0.32 -10000 0 -0.91 19 19
natural killer cell activation 0.008 0.024 -10000 0 -10000 0 0
RELB 0.008 0.066 -10000 0 -0.8 2 2
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.005 0.12 -10000 0 -0.64 10 10
IL2RA -0.086 0.27 -10000 0 -0.8 37 37
IFNG -0.15 0.32 -10000 0 -0.8 59 59
STAT3 (dimer) -0.073 0.32 -10000 0 -0.82 29 29
HLA-DRB5 -0.015 0.14 -10000 0 -0.75 11 11
FASLG -0.13 0.46 -10000 0 -1.3 31 31
NF kappa B2 p52/RelB -0.19 0.35 -10000 0 -1 34 34
CD4 0.007 0.06 -10000 0 -0.72 2 2
SOCS1 -0.054 0.22 -10000 0 -0.8 25 25
EntrezGene:6955 -0.006 0.017 -10000 0 -10000 0 0
CD3D -0.002 0.093 -10000 0 -0.71 5 5
CD3E -0.011 0.13 -10000 0 -0.77 8 8
CD3G -0.035 0.18 -10000 0 -0.74 18 18
IL12Rbeta2/JAK2 -0.099 0.26 -10000 0 -0.6 63 63
CCL3 -0.12 0.43 -10000 0 -1.2 28 28
CCL4 -0.12 0.43 -10000 0 -1.2 27 27
HLA-A 0.006 0.06 -10000 0 -0.72 2 2
IL18/IL18R 0.03 0.13 -10000 0 -0.45 19 19
NOS2 -0.13 0.43 -10000 0 -1.1 29 29
IL12/IL12R/TYK2/JAK2/SPHK2 -0.075 0.22 -10000 0 -0.58 31 31
IL1R1 -0.1 0.4 -10000 0 -1.1 26 26
IL4 -0.006 0.024 -10000 0 -10000 0 0
JAK2 0.018 0.02 -10000 0 -10000 0 0
EntrezGene:6957 -0.006 0.016 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.11 0.35 -10000 0 -0.85 42 42
RAB7A -0.026 0.27 -10000 0 -0.75 8 8
lysosomal transport -0.022 0.26 -10000 0 -0.71 8 8
FOS -0.21 0.52 -10000 0 -1.3 55 55
STAT4 (dimer) -0.071 0.35 -10000 0 -0.91 27 27
STAT5A (dimer) -0.26 0.41 -10000 0 -1.1 49 49
GZMA -0.14 0.48 -10000 0 -1.2 38 38
GZMB -0.15 0.47 -10000 0 -1.1 42 42
HLX 0.008 0.066 -10000 0 -0.8 2 2
LCK -0.14 0.46 -10000 0 -1.2 34 34
TCR/CD3/MHC II/CD4 -0.044 0.21 -10000 0 -0.67 19 19
IL2/IL2R -0.086 0.22 -10000 0 -0.57 45 45
MAPK14 -0.048 0.31 -10000 0 -0.82 18 18
CCR5 -0.07 0.35 -10000 0 -1.2 15 15
IL1B -0.059 0.24 -10000 0 -0.79 29 29
STAT6 -0.007 0.12 -10000 0 -10000 0 0
STAT4 -0.002 0.11 -10000 0 -0.78 6 6
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 -0.048 0.22 -10000 0 -0.8 23 23
NFKB1 0.013 0 -10000 0 -10000 0 0
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B -0.07 0.26 -10000 0 -0.81 33 33
CD8A -0.062 0.23 -10000 0 -0.76 29 29
CD8B -0.071 0.24 -10000 0 -0.77 32 32
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.098 0.24 0.6 38 -10000 0 38
IL2RB -0.003 0.11 -10000 0 -0.8 6 6
proteasomal ubiquitin-dependent protein catabolic process -0.06 0.32 -10000 0 -0.82 27 27
IL2RG -0.016 0.15 -10000 0 -0.79 11 11
IL12 -0.055 0.22 -10000 0 -0.59 43 43
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.026 0.17 -10000 0 -0.78 14 14
IL2 0.002 0.047 -10000 0 -0.8 1 1
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.004 0.12 -10000 0 -0.64 10 10
IL12/IL12R/TYK2/JAK2 -0.15 0.51 -10000 0 -1.3 34 34
MAP2K3 -0.049 0.3 -10000 0 -0.8 19 19
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.059 0.32 -10000 0 -0.84 21 21
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.008 0.053 -10000 0 -0.64 2 2
IL18RAP -0.002 0.12 -10000 0 -0.71 8 8
IL12Rbeta1/TYK2 -0.041 0.21 -10000 0 -0.63 32 32
EOMES -0.098 0.27 -10000 0 -0.65 53 53
STAT1 (dimer) -0.13 0.38 -10000 0 -0.89 41 41
T cell proliferation -0.018 0.26 0.44 2 -0.65 17 19
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.012 0.062 -10000 0 -0.74 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.22 -10000 0 -0.73 18 18
ATF2 -0.036 0.29 -10000 0 -0.79 14 14
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.067 0.16 -10000 0 -0.58 22 22
FYN -0.043 0.24 -10000 0 -0.71 28 28
LAT/GRAP2/SLP76 -0.052 0.2 -10000 0 -0.66 23 23
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.013 0.16 -10000 0 -0.47 25 25
B2M 0.013 0.005 -10000 0 -10000 0 0
IKBKG -0.02 0.045 -10000 0 -0.18 2 2
MAP3K8 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ -0.047 0.047 -10000 0 -0.13 19 19
integrin-mediated signaling pathway -0.001 0.023 -10000 0 -0.4 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.039 0.24 -10000 0 -0.68 29 29
TRPV6 -0.33 0.33 -10000 0 -0.65 153 153
CD28 -0.032 0.18 -10000 0 -0.79 17 17
SHC1 -0.045 0.24 -10000 0 -0.71 28 28
receptor internalization -0.042 0.25 -10000 0 -0.7 31 31
PRF1 -0.059 0.29 -10000 0 -0.86 30 30
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 0 0.13 -10000 0 -0.38 20 20
LAT -0.051 0.26 -10000 0 -0.78 28 28
EntrezGene:6955 -0.001 0.005 -10000 0 -10000 0 0
CD3D 0.001 0.093 -10000 0 -0.71 5 5
CD3E -0.007 0.13 -10000 0 -0.77 8 8
CD3G -0.031 0.18 -10000 0 -0.74 18 18
RASGRP2 0.005 0.024 -10000 0 -0.12 5 5
RASGRP1 -0.008 0.18 -10000 0 -0.5 26 26
HLA-A 0.008 0.06 -10000 0 -0.72 2 2
RASSF5 0.011 0.038 -10000 0 -0.64 1 1
RAP1A/GTP/RAPL -0.001 0.023 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.025 0.058 -10000 0 -0.13 17 17
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.04 0.078 -10000 0 -0.27 12 12
PRKCA -0.011 0.097 -10000 0 -0.31 15 15
GRAP2 -0.007 0.12 -10000 0 -0.74 8 8
mol:IP3 0.05 0.2 0.24 112 -0.49 17 129
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.039 0.24 -10000 0 -0.62 33 33
ORAI1 0.17 0.17 -10000 0 -10000 0 0
CSK -0.048 0.25 -10000 0 -0.72 28 28
B7 family/CD28 -0.19 0.29 -10000 0 -0.78 43 43
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.065 0.28 -10000 0 -0.8 31 31
PTPN6 -0.053 0.25 -10000 0 -0.73 28 28
VAV1 -0.048 0.25 -10000 0 -0.72 29 29
Monovalent TCR/CD3 -0.025 0.18 -10000 0 -0.58 23 23
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.052 0.26 -10000 0 -0.76 28 28
PAG1 -0.05 0.25 -10000 0 -0.7 30 30
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.068 0.28 -10000 0 -0.77 33 33
CD80 -0.24 0.38 -10000 0 -0.8 93 93
CD86 0.01 0.047 -10000 0 -0.8 1 1
PDK1/CARD11/BCL10/MALT1 -0.048 0.095 -10000 0 -0.3 22 22
HRAS 0.013 0 -10000 0 -10000 0 0
GO:0035030 -0.11 0.26 -10000 0 -0.62 43 43
CD8A -0.059 0.23 -10000 0 -0.75 29 29
CD8B -0.067 0.24 -10000 0 -0.76 32 32
PTPRC -0.013 0.14 -10000 0 -0.74 10 10
PDK1/PKC theta -0.015 0.2 -10000 0 -0.59 25 25
CSK/PAG1 -0.044 0.24 -10000 0 -0.69 29 29
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.01 0.047 -10000 0 -0.54 2 2
GRAP2/SLP76 -0.066 0.23 -10000 0 -0.68 29 29
STIM1 0.09 0.086 -10000 0 -10000 0 0
RAS family/GTP 0.024 0.074 -10000 0 -0.18 8 8
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.049 0.28 -10000 0 -0.77 31 31
mol:DAG -0.009 0.14 -10000 0 -0.43 20 20
RAP1A/GDP 0.012 0.025 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.023 0.17 -10000 0 -0.78 14 14
cytotoxic T cell degranulation -0.054 0.28 -10000 0 -0.81 30 30
RAP1A/GTP -0.002 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.025 0.2 -10000 0 -0.54 29 29
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.034 0.24 0.27 74 -0.66 18 92
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.022 0.16 -10000 0 -0.75 14 14
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.046 0.2 -10000 0 -0.62 24 24
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.013 0 -10000 0 -10000 0 0
CD8 heterodimer -0.094 0.29 -10000 0 -0.78 42 42
CARD11 -0.047 0.21 -10000 0 -0.79 23 23
PRKCB -0.014 0.11 -10000 0 -0.36 17 17
PRKCE -0.009 0.096 -10000 0 -0.31 15 15
PRKCQ -0.029 0.23 -10000 0 -0.65 29 29
LCP2 0.005 0.081 -10000 0 -0.8 3 3
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.007 0.14 -10000 0 -0.39 25 25
IKK complex 0.032 0.054 -10000 0 -0.13 5 5
RAS family/GDP -0.003 0.008 -10000 0 -10000 0 0
MAP3K14 0.01 0.1 -10000 0 -0.3 12 12
PDPK1 -0.009 0.16 -10000 0 -0.46 22 22
TCR/CD3/MHC I/CD8/Fyn -0.054 0.28 -10000 0 -0.76 34 34
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 -0.001 0.046 -9999 0 -0.64 1 1
SVIL 0.002 0.024 -9999 0 -10000 0 0
ZNF318 0.04 0.064 -9999 0 -10000 0 0
JMJD2C 0.006 0.027 -9999 0 -0.12 11 11
T-DHT/AR/Ubc9 -0.1 0.18 -9999 0 -0.46 57 57
CARM1 0.012 0.004 -9999 0 -10000 0 0
PRDX1 0.015 0.004 -9999 0 -10000 0 0
PELP1 0.018 0.01 -9999 0 -10000 0 0
CTNNB1 0.003 0.042 -9999 0 -0.64 1 1
AKT1 0.022 0.018 -9999 0 -10000 0 0
PTK2B 0.006 0.016 -9999 0 -10000 0 0
MED1 0.02 0.051 -9999 0 -0.8 1 1
MAK 0.028 0.11 -9999 0 -0.67 5 5
response to oxidative stress 0.002 0.005 -9999 0 -10000 0 0
HIP1 0.002 0.024 -9999 0 -10000 0 0
GSN 0.001 0.027 -9999 0 -10000 0 0
NCOA2 0.003 0.075 -9999 0 -0.64 4 4
NCOA6 0.003 0.023 -9999 0 -10000 0 0
DNA-PK 0.033 0.068 -9999 0 -10000 0 0
NCOA4 0.011 0.005 -9999 0 -10000 0 0
PIAS3 0.005 0.019 -9999 0 -10000 0 0
cell proliferation -0.011 0.12 -9999 0 -0.77 5 5
XRCC5 0.02 0.014 -9999 0 -10000 0 0
UBE3A -0.004 0.039 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.2 -9999 0 -0.48 63 63
FHL2 -0.024 0.12 -9999 0 -1 2 2
RANBP9 0.003 0.023 -9999 0 -10000 0 0
JMJD1A -0.06 0.077 -9999 0 -0.14 147 147
CDK6 0.001 0.1 -9999 0 -0.8 5 5
TGFB1I1 -0.019 0.13 -9999 0 -0.81 8 8
T-DHT/AR/CyclinD1 -0.12 0.2 -9999 0 -0.49 61 61
XRCC6 0.02 0.014 -9999 0 -10000 0 0
T-DHT/AR -0.12 0.21 -9999 0 -0.49 59 59
CTDSP1 0.011 0.005 -9999 0 -10000 0 0
CTDSP2 0.033 0.043 -9999 0 -10000 0 0
BRCA1 0.002 0.024 -9999 0 -10000 0 0
TCF4 0.028 0.031 -9999 0 -10000 0 0
CDKN2A -0.3 0.39 -9999 0 -0.76 124 124
SRF 0.03 0.024 -9999 0 -10000 0 0
NKX3-1 -0.13 0.14 -9999 0 -0.82 2 2
KLK3 -0.25 0.57 -9999 0 -1.4 57 57
TMF1 0.011 0.005 -9999 0 -10000 0 0
HNRNPA1 0.025 0.026 -9999 0 -10000 0 0
AOF2 -0.013 0.028 -9999 0 -0.071 55 55
APPL1 0.042 0.038 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.094 0.18 -9999 0 -0.46 57 57
AR -0.14 0.27 -9999 0 -0.68 57 57
UBA3 0.011 0.005 -9999 0 -10000 0 0
PATZ1 0.025 0.026 -9999 0 -10000 0 0
PAWR 0.011 0.005 -9999 0 -10000 0 0
PRKDC 0.02 0.014 -9999 0 -10000 0 0
PA2G4 0.026 0.029 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.081 0.17 -9999 0 -0.42 57 57
RPS6KA3 0.001 0.027 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.1 0.18 -9999 0 -0.46 57 57
LATS2 0.024 0.023 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.077 0.17 -9999 0 -0.42 57 57
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.041 0.17 -9999 0 -0.65 21 21
KLK2 -0.08 0.19 -9999 0 -0.97 11 11
CASP8 0.017 0.008 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.093 0.18 -9999 0 -0.46 43 43
TMPRSS2 -0.52 0.52 -9999 0 -1.1 145 145
CCND1 -0.007 0.11 -9999 0 -0.72 7 7
PIAS1 -0.004 0.039 -9999 0 -10000 0 0
mol:T-DHT -0.026 0.037 -9999 0 -0.069 103 103
CDC2L1 0.001 0.002 -9999 0 -10000 0 0
PIAS4 -0.014 0.059 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.11 0.19 -9999 0 -0.47 61 61
CMTM2 -0.014 0.15 -9999 0 -0.8 11 11
SNURF -0.007 0.11 -9999 0 -0.64 9 9
ZMIZ1 -0.007 0.031 -9999 0 -10000 0 0
CCND3 0.014 0.002 -9999 0 -10000 0 0
TGIF1 0.025 0.026 -9999 0 -10000 0 0
FKBP4 0.003 0.023 -9999 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 -0.049 0.21 -10000 0 -0.8 22 22
GNB1/GNG2 -0.057 0.077 -10000 0 -0.21 20 20
AKT1 -0.002 0.12 -10000 0 -0.26 1 1
EGF -0.14 0.27 -10000 0 -0.64 69 69
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.018 0.1 -10000 0 -0.48 5 5
mol:Ca2+ -0.029 0.16 -10000 0 -0.3 58 58
LYN -0.016 0.1 -10000 0 -0.51 4 4
RhoA/GTP -0.034 0.051 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.033 0.18 -10000 0 -0.36 25 25
GNG2 0.011 0.047 -10000 0 -0.8 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.007 0.067 -10000 0 -10000 0 0
G beta5/gamma2 -0.074 0.1 -10000 0 -0.29 21 21
PRKCH -0.038 0.18 -10000 0 -0.38 26 26
DNM1 -0.043 0.21 -10000 0 -0.8 21 21
TXA2/TP beta/beta Arrestin3 -0.023 0.065 -10000 0 -0.26 18 18
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.006 0.076 -10000 0 -0.75 3 3
G12 family/GTP -0.084 0.12 -10000 0 -0.33 23 23
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.011 0.047 -10000 0 -0.8 1 1
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.12 0.36 15 -10000 0 15
mol:NADP 0 0.1 -10000 0 -0.8 5 5
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.008 0.12 -10000 0 -0.71 9 9
mol:IP3 -0.045 0.2 -10000 0 -0.38 59 59
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.074 0.26 -10000 0 -0.51 59 59
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.079 0.17 -10000 0 -0.57 13 13
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.021 0.11 -10000 0 -0.48 5 5
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR -0.008 0.13 -10000 0 -0.8 8 8
PRKCB1 -0.046 0.2 -10000 0 -0.37 59 59
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0 0.1 -10000 0 -0.8 5 5
TXA2/TXA2-R family -0.075 0.26 -10000 0 -0.52 62 62
LCK -0.029 0.12 -10000 0 -0.43 14 14
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.038 0.13 -10000 0 -0.46 22 22
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.046 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.037 0.12 -10000 0 -0.45 22 22
MAPK14 -0.008 0.13 -10000 0 -10000 0 0
TGM2/GTP -0.058 0.22 -10000 0 -0.49 28 28
MAPK11 -0.008 0.13 -10000 0 -0.25 3 3
ARHGEF1 -0.007 0.1 -10000 0 -0.23 1 1
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.045 0.2 -10000 0 -0.38 59 59
RAB11/GDP 0.013 0.002 -10000 0 -10000 0 0
ICAM1 -0.03 0.16 -10000 0 -0.33 34 34
cAMP biosynthetic process -0.044 0.19 -10000 0 -0.38 29 29
Gq family/GTP/EBP50 -0.008 0.088 -10000 0 -0.36 2 2
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.016 0.1 -10000 0 -0.51 4 4
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.013 0.12 -10000 0 -0.34 10 10
VCAM1 -0.04 0.18 -10000 0 -0.33 73 73
TP beta/Gq family/GDP/G beta5/gamma2 0.007 0.067 -10000 0 -10000 0 0
platelet activation -0.014 0.17 -10000 0 -0.32 22 22
PGI2/IP -0.016 0.1 -10000 0 -0.62 8 8
PRKACA 0.009 0.067 -10000 0 -0.34 10 10
Gq family/GDP/G beta5/gamma2 0.011 0.067 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2 -0.028 0.09 -10000 0 -0.35 21 21
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.015 0.15 -10000 0 -0.52 22 22
mol:DAG -0.054 0.22 -10000 0 -0.42 59 59
EGFR -0.014 0.15 -10000 0 -0.8 10 10
TXA2/TP alpha -0.066 0.24 -10000 0 -0.53 30 30
Gq family/GTP -0.038 0.094 -10000 0 -0.25 50 50
YES1 -0.016 0.1 -10000 0 -0.51 4 4
GNAI2/GTP -0.035 0.11 -10000 0 -0.43 14 14
PGD2/DP -0.006 0.057 -10000 0 -0.57 3 3
SLC9A3R1 0.009 0.053 -10000 0 -0.64 2 2
FYN -0.017 0.11 -10000 0 -0.54 5 5
mol:NO 0 0.1 -10000 0 -0.8 5 5
GNA15 0.013 0 -10000 0 -10000 0 0
PGK/cGMP -0.023 0.1 -10000 0 -0.49 14 14
RhoA/GDP 0.013 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.067 0.18 -10000 0 -0.79 9 9
NOS3 0 0.1 -10000 0 -0.8 5 5
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.039 0.18 -10000 0 -0.38 26 26
PRKCB -0.044 0.19 -10000 0 -0.37 58 58
PRKCE -0.037 0.19 -10000 0 -0.36 53 53
PRKCD -0.043 0.2 -10000 0 -0.38 55 55
PRKCG -0.064 0.22 -10000 0 -0.43 63 63
muscle contraction -0.063 0.25 -10000 0 -0.48 62 62
PRKCZ -0.032 0.18 -10000 0 -0.37 22 22
ARR3 0.001 0.004 -10000 0 -10000 0 0
TXA2/TP beta -0.039 0.13 -10000 0 -0.45 23 23
PRKCQ -0.043 0.19 -10000 0 -0.37 56 56
MAPKKK cascade -0.059 0.23 -10000 0 -0.44 61 61
SELE -0.045 0.19 -10000 0 -0.4 53 53
TP beta/GNAI2/GDP/G beta/gamma -0.038 0.12 -10000 0 -0.7 4 4
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.095 0.24 -10000 0 -0.64 50 50
chemotaxis -0.09 0.3 -10000 0 -0.6 64 64
GNA12 0.008 0.066 -10000 0 -0.8 2 2
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 0.013 0 -10000 0 -10000 0 0
Rac1/GTP 0 0 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.013 0.061 -10000 0 -10000 0 0
SMARCC2 0.015 0.003 -10000 0 -10000 0 0
SMARCC1 0.015 0.003 -10000 0 -10000 0 0
TBX21 -0.089 0.23 -10000 0 -0.84 21 21
SUMO2 0.014 0.007 -10000 0 -10000 0 0
STAT1 (dimer) -0.039 0.21 -10000 0 -0.78 23 23
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.009 0.053 -10000 0 -0.64 2 2
GR alpha/HSP90/FKBP51/HSP90 0.091 0.095 0.36 6 -10000 0 6
PRL -0.089 0.17 -10000 0 -0.8 5 5
cortisol/GR alpha (dimer)/TIF2 0.2 0.22 0.57 40 -10000 0 40
RELA -0.007 0.089 -10000 0 -10000 0 0
FGG 0.12 0.24 0.57 12 -0.66 15 27
GR beta/TIF2 0.09 0.11 0.41 6 -0.44 1 7
IFNG -0.35 0.31 -10000 0 -0.82 78 78
apoptosis 0.025 0.16 0.44 10 -0.71 1 11
CREB1 0.017 0.019 -10000 0 -10000 0 0
histone acetylation 0.006 0.12 0.5 2 -0.42 3 5
BGLAP -0.039 0.11 -10000 0 -10000 0 0
GR/PKAc 0.09 0.09 0.36 4 -10000 0 4
NF kappa B1 p50/RelA -0.019 0.16 -10000 0 -0.46 5 5
SMARCD1 0.015 0.003 -10000 0 -10000 0 0
MDM2 0.078 0.08 0.32 9 -10000 0 9
GATA3 -0.008 0.14 -10000 0 -0.76 10 10
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.29 0.28 -10000 0 -0.55 149 149
GSK3B 0.014 0.007 -10000 0 -10000 0 0
NR1I3 0.058 0.16 0.48 4 -0.76 2 6
CSN2 0.12 0.14 0.47 7 -0.49 1 8
BRG1/BAF155/BAF170/BAF60A 0.022 0.024 -10000 0 -10000 0 0
NFATC1 0.014 0.003 -10000 0 -10000 0 0
POU2F1 0.015 0.015 -10000 0 -10000 0 0
CDKN1A 0.03 0.042 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN 0.011 0.038 -10000 0 -0.64 1 1
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.092 0.092 0.36 4 -10000 0 4
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.038 0.21 0.46 4 -0.86 11 15
JUN -0.2 0.16 -10000 0 -0.66 15 15
IL4 -0.063 0.11 -10000 0 -0.58 1 1
CDK5R1 0.011 0.047 -10000 0 -0.8 1 1
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.15 0.31 -10000 0 -0.66 40 40
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.094 0.091 0.35 6 -10000 0 6
cortisol/GR alpha (monomer) 0.23 0.26 0.67 46 -10000 0 46
NCOA2 0.005 0.075 -10000 0 -0.64 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.17 0.24 -10000 0 -0.71 49 49
AP-1/NFAT1-c-4 -0.41 0.25 -10000 0 -0.83 49 49
AFP -0.14 0.19 -10000 0 -0.84 15 15
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.1 0.17 0.49 9 -0.48 1 10
TP53 0.031 0.065 -10000 0 -0.62 3 3
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.38 0.37 -10000 0 -0.95 79 79
KRT14 -0.22 0.38 -10000 0 -1.2 36 36
TBP 0.024 0 -10000 0 -10000 0 0
CREBBP 0.066 0.087 0.36 3 -10000 0 3
HDAC1 0.012 0.012 -10000 0 -10000 0 0
HDAC2 0.042 0.031 -10000 0 -10000 0 0
AP-1 -0.41 0.25 -10000 0 -0.83 49 49
MAPK14 0.014 0.007 -10000 0 -10000 0 0
MAPK10 -0.017 0.14 -10000 0 -0.65 14 14
MAPK11 0.014 0.007 -10000 0 -10000 0 0
KRT5 -0.26 0.21 -10000 0 -0.86 14 14
interleukin-1 receptor activity 0.029 0.031 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 -0.039 0.21 -10000 0 -0.78 23 23
CGA -0.055 0.13 -10000 0 -0.65 5 5
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.2 0.42 145 -10000 0 145
MAPK3 0.014 0.007 -10000 0 -10000 0 0
MAPK1 0.014 0.007 -10000 0 -10000 0 0
ICAM1 -0.14 0.25 -10000 0 -0.75 28 28
NFKB1 -0.007 0.089 -10000 0 -10000 0 0
MAPK8 -0.16 0.15 -10000 0 -0.58 16 16
MAPK9 0.014 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.017 0.16 0.44 10 -0.76 1 11
BAX 0.03 0.042 -10000 0 -10000 0 0
POMC -0.16 0.31 -10000 0 -0.86 35 35
EP300 0.068 0.088 0.35 7 -10000 0 7
cortisol/GR alpha (dimer)/p53 0.22 0.22 0.59 42 -0.58 1 43
proteasomal ubiquitin-dependent protein catabolic process 0.054 0.062 0.28 1 -10000 0 1
SGK1 0.12 0.13 -10000 0 -1.4 1 1
IL13 -0.21 0.18 -10000 0 -0.71 16 16
IL6 -0.18 0.36 -10000 0 -1.1 33 33
PRKACG 0.001 0.047 -10000 0 -0.8 1 1
IL5 -0.19 0.16 -10000 0 -0.82 6 6
IL2 -0.26 0.19 -10000 0 -0.74 17 17
CDK5 0.013 0.005 -10000 0 -10000 0 0
PRKACB 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.22 0.34 -10000 0 -0.74 74 74
CDK5R1/CDK5 0.002 0.038 -10000 0 -0.61 1 1
NF kappa B1 p50/RelA/PKAc 0.01 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.2 0.2 0.57 33 -10000 0 33
SMARCA4 0.015 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.13 0.4 24 -10000 0 24
NF kappa B1 p50/RelA/Cbp 0.065 0.16 0.45 2 -10000 0 2
JUN (dimer) -0.2 0.16 -10000 0 -0.66 15 15
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.076 0.2 -10000 0 -0.89 13 13
NR3C1 0.14 0.15 0.49 22 -10000 0 22
NR4A1 -0.022 0.13 -10000 0 -0.55 11 11
TIF2/SUV420H1 -0.006 0.054 -10000 0 -0.47 4 4
MAPKKK cascade 0.025 0.16 0.44 10 -0.71 1 11
cortisol/GR alpha (dimer)/Src-1 0.21 0.22 0.58 41 -10000 0 41
PBX1 -0.082 0.23 -10000 0 -0.64 45 45
POU1F1 0.003 0.016 -10000 0 -10000 0 0
SELE -0.23 0.42 -10000 0 -1.1 49 49
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.13 0.4 24 -10000 0 24
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.2 0.2 0.57 33 -10000 0 33
mol:cortisol 0.12 0.16 0.4 46 -10000 0 46
MMP1 -0.64 0.21 -10000 0 -0.71 271 271
LPA4-mediated 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
ADCY4 0.022 0 -9999 0 -10000 0 0
ADCY5 -0.072 0.18 -9999 0 -0.42 65 65
ADCY6 0.009 0.072 -9999 0 -0.4 9 9
ADCY7 0.022 0 -9999 0 -10000 0 0
ADCY1 -0.002 0.11 -9999 0 -0.54 13 13
ADCY2 -0.11 0.2 -9999 0 -0.41 95 95
ADCY3 0.022 0 -9999 0 -10000 0 0
ADCY8 -0.002 0.094 -9999 0 -0.54 9 9
PRKCE 0.012 0 -9999 0 -10000 0 0
ADCY9 0.022 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.048 0.11 -9999 0 -0.43 5 5
Caspase cascade in apoptosis

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
TOP1 -0.038 0.18 -10000 0 -0.42 49 49
ACTA1 -0.14 0.24 -10000 0 -0.63 51 51
NUMA1 -0.039 0.18 -10000 0 -0.53 25 25
SPTAN1 -0.063 0.24 -10000 0 -0.56 49 49
LIMK1 -0.063 0.24 -10000 0 -0.57 47 47
BIRC3 -0.024 0.17 -10000 0 -0.8 14 14
BIRC2 -0.003 0.11 -10000 0 -0.8 6 6
BAX 0.013 0 -10000 0 -10000 0 0
CASP10 -0.097 0.3 -10000 0 -0.72 52 52
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 -0.038 0.18 -10000 0 -0.42 49 49
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.061 0.23 -10000 0 -0.55 49 49
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN -0.063 0.24 -10000 0 -0.56 49 49
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.001 0.1 -10000 0 -0.6 5 5
BID -0.027 0.12 -10000 0 -0.35 23 23
MAP3K1 -0.011 0.075 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.063 0.24 -10000 0 -0.56 49 49
CASP9 0.013 0.002 -10000 0 -10000 0 0
DNA repair 0.006 0.063 -10000 0 -0.2 6 6
neuron apoptosis 0.018 0.024 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.053 0.23 -10000 0 -0.72 23 23
APAF1 0.013 0 -10000 0 -10000 0 0
CASP6 -0.002 0.1 -10000 0 -0.47 1 1
TRAF2 0.008 0.066 -10000 0 -0.8 2 2
ICAD/CAD -0.053 0.23 -10000 0 -0.74 22 22
CASP7 0.007 0.065 0.31 10 -10000 0 10
KRT18 0.004 0.065 -10000 0 -0.48 4 4
apoptosis -0.042 0.21 -10000 0 -0.66 22 22
DFFA -0.063 0.24 -10000 0 -0.56 49 49
DFFB -0.063 0.24 -10000 0 -0.57 46 46
PARP1 -0.006 0.063 0.2 6 -10000 0 6
actin filament polymerization 0.049 0.22 0.69 22 -10000 0 22
TNF -0.025 0.17 -10000 0 -0.76 15 15
CYCS -0.017 0.094 -10000 0 -0.27 22 22
SATB1 -0.006 0.12 -10000 0 -0.47 3 3
SLK -0.063 0.24 -10000 0 -0.56 49 49
p15 BID/BAX -0.018 0.11 -10000 0 -0.32 22 22
CASP2 0.034 0.071 -10000 0 -10000 0 0
JNK cascade 0.011 0.075 -10000 0 -10000 0 0
CASP3 -0.075 0.25 -10000 0 -0.6 49 49
LMNB2 0.028 0.06 -10000 0 -0.37 1 1
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.011 0.038 -10000 0 -0.64 1 1
Mammalian IAPs/DIABLO -0.031 0.14 -10000 0 -0.59 16 16
negative regulation of DNA binding -0.001 0.099 -10000 0 -0.6 5 5
stress fiber formation -0.061 0.23 -10000 0 -0.55 49 49
GZMB -0.12 0.34 -10000 0 -0.82 52 52
CASP1 0.016 0.032 -10000 0 -0.37 2 2
LMNB1 0.028 0.06 -10000 0 -0.37 1 1
APP 0.018 0.024 -10000 0 -10000 0 0
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM -0.045 0.2 -10000 0 -0.62 24 24
LMNA 0.028 0.06 -10000 0 -0.34 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.027 0.075 -10000 0 -0.37 4 4
LRDD 0.011 0.047 -10000 0 -0.8 1 1
SREBF1 -0.063 0.24 -10000 0 -0.56 49 49
APAF-1/Caspase 9 -0.001 0.075 0.48 5 -10000 0 5
nuclear fragmentation during apoptosis -0.038 0.18 -10000 0 -0.52 25 25
CFL2 -0.051 0.22 -10000 0 -0.72 22 22
GAS2 -0.12 0.26 -10000 0 -0.62 49 49
positive regulation of apoptosis 0.032 0.06 -10000 0 -0.37 1 1
PRF1 -0.051 0.22 -10000 0 -0.8 24 24
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.026 0.054 -9999 0 -0.39 5 5
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.024 0.063 -9999 0 -0.42 6 6
MAPK12 -0.011 0.14 -9999 0 -0.44 27 27
CCND1 -0.002 0.086 -9999 0 -0.38 9 9
p38 gamma/SNTA1 -0.003 0.13 -9999 0 -0.49 14 14
MAP2K3 0.011 0.038 -9999 0 -0.64 1 1
PKN1 0.008 0.066 -9999 0 -0.8 2 2
G2/M transition checkpoint -0.01 0.14 -9999 0 -0.44 27 27
MAP2K6 0.004 0.093 -9999 0 -0.38 17 17
MAPT -0.14 0.19 -9999 0 -0.35 131 131
MAPK13 0.017 0.063 -9999 0 -0.47 5 5
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0.037 -9999 0 -0.36 3 3
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.003 0.016 -10000 0 -10000 0 0
AES 0.002 0.014 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.01 0.078 -10000 0 -0.61 5 5
SMAD4 0.011 0.038 -10000 0 -0.64 1 1
DKK2 -0.012 0.14 -10000 0 -0.74 10 10
TLE1 0.002 0.014 -10000 0 -10000 0 0
MACF1 0.014 0.001 -10000 0 -10000 0 0
CTNNB1 0.047 0.12 -10000 0 -0.41 1 1
WIF1 -0.31 0.33 -10000 0 -0.65 145 145
beta catenin/RanBP3 -0.013 0.082 0.38 6 -10000 0 6
KREMEN2 -0.27 0.39 -10000 0 -0.8 106 106
DKK1 -0.23 0.37 -10000 0 -0.78 93 93
beta catenin/beta TrCP1 0.053 0.11 -10000 0 -10000 0 0
FZD1 0 0.1 -10000 0 -0.8 5 5
AXIN2 0.004 0.16 -10000 0 -1.5 3 3
AXIN1 0.014 0.001 -10000 0 -10000 0 0
RAN 0.013 0 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.025 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.088 0.065 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.005 0.041 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.058 0.072 -10000 0 -10000 0 0
HNF1A -0.014 0.11 -10000 0 -0.8 6 6
CTBP1 0.002 0.015 -10000 0 -10000 0 0
MYC 0.016 0.045 -10000 0 -0.53 1 1
RANBP3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.2 0.26 -10000 0 -0.53 114 114
NKD1 -0.015 0.14 -10000 0 -0.76 11 11
TCF4 0.002 0.015 -10000 0 -10000 0 0
TCF3 0.002 0.015 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.011 0.072 -10000 0 -0.48 7 7
Ran/GTP 0 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.008 0.084 0.53 5 -10000 0 5
LEF1 -0.003 0.067 -10000 0 -0.81 2 2
DVL1 0.066 0.06 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.1 0.072 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.34 0.34 -10000 0 -0.62 163 163
LRP6 0.014 0.001 -10000 0 -10000 0 0
CSNK1A1 0.003 0.016 -10000 0 -10000 0 0
NLK 0.014 0.003 -10000 0 -10000 0 0
CCND1 -0.006 0.19 -10000 0 -1.1 7 7
WNT1 0.006 0.066 -10000 0 -0.8 2 2
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
PPP2R5D 0.052 0.066 0.36 11 -10000 0 11
APC 0.031 0.073 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.12 0.13 0.25 145 -10000 0 145
CREBBP 0.002 0.015 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.13 0.24 -10000 0 -0.54 75 75
cell-cell adhesion 0.12 0.16 0.56 3 -10000 0 3
Ephrin B/EPHB2/RasGAP -0.12 0.19 -10000 0 -0.45 67 67
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.013 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.012 0.069 -10000 0 -0.4 9 9
Ephrin B1/EPHB1 -0.033 0.12 -10000 0 -0.5 20 20
HRAS/GDP -0.057 0.11 -10000 0 -0.57 2 2
Ephrin B/EPHB1/GRB7 -0.052 0.14 -10000 0 -0.47 19 19
Endophilin/SYNJ1 -0.081 0.2 -10000 0 -0.42 67 67
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.046 0.13 -10000 0 -0.47 16 16
endothelial cell migration 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 0.003 0.089 -10000 0 -0.76 4 4
PAK1 -0.096 0.22 -10000 0 -0.68 8 8
HRAS 0.013 0 -10000 0 -10000 0 0
RRAS -0.082 0.2 -10000 0 -0.43 67 67
DNM1 -0.043 0.21 -10000 0 -0.8 21 21
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.007 0.14 -10000 0 -0.45 16 16
lamellipodium assembly -0.12 0.16 -10000 0 -0.56 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.009 0.097 -10000 0 -0.5 2 2
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 -0.17 0.34 -10000 0 -0.8 67 67
EPHB3 -0.006 0.11 -10000 0 -0.64 9 9
EPHB1 -0.037 0.19 -10000 0 -0.75 20 20
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.054 0.11 -10000 0 -0.52 3 3
Ephrin B/EPHB2 -0.12 0.2 -10000 0 -0.46 67 67
Ephrin B/EPHB3 -0.03 0.099 -10000 0 -0.68 1 1
JNK cascade -0.093 0.22 -10000 0 -0.44 81 81
Ephrin B/EPHB1 -0.047 0.13 -10000 0 -0.48 16 16
RAP1/GDP -0.045 0.096 -10000 0 -0.48 2 2
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.025 0.16 -10000 0 -0.64 18 18
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.14 0.22 -10000 0 -0.48 87 87
RAP1B 0.011 0.047 -10000 0 -0.8 1 1
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.17 -10000 0 -0.62 3 3
Rap1/GTP -0.12 0.16 -10000 0 -0.57 3 3
axon guidance -0.13 0.23 -10000 0 -0.53 75 75
MAPK3 0.026 0.088 -10000 0 -0.44 2 2
MAPK1 0.026 0.088 -10000 0 -0.44 2 2
Rac1/GDP -0.012 0.12 -10000 0 -0.5 2 2
actin cytoskeleton reorganization -0.091 0.13 -10000 0 -0.44 3 3
CDC42/GDP -0.012 0.12 -10000 0 -0.5 2 2
PI3K 0 0 -10000 0 -10000 0 0
EFNA5 -0.01 0.12 -10000 0 -0.64 11 11
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.042 0.13 -10000 0 -0.54 1 1
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.16 -10000 0 -0.55 3 3
PTK2 0.029 0.046 -10000 0 -10000 0 0
MAP4K4 -0.094 0.22 -10000 0 -0.44 81 81
SRC 0.013 0 -10000 0 -10000 0 0
KALRN -0.025 0.16 -10000 0 -0.64 18 18
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.047 0.17 -10000 0 -0.49 5 5
MAP2K1 0.018 0.092 -10000 0 -0.47 2 2
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.14 0.21 -10000 0 -0.48 81 81
cell migration 0.022 0.1 -10000 0 -0.54 2 2
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 -0.082 0.2 -10000 0 -0.43 67 67
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.3 0.25 -10000 0 -0.7 62 62
HRAS/GTP -0.12 0.18 -10000 0 -0.61 3 3
Ephrin B1/EPHB1-2 -0.14 0.22 -10000 0 -0.48 87 87
cell adhesion mediated by integrin 0.014 0.087 0.34 16 -10000 0 16
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.13 0.19 -10000 0 -0.66 3 3
RAC1-CDC42/GTP -0.12 0.17 -10000 0 -0.58 6 6
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.043 0.094 -10000 0 -0.48 2 2
ruffle organization -0.068 0.2 -10000 0 -0.57 3 3
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization -0.1 0.24 -10000 0 -0.82 11 11
Ephrin B/EPHB2/KALRN -0.14 0.21 -10000 0 -0.47 72 72
ROCK1 0.016 0.066 -10000 0 -10000 0 0
RAS family/GDP -0.088 0.13 -10000 0 -0.5 1 1
Rac1/GTP -0.12 0.17 -10000 0 -0.6 3 3
Ephrin B/EPHB1/Src/Paxillin 0.003 0.1 -10000 0 -0.55 2 2
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.012 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.071 0.15 -10000 0 -0.37 58 58
regulation of S phase of mitotic cell cycle -0.025 0.12 -10000 0 -10000 0 0
GNAO1 0.008 0.06 -10000 0 -0.72 2 2
HRAS 0.013 0.001 -10000 0 -10000 0 0
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.029 0.14 -10000 0 -0.5 2 2
T-DHT/AR -0.092 0.19 -10000 0 -0.49 57 57
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 49 49
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.011 0.038 -10000 0 -0.64 1 1
mol:GDP -0.09 0.19 -10000 0 -0.48 57 57
cell proliferation -0.046 0.2 -10000 0 -0.61 13 13
PIK3CA 0.013 0 -10000 0 -10000 0 0
FOS -0.1 0.33 -10000 0 -0.84 49 49
mol:Ca2+ -0.011 0.02 -10000 0 -0.092 4 4
MAPK3 -0.036 0.17 -10000 0 -0.53 13 13
MAPK1 -0.016 0.099 -10000 0 -0.28 13 13
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.005 49 49
cAMP biosynthetic process 0.01 0.02 -10000 0 -10000 0 0
GNG2 0.011 0.047 -10000 0 -0.8 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.005 49 49
HRAS/GTP -0.066 0.13 -10000 0 -0.46 4 4
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.013 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.005 49 49
PI3K 0 0 -10000 0 -10000 0 0
apoptosis 0.044 0.19 0.42 49 -10000 0 49
T-DHT/AR/PELP1 -0.077 0.16 -10000 0 -0.42 57 57
HRAS/GDP -0.083 0.18 -10000 0 -0.45 57 57
CREB1 -0.049 0.2 -10000 0 -0.46 49 49
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.11 0.26 -10000 0 -0.65 57 57
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.034 0.14 -10000 0 -0.5 2 2
RAC1-CDC42/GDP -0.08 0.17 -10000 0 -0.43 53 53
T-DHT/AR/PELP1/Src -0.07 0.15 -10000 0 -0.42 15 15
MAP2K2 -0.029 0.14 -10000 0 -0.5 2 2
T-DHT/AR/PELP1/Src/PI3K -0.025 0.12 -10000 0 -10000 0 0
GNAZ -0.004 0.11 -10000 0 -0.73 7 7
SHBG 0.013 0.003 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.022 0.066 -10000 0 -0.44 1 1
mol:T-DHT 0 0.001 -10000 0 -0.003 36 36
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 -0.004 0.099 -10000 0 -0.61 8 8
Gi family/GTP -0.035 0.076 -10000 0 -0.4 4 4
CDC42 0.013 0 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.037 0.16 -10000 0 -0.45 17 17
IKBKB -0.015 0.082 -10000 0 -0.27 4 4
AKT1 -0.035 0.12 -10000 0 -0.29 26 26
IKBKG -0.014 0.086 -10000 0 -0.29 4 4
CALM1 -0.052 0.13 -10000 0 -0.41 22 22
PIK3CA 0.013 0 -10000 0 -10000 0 0
MAP3K1 -0.069 0.22 -10000 0 -0.65 21 21
MAP3K7 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ -0.064 0.13 -10000 0 -0.44 22 22
DOK1 0.013 0 -10000 0 -10000 0 0
AP-1 -0.033 0.1 -10000 0 -0.29 5 5
LYN 0.013 0 -10000 0 -10000 0 0
BLNK -0.056 0.2 -10000 0 -0.64 32 32
SHC1 0.013 0 -10000 0 -10000 0 0
BCR complex -0.16 0.31 -10000 0 -0.67 71 71
CD22 -0.14 0.29 -10000 0 -0.86 34 34
CAMK2G -0.041 0.12 -10000 0 -0.42 9 9
CSNK2A1 0.013 0 -10000 0 -10000 0 0
INPP5D 0.011 0.038 -10000 0 -0.64 1 1
SHC/GRB2/SOS1 -0.13 0.22 -10000 0 -0.72 22 22
GO:0007205 -0.064 0.14 -10000 0 -0.45 22 22
SYK 0.011 0.038 -10000 0 -0.64 1 1
ELK1 -0.055 0.13 -10000 0 -0.42 23 23
NFATC1 -0.082 0.21 -10000 0 -0.48 50 50
B-cell antigen/BCR complex -0.16 0.31 -10000 0 -0.67 71 71
PAG1/CSK -0.004 0.05 -10000 0 -0.61 2 2
NFKBIB 0.006 0.031 0.083 1 -10000 0 1
HRAS -0.058 0.14 -10000 0 -0.46 22 22
NFKBIA 0.006 0.031 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.012 0.026 -10000 0 -10000 0 0
RasGAP/Csk -0.12 0.24 -10000 0 -0.86 18 18
mol:GDP -0.062 0.13 -10000 0 -0.42 22 22
PTEN 0.013 0 -10000 0 -10000 0 0
CD79B -0.029 0.18 -10000 0 -0.78 16 16
NF-kappa-B/RelA/I kappa B alpha 0.013 0.025 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.11 0.24 -10000 0 -0.55 55 55
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.073 0.13 -10000 0 -0.45 22 22
CSK 0.013 0 -10000 0 -10000 0 0
FOS -0.095 0.18 -10000 0 -0.5 25 25
CHUK -0.014 0.086 -10000 0 -0.29 4 4
IBTK 0.013 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.08 0.14 -10000 0 -0.57 10 10
PTPN6 -0.13 0.27 -10000 0 -0.85 30 30
RELA 0.013 0 -10000 0 -10000 0 0
BCL2A1 0.007 0.038 -10000 0 -0.12 18 18
VAV2 -0.17 0.29 -10000 0 -0.76 51 51
ubiquitin-dependent protein catabolic process 0.01 0.03 0.086 1 -10000 0 1
BTK -0.004 0.03 0.38 1 -10000 0 1
CD19 -0.17 0.33 -10000 0 -0.81 55 55
MAP4K1 -0.012 0.14 -10000 0 -0.75 10 10
CD72 -0.083 0.26 -10000 0 -0.8 36 36
PAG1 0.008 0.066 -10000 0 -0.8 2 2
MAPK14 -0.048 0.19 -10000 0 -0.55 19 19
SH3BP5 0.011 0.038 -10000 0 -0.64 1 1
PIK3AP1 -0.073 0.16 -10000 0 -0.47 33 33
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.099 0.22 -10000 0 -0.66 25 25
RAF1 -0.047 0.14 -10000 0 -0.42 22 22
RasGAP/p62DOK/SHIP -0.12 0.23 -10000 0 -0.81 19 19
CD79A -0.16 0.32 -10000 0 -0.75 70 70
re-entry into mitotic cell cycle -0.034 0.1 -10000 0 -0.28 6 6
RASA1 0.013 0 -10000 0 -10000 0 0
MAPK3 -0.024 0.12 -10000 0 -0.51 1 1
MAPK1 -0.024 0.12 -10000 0 -0.51 1 1
CD72/SHP1 -0.12 0.32 -10000 0 -0.91 32 32
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.05 0.19 -10000 0 -0.55 19 19
actin cytoskeleton organization -0.11 0.26 -10000 0 -0.62 50 50
NF-kappa-B/RelA 0.031 0.048 -10000 0 -10000 0 0
Calcineurin -0.053 0.095 -10000 0 -0.55 1 1
PI3K -0.14 0.23 -10000 0 -0.62 50 50
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.077 0.14 -10000 0 -0.48 22 22
SOS1 0.013 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.067 0.23 -10000 0 -0.76 22 22
DAPP1 -0.094 0.21 -10000 0 -0.73 21 21
cytokine secretion -0.075 0.19 -10000 0 -0.45 50 50
mol:DAG -0.073 0.13 -10000 0 -0.45 22 22
PLCG2 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.035 0.13 -10000 0 -0.52 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.14 0.28 -10000 0 -0.68 53 53
mol:PI-3-4-5-P3 -0.099 0.16 -10000 0 -0.41 48 48
ETS1 -0.033 0.12 -10000 0 -0.43 4 4
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.15 0.25 -10000 0 -0.83 22 22
B-cell antigen/BCR complex/LYN -0.1 0.22 -10000 0 -0.78 19 19
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.013 0 -10000 0 -10000 0 0
RAC1 -0.12 0.28 -10000 0 -0.68 50 50
B-cell antigen/BCR complex/LYN/SYK -0.14 0.29 -10000 0 -0.92 29 29
CARD11 -0.086 0.18 -10000 0 -0.48 41 41
FCGR2B 0 0.091 -10000 0 -0.64 6 6
PPP3CA 0.013 0 -10000 0 -10000 0 0
BCL10 0.013 0 -10000 0 -10000 0 0
IKK complex 0.004 0.04 -10000 0 -10000 0 0
PTPRC -0.011 0.14 -10000 0 -0.74 10 10
PDPK1 -0.034 0.12 -10000 0 -0.29 27 27
PPP3CB 0.013 0 -10000 0 -10000 0 0
PPP3CC 0.013 0 -10000 0 -10000 0 0
POU2F2 0.006 0.044 -10000 0 -0.14 24 24
Reelin signaling pathway

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
CDK5R1/CDK5 -0.002 0.035 -9999 0 -0.61 1 1
VLDLR 0.003 0.083 -9999 0 -0.64 5 5
CRKL 0.011 0.047 -9999 0 -0.8 1 1
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.011 0.047 -9999 0 -0.8 1 1
ITGA3 -0.026 0.18 -9999 0 -0.79 15 15
RELN/VLDLR/Fyn -0.083 0.16 -9999 0 -0.4 63 63
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.004 0.037 -9999 0 -0.45 1 1
AKT1 -0.031 0.13 -9999 0 -0.54 4 4
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 -0.022 0.16 -9999 0 -0.8 12 12
RELN/LRP8/DAB1 -0.1 0.19 -9999 0 -0.42 72 72
LRPAP1/LRP8 -0.016 0.098 -9999 0 -0.61 8 8
RELN/LRP8/DAB1/Fyn -0.095 0.18 -9999 0 -0.54 21 21
DAB1/alpha3/beta1 Integrin -0.11 0.18 -9999 0 -0.72 7 7
long-term memory -0.16 0.23 -9999 0 -0.77 18 18
DAB1/LIS1 -0.09 0.17 -9999 0 -0.75 6 6
DAB1/CRLK/C3G -0.088 0.16 -9999 0 -0.72 7 7
PIK3CA 0.013 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.091 0.17 -9999 0 -0.75 6 6
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.12 0.29 -9999 0 -0.72 56 56
CDK5R1 0.011 0.047 -9999 0 -0.8 1 1
RELN -0.11 0.26 -9999 0 -0.64 57 57
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.09 0.18 -9999 0 -0.42 64 64
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.23 -9999 0 -0.56 54 54
MAPK8 0.009 0.053 -9999 0 -0.64 2 2
RELN/VLDLR/DAB1 -0.093 0.18 -9999 0 -0.4 70 70
ITGB1 0.011 0.047 -9999 0 -0.8 1 1
MAP1B -0.08 0.22 -9999 0 -0.64 19 19
RELN/LRP8 -0.088 0.18 -9999 0 -0.42 63 63
GRIN2B/RELN/LRP8/DAB1/Fyn -0.098 0.19 -9999 0 -0.54 23 23
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.032 0.14 -9999 0 -0.6 16 16
RAP1A -0.036 0.18 -9999 0 -0.67 7 7
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.011 0.047 -9999 0 -0.8 1 1
CRLK/C3G -0.002 0.035 -9999 0 -0.61 1 1
GRIN2B -0.003 0.08 -9999 0 -0.8 3 3
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.012 0.11 -9999 0 -0.42 7 7
neuron adhesion -0.041 0.19 -9999 0 -0.63 8 8
LRP8 -0.008 0.13 -9999 0 -0.8 8 8
GSK3B -0.021 0.13 -9999 0 -0.5 4 4
RELN/VLDLR/DAB1/Fyn -0.088 0.17 -9999 0 -0.56 13 13
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.042 0.14 -9999 0 -0.57 4 4
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT -0.25 0.3 -9999 0 -0.6 131 131
neuron migration -0.025 0.18 -9999 0 -0.56 6 6
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.012 0.11 -9999 0 -0.42 7 7
RELN/VLDLR -0.085 0.16 -9999 0 -0.56 8 8
IL1-mediated signaling events

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.038 -10000 0 -0.64 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.013 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.021 0.062 -10000 0 -10000 0 0
IRAK/TOLLIP 0.034 0.003 -10000 0 -10000 0 0
IKBKB 0.013 0 -10000 0 -10000 0 0
IKBKG 0.013 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.24 0.3 -10000 0 -0.58 128 128
IL1A -0.18 0.34 -10000 0 -0.8 72 72
IL1B -0.037 0.19 -10000 0 -0.6 30 30
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.016 -10000 0 -10000 0 0
IL1R2 -0.13 0.27 -10000 0 -0.65 64 64
IL1R1 0.013 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.011 0.056 0.22 5 -10000 0 5
TOLLIP 0.013 0 -10000 0 -10000 0 0
TICAM2 0.013 0 -10000 0 -10000 0 0
MAP3K3 0.013 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.073 0.007 -10000 0 -10000 0 0
JUN 0.036 0.07 -10000 0 -10000 0 0
MAP3K7 0.013 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.042 0.12 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.11 0.2 -10000 0 -0.48 70 70
PIK3R1 0.013 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.11 0.19 -10000 0 -0.45 70 70
IL1 beta fragment/IL1R1/IL1RAP -0.048 0.14 -10000 0 -0.48 28 28
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.029 0.074 -10000 0 -10000 0 0
IRAK1 0.029 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.14 0.22 -10000 0 -0.47 90 90
IRAK4 0.013 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
TRAF6 0.013 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.017 0.079 -10000 0 -10000 0 0
CHUK 0.013 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.048 0.14 -10000 0 -0.48 28 28
IL1 beta/IL1R2 -0.14 0.22 -10000 0 -0.56 35 35
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.037 0.11 -10000 0 -10000 0 0
IRAK3 -0.004 0.12 -10000 0 -0.76 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.042 0.12 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.03 0.12 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.13 0.22 -10000 0 -0.52 73 73
RELA 0.013 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
MYD88 0.013 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -10000 0 -10000 0 0
IL1RAP 0.011 0.047 -10000 0 -0.8 1 1
UBE2N 0.013 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.034 0.1 -10000 0 -10000 0 0
CASP1 0.011 0.038 -10000 0 -0.64 1 1
IL1RN/IL1R2 -0.23 0.31 -10000 0 -0.59 119 119
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.044 0.13 -10000 0 -0.45 28 28
TMEM189-UBE2V1 0.011 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.036 0.078 -10000 0 -10000 0 0
PIK3CA 0.013 0 -10000 0 -10000 0 0
IL1RN -0.18 0.3 -10000 0 -0.64 90 90
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 0.023 0.072 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.015 0.15 -10000 0 -0.46 2 2
CRKL -0.011 0.14 -10000 0 -0.4 30 30
HRAS -0.007 0.15 -10000 0 -0.53 5 5
mol:PIP3 -0.025 0.13 -10000 0 -0.4 29 29
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.013 0 -10000 0 -10000 0 0
GAB1 -0.019 0.14 -10000 0 -0.43 29 29
FOXO3 -0.003 0.13 -10000 0 -0.4 3 3
AKT1 -0.013 0.14 -10000 0 -0.4 29 29
BAD -0.003 0.13 -10000 0 -0.39 4 4
megakaryocyte differentiation -0.033 0.16 -10000 0 -0.43 39 39
GSK3B -0.003 0.13 -10000 0 -0.4 3 3
RAF1 0.006 0.13 -10000 0 -0.49 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.019 0.14 -10000 0 -0.43 29 29
STAT1 -0.086 0.35 -10000 0 -1.1 29 29
HRAS/SPRED1 -0.049 0.097 -10000 0 -0.42 5 5
cell proliferation -0.02 0.15 -10000 0 -0.43 29 29
PIK3CA 0.013 0 -10000 0 -10000 0 0
TEC -0.023 0.15 -10000 0 -0.64 17 17
RPS6KB1 -0.019 0.14 -10000 0 -0.43 29 29
HRAS/SPRED2 -0.049 0.097 -10000 0 -0.42 5 5
LYN/TEC/p62DOK -0.063 0.14 -10000 0 -0.66 6 6
MAPK3 0.02 0.096 -10000 0 -10000 0 0
STAP1 -0.056 0.18 -10000 0 -0.44 53 53
GRAP2 -0.007 0.12 -10000 0 -0.74 8 8
JAK2 -0.11 0.25 -10000 0 -0.84 29 29
STAT1 (dimer) -0.083 0.34 -10000 0 -1 29 29
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.084 0.17 -10000 0 -0.59 9 9
actin filament polymerization -0.019 0.15 -10000 0 -0.44 29 29
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.059 0.22 -10000 0 -0.59 32 32
PIK3R1 0.013 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.042 0.11 -10000 0 -10000 0 0
PI3K -0.047 0.12 -10000 0 -0.4 25 25
PTEN 0.013 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.11 0.42 -10000 0 -1.3 29 29
MAPK8 -0.021 0.15 -10000 0 -0.44 29 29
STAT3 (dimer) -0.018 0.14 -10000 0 -0.42 29 29
positive regulation of transcription 0.022 0.083 -10000 0 -10000 0 0
mol:GDP -0.071 0.14 -10000 0 -0.6 6 6
PIK3C2B -0.02 0.15 -10000 0 -0.44 29 29
CBL/CRKL -0.002 0.13 -10000 0 -0.4 2 2
FER -0.019 0.14 -10000 0 -0.43 29 29
SH2B3 -0.02 0.15 -10000 0 -0.43 30 30
PDPK1 -0.015 0.12 -10000 0 -0.44 3 3
SNAI2 -0.025 0.16 -10000 0 -0.44 32 32
positive regulation of cell proliferation -0.046 0.25 -10000 0 -0.74 29 29
KITLG 0.015 0.009 -10000 0 -10000 0 0
cell motility -0.046 0.25 -10000 0 -0.74 29 29
PTPN6 0.007 0.012 -10000 0 -10000 0 0
EPOR 0.002 0.14 -10000 0 -0.91 1 1
STAT5A (dimer) -0.03 0.2 -10000 0 -0.6 29 29
SOCS1 -0.054 0.22 -10000 0 -0.8 25 25
cell migration 0.03 0.16 0.43 36 -10000 0 36
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.055 0.22 -10000 0 -0.8 25 25
VAV1 0.003 0.083 -10000 0 -0.64 5 5
GRB10 -0.02 0.15 -10000 0 -0.43 30 30
PTPN11 0.006 0.01 -10000 0 -10000 0 0
SCF/KIT -0.054 0.14 -10000 0 -0.46 29 29
GO:0007205 0.001 0.009 -10000 0 -10000 0 0
MAP2K1 0.017 0.1 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.093 0.41 -10000 0 -1.3 30 30
MAP2K2 0.017 0.1 -10000 0 -0.36 1 1
SHC/Grb2/SOS1 -0.046 0.12 -10000 0 -0.43 2 2
STAT5A -0.032 0.21 -10000 0 -0.62 29 29
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.024 0.15 -10000 0 -0.44 32 32
SHC/GRAP2 -0.015 0.09 -10000 0 -0.56 8 8
PTPRO -0.034 0.16 -10000 0 -0.44 39 39
SH2B2 -0.02 0.15 -10000 0 -0.44 29 29
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.031 0.16 -10000 0 -0.44 36 36
CREBBP 0.035 0.014 -10000 0 -10000 0 0
BCL2 0.002 0.17 -10000 0 -1.2 4 4
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 -0.25 0.21 -10000 0 -0.91 2 2
IHH -0.049 0.062 -10000 0 -0.76 1 1
SHH Np/Cholesterol/GAS1 -0.044 0.14 -10000 0 -0.48 28 28
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.044 0.14 0.48 28 -10000 0 28
SMO/beta Arrestin2 -0.13 0.13 -10000 0 -0.53 8 8
SMO -0.14 0.14 -10000 0 -0.57 8 8
AKT1 -0.051 0.071 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.047 0.19 -10000 0 -0.64 28 28
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.14 0.14 -10000 0 -0.56 8 8
STIL -0.12 0.15 -10000 0 -0.58 18 18
DHH N/PTCH2 -0.025 0.11 -10000 0 -0.51 15 15
DHH N/PTCH1 -0.13 0.13 -10000 0 -0.59 5 5
PIK3CA 0.013 0 -10000 0 -10000 0 0
DHH -0.004 0.11 -10000 0 -0.69 7 7
PTHLH -0.43 0.32 -10000 0 -1.2 1 1
determination of left/right symmetry -0.14 0.14 -10000 0 -0.56 8 8
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.43 0.32 -10000 0 -0.64 77 77
IHH N/Hhip -0.057 0.17 -10000 0 -0.67 22 22
DHH N/Hhip -0.054 0.17 -10000 0 -0.58 28 28
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.14 0.14 -10000 0 -0.56 8 8
pancreas development -0.045 0.2 -10000 0 -0.79 21 21
HHAT 0.013 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.004 0.084 -10000 0 -0.72 4 4
somite specification -0.14 0.14 -10000 0 -0.56 8 8
SHH Np/Cholesterol/PTCH1 -0.13 0.16 -10000 0 -0.62 17 17
SHH Np/Cholesterol/PTCH2 -0.049 0.15 -10000 0 -0.53 24 24
SHH Np/Cholesterol/Megalin -0.061 0.18 -10000 0 -0.54 34 34
SHH -0.03 0.17 -10000 0 -0.62 24 24
catabolic process -0.15 0.13 -10000 0 -10000 0 0
SMO/Vitamin D3 -0.14 0.16 -10000 0 -0.6 17 17
SHH Np/Cholesterol/Hhip -0.071 0.2 -10000 0 -0.57 38 38
LRP2 -0.026 0.17 -10000 0 -0.8 14 14
receptor-mediated endocytosis -0.16 0.15 -10000 0 -0.58 20 20
SHH Np/Cholesterol/BOC -0.072 0.16 -10000 0 -0.43 51 51
SHH Np/Cholesterol/CDO -0.043 0.14 -10000 0 -0.47 28 28
mesenchymal cell differentiation 0.071 0.2 0.56 38 -10000 0 38
mol:Vitamin D3 -0.13 0.16 -10000 0 -0.62 17 17
IHH N/PTCH2 -0.023 0.098 -10000 0 -0.57 9 9
CDON 0.005 0.075 -10000 0 -0.64 4 4
IHH N/PTCH1 -0.15 0.13 -10000 0 -10000 0 0
Megalin/LRPAP1 -0.028 0.13 -10000 0 -0.61 14 14
PTCH2 -0.005 0.11 -10000 0 -0.68 8 8
SHH Np/Cholesterol -0.039 0.13 -10000 0 -0.5 24 24
PTCH1 -0.15 0.13 -10000 0 -10000 0 0
HHIP -0.045 0.2 -10000 0 -0.8 21 21
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.008 0.061 -10000 0 -0.62 2 2
HDAC1 0.001 0.007 -10000 0 -10000 0 0
AES 0.012 0.001 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 0.011 0.038 -10000 0 -0.64 1 1
LRP6/FZD1 -0.01 0.078 -10000 0 -0.61 5 5
TLE1 0.013 0.001 -10000 0 -10000 0 0
AP1 -0.037 0.14 -10000 0 -0.32 51 51
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 0.013 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.038 0.048 -10000 0 -10000 0 0
NICD/RBPSUH -0.004 0.05 -10000 0 -0.61 2 2
WIF1 -0.31 0.33 -10000 0 -0.65 145 145
NOTCH1 -0.005 0.053 -10000 0 -0.65 2 2
PSENEN 0.011 0.047 -10000 0 -0.8 1 1
KREMEN2 -0.27 0.39 -10000 0 -0.8 106 106
DKK1 -0.23 0.37 -10000 0 -0.78 93 93
beta catenin/beta TrCP1 0.017 0.04 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0.002 0.024 -10000 0 -0.27 1 1
CtBP/CBP/TCF1/TLE1/AES -0.002 0.044 -10000 0 -10000 0 0
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.092 0.24 -10000 0 -0.64 49 49
JUN 0.013 0 -10000 0 -10000 0 0
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.01 0.043 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.2 0.26 -10000 0 -0.53 114 114
HNF1A -0.004 0.11 -10000 0 -0.8 6 6
CTBP1 0.012 0.001 -10000 0 -10000 0 0
MYC 0.025 0.014 -10000 0 -10000 0 0
NKD1 -0.015 0.14 -10000 0 -0.76 11 11
FZD1 0 0.1 -10000 0 -0.8 5 5
NOTCH1 precursor/Deltex homolog 1 -0.005 0.064 -10000 0 -0.78 2 2
apoptosis -0.037 0.14 -10000 0 -0.31 51 51
Delta 1/NOTCHprecursor -0.008 0.061 -10000 0 -0.61 2 2
DLL1 0.005 0.075 -10000 0 -0.64 4 4
PPARD 0.025 0.014 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.026 -10000 0 -0.45 1 1
APC 0.002 0.024 -10000 0 -0.27 1 1
DVL1 -0.026 0.026 -10000 0 -10000 0 0
CSNK2A1 0.014 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.34 0.34 -10000 0 -0.62 164 164
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.002 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -10000 0 0
CCND1 0.001 0.18 -10000 0 -1.1 7 7
WNT1 0.005 0.066 -10000 0 -0.8 2 2
Axin1/APC/beta catenin 0.023 0.04 -10000 0 -10000 0 0
DKK2 -0.011 0.14 -10000 0 -0.74 10 10
NOTCH1 precursor/DVL1 -0.011 0.049 -10000 0 -0.61 2 2
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.005 0.064 -10000 0 -0.78 2 2
PPP2R5D -0.001 0.063 0.31 11 -10000 0 11
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.18 0.18 -10000 0 -0.48 15 15
RBPJ 0.013 0 -10000 0 -10000 0 0
CREBBP 0.017 0.003 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.007 0.011 -10000 0 -10000 0 0
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.053 0.17 -10000 0 -0.54 12 12
AKT1 0.002 0.031 -10000 0 -10000 0 0
GSC -0.017 0.18 -10000 0 -0.63 23 23
NKX2-5 -0.2 0.35 -10000 0 -0.79 80 80
muscle cell differentiation 0.15 0.22 0.66 29 -10000 0 29
SMAD2-3/SMAD4/SP1 -0.059 0.1 -10000 0 -10000 0 0
SMAD4 -0.001 0.054 -10000 0 -0.61 1 1
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.014 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.001 0.048 -10000 0 -0.53 2 2
SMAD3/SMAD4/VDR 0.005 0.039 -10000 0 -10000 0 0
MYC 0.025 0.032 -10000 0 -10000 0 0
CDKN2B -0.22 0.56 -10000 0 -1.4 57 57
AP1 -0.02 0.13 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.057 0.038 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.054 0.16 -10000 0 -0.59 7 7
SP3 0.016 0.001 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.08 0.26 -10000 0 -0.79 34 34
SMAD3/SMAD4/GR 0.035 0.073 -10000 0 -10000 0 0
GATA3 -0.013 0.14 -10000 0 -0.76 10 10
SKI/SIN3/HDAC complex/NCoR1 0.058 0.017 -10000 0 -10000 0 0
MEF2C/TIF2 -0.16 0.25 -10000 0 -0.77 21 21
endothelial cell migration 0.37 0.32 0.64 181 -10000 0 181
MAX 0.035 0.02 -10000 0 -10000 0 0
RBBP7 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.014 0.002 -10000 0 -10000 0 0
RUNX2 0.011 0.038 -10000 0 -0.64 1 1
RUNX3 0.005 0.081 -10000 0 -0.8 3 3
RUNX1 0.013 0 -10000 0 -10000 0 0
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.035 0.02 -10000 0 -10000 0 0
VDR 0.013 0 -10000 0 -10000 0 0
CDKN1A -0.001 0.095 -10000 0 -10000 0 0
KAT2B -0.019 0.13 -10000 0 -0.65 13 13
SMAD2/SMAD2/SMAD4/FOXH1 -0.06 0.18 -10000 0 -0.54 34 34
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.014 0.002 -10000 0 -10000 0 0
SERPINE1 -0.37 0.33 -10000 0 -0.64 181 181
SMAD3/SMAD4/ATF2 0.009 0.054 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.002 0.084 -10000 0 -0.52 4 4
SAP30 0.014 0.002 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.002 0.028 -10000 0 -10000 0 0
JUN -0.005 0.13 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.001 0.1 -10000 0 -0.63 4 4
TFE3 0 0.017 -10000 0 -10000 0 0
COL1A2 -0.34 0.35 -10000 0 -0.68 155 155
mesenchymal cell differentiation -0.008 0.059 0.39 1 -10000 0 1
DLX1 -0.38 0.41 -10000 0 -0.8 146 146
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.087 0.24 -10000 0 -0.63 49 49
SMAD3/SMAD4/Max 0.035 0.073 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.002 0.01 -10000 0 -10000 0 0
ZBTB17 0.023 0.025 -10000 0 -10000 0 0
LAMC1 0.005 0.048 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.007 0.066 -10000 0 -0.64 1 1
IRF7 0 0.1 -10000 0 -0.8 5 5
ESR1 -0.009 0.18 -10000 0 -0.74 17 17
HNF4A -0.07 0.24 -10000 0 -0.8 30 30
MEF2C -0.15 0.28 -10000 0 -0.76 24 24
SMAD2-3/SMAD4 -0.003 0.067 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.005 0.018 -10000 0 -10000 0 0
IGHV3OR16-13 -0.002 0.012 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.011 0.047 -10000 0 -0.8 1 1
CREBBP 0.007 0.01 -10000 0 -10000 0 0
SKIL 0.013 0 -10000 0 -10000 0 0
HDAC1 0.014 0.002 -10000 0 -10000 0 0
HDAC2 0.014 0.002 -10000 0 -10000 0 0
SNIP1 0.015 0.005 -10000 0 -10000 0 0
GCN5L2 -0.009 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.009 0.05 -10000 0 -10000 0 0
MSG1/HSC70 0.014 0.053 -10000 0 -0.61 2 2
SMAD2 0.002 0.036 -10000 0 -10000 0 0
SMAD3 0.004 0.051 -10000 0 -0.59 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.023 0.043 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.025 0.084 -10000 0 -0.39 14 14
NCOR1 0.014 0.002 -10000 0 -10000 0 0
NCOA2 0.005 0.075 -10000 0 -0.64 4 4
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.088 0.19 -10000 0 -0.48 56 56
SMAD2-3/SMAD4/SP1/MIZ-1 -0.048 0.098 -10000 0 -10000 0 0
IFNB1 0.01 0.13 -10000 0 -0.72 6 6
SMAD3/SMAD4/MEF2C -0.14 0.27 -10000 0 -0.79 19 19
CITED1 0.008 0.066 -10000 0 -0.8 2 2
SMAD2-3/SMAD4/ARC105 0.004 0.068 -10000 0 -0.54 1 1
RBL1 0.013 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.054 0.22 -10000 0 -0.5 57 57
RUNX1-3/PEBPB2 -0.005 0.052 -10000 0 -0.53 3 3
SMAD7 -0.042 0.13 -10000 0 -10000 0 0
MYC/MIZ-1 0.03 0.063 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.13 0.15 0.35 4 -0.41 3 7
IL10 0 0.17 -10000 0 -0.72 10 10
PIASy/HDAC complex 0.023 0.012 -10000 0 -10000 0 0
PIAS3 0.006 0.008 -10000 0 -10000 0 0
CDK2 0.007 0.009 -10000 0 -10000 0 0
IL5 0.002 0.14 -10000 0 -0.71 5 5
CDK4 0.007 0.01 -10000 0 -10000 0 0
PIAS4 0.023 0.012 -10000 0 -10000 0 0
ATF3 0.002 0.092 -10000 0 -0.71 5 5
SMAD3/SMAD4/SP1 -0.077 0.087 -10000 0 -10000 0 0
FOXG1 -0.1 0.26 -10000 0 -0.72 44 44
FOXO3 0.01 0.042 -10000 0 -10000 0 0
FOXO1 0.01 0.042 -10000 0 -10000 0 0
FOXO4 0.007 0.057 -10000 0 -0.47 2 2
heart looping -0.14 0.28 -10000 0 -0.75 24 24
CEBPB 0.008 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.27 0.29 -10000 0 -0.57 146 146
MYOD1 -0.11 0.26 -10000 0 -0.65 56 56
SMAD3/SMAD4/HNF4 -0.049 0.18 -10000 0 -0.56 30 30
SMAD3/SMAD4/GATA3 -0.012 0.13 -10000 0 -0.57 8 8
SnoN/SIN3/HDAC complex/NCoR1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.013 0.068 -10000 0 -0.47 3 3
SMAD3/SMAD4/SP1-3 -0.056 0.07 -10000 0 -10000 0 0
MED15 0.011 0.047 -10000 0 -0.8 1 1
SP1 -0.053 0.075 -10000 0 -10000 0 0
SIN3B 0.014 0.002 -10000 0 -10000 0 0
SIN3A 0.014 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.18 0.28 -10000 0 -0.56 85 85
ITGB5 -0.012 0.093 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.054 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.069 0.18 -10000 0 -0.45 37 37
AR -0.11 0.26 -10000 0 -0.65 57 57
negative regulation of cell growth 0.025 0.056 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.075 0.18 -10000 0 -0.45 46 46
E2F5 0.013 0 -10000 0 -10000 0 0
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.054 0.15 -10000 0 -0.48 15 15
SMAD2-3/SMAD4/FOXO1-3a-4 -0.026 0.15 -10000 0 -0.38 1 1
TFDP1 0.011 0.047 -10000 0 -0.8 1 1
SMAD3/SMAD4/AP1 -0.012 0.14 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.008 0.059 -10000 0 -0.39 1 1
TGIF2 0.011 0.047 -10000 0 -0.8 1 1
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 0.013 0 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.046 0.16 0.62 22 -10000 0 22
KIRREL 0.006 0.042 -10000 0 -0.64 1 1
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.047 0.16 -10000 0 -0.62 22 22
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.046 0.16 -10000 0 -0.55 25 25
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.002 0.1 -10000 0 -0.56 5 5
FYN -0.025 0.15 -10000 0 -0.49 26 26
mol:Ca2+ -0.046 0.16 -10000 0 -0.54 25 25
mol:DAG -0.046 0.16 -10000 0 -0.54 25 25
NPHS2 -0.025 0.14 -10000 0 -0.84 9 9
mol:IP3 -0.046 0.16 -10000 0 -0.54 25 25
regulation of endocytosis -0.04 0.14 -10000 0 -0.48 20 20
Nephrin/NEPH1/podocin/Cholesterol -0.047 0.16 -10000 0 -0.55 26 26
establishment of cell polarity -0.046 0.16 -10000 0 -0.62 22 22
Nephrin/NEPH1/podocin/NCK1-2 -0.042 0.15 -10000 0 -0.85 5 5
Nephrin/NEPH1/beta Arrestin2 -0.041 0.14 -10000 0 -0.73 6 6
NPHS1 -0.05 0.21 -10000 0 -0.81 21 21
Nephrin/NEPH1/podocin -0.044 0.15 -10000 0 -0.5 26 26
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.046 0.16 -10000 0 -0.55 25 25
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.046 0.16 -10000 0 -0.55 25 25
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.063 0.21 -10000 0 -0.51 49 49
cytoskeleton organization 0 0.14 -10000 0 -0.75 5 5
Nephrin/NEPH1 -0.035 0.12 -10000 0 -0.47 22 22
Nephrin/NEPH1/ZO-1 -0.038 0.13 -10000 0 -0.52 21 21
Signaling events mediated by PTP1B

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
PDGFRB -0.22 0.37 -10000 0 -0.8 85 85
Jak2/Leptin Receptor -0.074 0.1 -10000 0 -0.38 6 6
PTP1B/AKT1 -0.029 0.078 0.23 1 -10000 0 1
FYN 0.011 0.047 -10000 0 -0.8 1 1
p210 bcr-abl/PTP1B -0.041 0.087 0.26 1 -0.32 2 3
EGFR -0.017 0.14 -10000 0 -0.8 10 10
EGF/EGFR -0.13 0.16 -10000 0 -0.42 44 44
CSF1 0.009 0.053 -10000 0 -0.64 2 2
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.013 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.12 0.21 0.23 1 -0.53 53 54
Insulin Receptor/Insulin -0.033 0.043 -10000 0 -10000 0 0
HCK 0.004 0.084 -10000 0 -0.72 4 4
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.031 0.083 0.25 1 -0.33 1 2
EGF -0.14 0.28 -10000 0 -0.65 69 69
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.062 0.11 0.25 1 -0.36 11 12
TXN 0.01 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.036 0.067 -10000 0 -10000 0 0
cell migration 0.041 0.087 0.32 2 -0.26 1 3
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.13 0.27 -10000 0 -0.65 64 64
ITGA2B -0.041 0.2 -10000 0 -0.8 20 20
CSF1R 0.009 0.053 -10000 0 -0.64 2 2
Prolactin Receptor/Prolactin -0.1 0.21 -10000 0 -0.49 66 66
FGR 0.011 0.047 -10000 0 -0.8 1 1
PTP1B/p130 Cas -0.032 0.082 0.23 1 -0.33 1 2
Crk/p130 Cas -0.036 0.067 -10000 0 -10000 0 0
DOK1 -0.079 0.15 0.25 1 -0.39 13 14
JAK2 -0.07 0.12 -10000 0 -0.36 18 18
Jak2/Leptin Receptor/Leptin -0.086 0.12 -10000 0 -0.49 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.042 0.088 0.26 1 -0.32 2 3
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.13 0.31 -10000 0 -0.79 55 55
SRC 0 0.037 -10000 0 -10000 0 0
ITGB3 -0.018 0.15 -10000 0 -0.76 12 12
CAT1/PTP1B -0.14 0.16 0.26 1 -0.44 24 25
CAPN1 0.011 0.005 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.022 0.037 -10000 0 -10000 0 0
mol:H2O2 0 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.076 0.11 -10000 0 -0.46 1 1
negative regulation of transcription -0.069 0.12 -10000 0 -0.36 18 18
FCGR2A -0.046 0.21 -10000 0 -0.8 22 22
FER 0.01 0.006 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.063 0.19 -10000 0 -0.62 31 31
BLK -0.12 0.3 -10000 0 -0.77 53 53
Insulin Receptor/Insulin/Shc 0 0.002 -10000 0 -10000 0 0
RHOA 0.011 0.005 -10000 0 -10000 0 0
LEPR 0.013 0.001 -10000 0 -10000 0 0
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH -0.002 0.004 -10000 0 -10000 0 0
TRPV6 -0.13 0.16 -10000 0 -0.46 33 33
PRL -0.004 0.08 -10000 0 -0.8 3 3
SOCS3 0.018 0.082 -10000 0 -1.4 1 1
SPRY2 0.004 0.075 -10000 0 -0.65 4 4
Insulin Receptor/Insulin/IRS1 0 0.002 -10000 0 -10000 0 0
CSF1/CSF1R -0.041 0.074 -10000 0 -0.39 1 1
Ras protein signal transduction 0.03 0.028 -10000 0 -10000 0 0
IRS1 0.013 0 -10000 0 -10000 0 0
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.11 0.26 -10000 0 -0.7 50 50
STAT5B -0.048 0.085 0.21 1 -0.29 4 5
STAT5A -0.048 0.085 0.21 1 -0.29 4 5
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.16 0.26 0.23 1 -0.56 85 86
CSN2 -0.025 0.09 -10000 0 -0.66 1 1
PIK3CA 0.013 0 -10000 0 -10000 0 0
LAT -0.027 0.093 -10000 0 -0.32 14 14
YBX1 0.02 0.002 -10000 0 -10000 0 0
LCK -0.014 0.15 -10000 0 -0.8 10 10
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.21 0.36 -10000 0 -0.8 83 83
Syndecan-3-mediated signaling events

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.005 0.12 -9999 0 -0.8 7 7
Syndecan-3/Src/Cortactin -0.12 0.16 -9999 0 -0.72 4 4
Syndecan-3/Neurocan -0.012 0.07 -9999 0 -0.45 7 7
POMC -0.067 0.24 -9999 0 -0.77 31 31
EGFR -0.014 0.15 -9999 0 -0.8 10 10
Syndecan-3/EGFR -0.016 0.082 -9999 0 -0.44 11 11
AGRP 0.005 0.006 -9999 0 -10000 0 0
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.011 0.047 -9999 0 -0.8 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.009 0.12 -9999 0 -0.8 7 7
long-term memory -0.012 0.069 -9999 0 -0.42 8 8
Syndecan-3/IL8 -0.097 0.18 -9999 0 -0.45 65 65
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin -0.014 0.092 -9999 0 -0.61 7 7
FYN 0.011 0.047 -9999 0 -0.8 1 1
limb bud formation -0.001 0.021 -9999 0 -0.36 1 1
MC4R 0.006 0.007 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PTN -0.23 0.32 -9999 0 -0.64 111 111
FGFR/FGF/Syndecan-3 -0.001 0.022 -9999 0 -0.37 1 1
neuron projection morphogenesis -0.12 0.16 -9999 0 -0.69 5 5
Syndecan-3/AgRP -0.001 0.021 -9999 0 -0.35 1 1
Syndecan-3/AgRP/MC4R -0.001 0.019 -9999 0 -10000 0 0
Fyn/Cortactin -0.016 0.098 -9999 0 -0.61 8 8
SDC3 -0.002 0.022 -9999 0 -0.37 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.096 0.18 -9999 0 -0.44 66 66
IL8 -0.16 0.33 -9999 0 -0.8 65 65
Syndecan-3/Fyn/Cortactin -0.013 0.071 -9999 0 -0.43 8 8
Syndecan-3/CASK -0.001 0.021 -9999 0 -0.35 1 1
alpha-MSH/MC4R -0.06 0.18 -9999 0 -0.59 31 31
Gamma Secretase -0.001 0.026 -9999 0 -0.45 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.004 0.05 -9999 0 -0.61 2 2
alphaV beta3 Integrin -0.04 0.14 -9999 0 -0.58 16 16
PTK2 -0.002 0.15 -9999 0 -0.68 3 3
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
CDKN1B -0.047 0.12 -9999 0 -0.4 27 27
VEGFA 0.011 0.047 -9999 0 -0.8 1 1
ILK -0.047 0.12 -9999 0 -0.4 27 27
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.042 0.11 -9999 0 -0.49 3 3
PTK2B 0.018 0.11 -9999 0 -0.66 1 1
alphaV/beta3 Integrin/JAM-A -0.073 0.18 -9999 0 -0.87 5 5
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.028 0.12 -9999 0 -0.55 14 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.037 0.11 -9999 0 -0.48 5 5
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.013 0.089 -9999 0 -0.42 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.024 0.11 -9999 0 -0.55 12 12
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.29 0.25 -9999 0 -0.82 26 26
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.32 0.28 -9999 0 -0.55 176 176
RPS6KB1 -0.24 0.26 -9999 0 -0.75 26 26
TLN1 0.011 0.047 -9999 0 -0.8 1 1
MAPK3 -0.12 0.16 -9999 0 -0.7 12 12
GPR124 0.008 0.066 -9999 0 -0.8 2 2
MAPK1 -0.12 0.16 -9999 0 -0.7 12 12
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.086 0.2 -9999 0 -0.57 38 38
cell adhesion -0.023 0.1 -9999 0 -0.48 7 7
ANGPTL3 -0.001 0.066 -9999 0 -0.8 2 2
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.043 -9999 0 -0.53 2 2
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.013 0 -9999 0 -10000 0 0
ITGB3 -0.017 0.15 -9999 0 -0.76 12 12
IGF1 -0.054 0.2 -9999 0 -0.67 30 30
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.027 0.12 -9999 0 -0.58 13 13
apoptosis 0.006 0.076 -9999 0 -0.75 3 3
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.024 0.11 -9999 0 -0.55 12 12
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.075 0.2 -9999 0 -0.58 36 36
CSF1 0.009 0.053 -9999 0 -0.64 2 2
PIK3C2A -0.047 0.12 -9999 0 -0.4 27 27
PI4 Kinase/Pyk2 -0.063 0.15 -9999 0 -0.74 5 5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.025 0.11 -9999 0 -0.5 14 14
FAK1/Vinculin 0.009 0.12 -9999 0 -0.51 3 3
alphaV beta3/Integrin/ppsTEM5 -0.028 0.12 -9999 0 -0.58 13 13
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.059 0.23 -9999 0 -0.8 27 27
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 -0.012 0.13 -9999 0 -0.68 11 11
F11R 0.005 0.1 -9999 0 -0.51 11 11
alphaV/beta3 Integrin/Lactadherin -0.024 0.11 -9999 0 -0.55 12 12
alphaV/beta3 Integrin/TGFBR2 -0.024 0.11 -9999 0 -0.55 12 12
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.007 0.052 -9999 0 -0.48 2 2
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.024 0.11 -9999 0 -0.5 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.44 0.4 -9999 0 -0.8 170 170
alphaV/beta3 Integrin/Pyk2 -0.023 0.1 -9999 0 -0.67 1 1
SDC1 0.013 0 -9999 0 -10000 0 0
VAV3 0.011 0.11 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.009 0.12 -9999 0 -0.51 3 3
cell migration 0.019 0.12 -9999 0 -0.45 3 3
ITGAV 0.006 0.076 -9999 0 -0.75 3 3
PI3K -0.065 0.16 -9999 0 -0.79 5 5
SPP1 -0.45 0.4 -9999 0 -0.8 171 171
KDR 0.011 0.047 -9999 0 -0.8 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.006 0.076 -9999 0 -0.75 3 3
COL4A3 -0.084 0.26 -9999 0 -0.76 38 38
angiogenesis -0.094 0.18 -9999 0 -0.77 9 9
Rac1/GTP -0.026 0.085 -9999 0 -10000 0 0
EDIL3 -0.067 0.24 -9999 0 -0.77 31 31
cell proliferation -0.024 0.11 -9999 0 -0.55 12 12
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.057 0.12 -9999 0 -0.76 2 2
NF kappa B1 p50/RelA/I kappa B alpha -0.022 0.048 -9999 0 -10000 0 0
AP1 -0.097 0.14 -9999 0 -0.55 8 8
mol:PIP3 -0.055 0.1 -9999 0 -0.63 1 1
AKT1 -0.034 0.071 -9999 0 -0.5 2 2
PTK2B -0.008 0.079 -9999 0 -0.29 1 1
RHOA 0.003 0.063 -9999 0 -10000 0 0
PIK3CB 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.008 0.07 -9999 0 -0.46 2 2
MAGI3 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.031 0.12 -9999 0 -0.34 10 10
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.13 0.17 -9999 0 -0.45 23 23
NF kappa B1 p50/RelA -0.039 0.088 -9999 0 -0.56 2 2
endothelial cell migration -0.13 0.31 -9999 0 -0.72 66 66
ADCY4 -0.015 0.13 -9999 0 -0.48 8 8
ADCY5 -0.059 0.15 -9999 0 -0.57 11 11
ADCY6 -0.022 0.14 -9999 0 -0.57 9 9
ADCY7 -0.015 0.13 -9999 0 -0.48 8 8
ADCY1 -0.023 0.13 -9999 0 -0.47 9 9
ADCY2 -0.08 0.15 -9999 0 -0.54 12 12
ADCY3 -0.015 0.13 -9999 0 -0.48 8 8
ADCY8 -0.023 0.13 -9999 0 -0.44 12 12
ADCY9 -0.015 0.13 -9999 0 -0.48 8 8
GSK3B 0 0.076 -9999 0 -10000 0 0
arachidonic acid secretion -0.008 0.12 -9999 0 -0.44 8 8
GNG2 0.011 0.047 -9999 0 -0.8 1 1
TRIP6 0.015 0.025 -9999 0 -10000 0 0
GNAO1 -0.043 0.14 -9999 0 -0.47 8 8
HRAS 0.013 0 -9999 0 -10000 0 0
NFKBIA 0.011 0.082 -9999 0 -0.43 2 2
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.004 0.09 -9999 0 -0.9 3 3
JUN 0.013 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.019 0.049 -9999 0 -0.62 1 1
TIAM1 -0.007 0.11 -9999 0 -1.1 3 3
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
mol:IP3 0.008 0.071 -9999 0 -0.47 2 2
PLCB3 0.01 0.051 -9999 0 -0.57 1 1
FOS -0.092 0.24 -9999 0 -0.64 49 49
positive regulation of mitosis -0.008 0.12 -9999 0 -0.44 8 8
LPA/LPA1-2-3 -0.06 0.12 -9999 0 -0.81 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation -0.004 0.093 -9999 0 -0.43 1 1
GNAZ -0.051 0.16 -9999 0 -0.53 12 12
EGFR/PI3K-beta/Gab1 -0.057 0.1 -9999 0 -0.67 1 1
positive regulation of dendritic cell cytokine production -0.06 0.12 -9999 0 -0.8 1 1
LPA/LPA2/MAGI-3 -0.017 0.034 -9999 0 -10000 0 0
ARHGEF1 -0.02 0.12 -9999 0 -0.62 3 3
GNAI2 -0.039 0.14 -9999 0 -0.47 6 6
GNAI3 -0.039 0.14 -9999 0 -0.47 6 6
GNAI1 -0.041 0.14 -9999 0 -0.46 7 7
LPA/LPA3 -0.03 0.07 -9999 0 -0.48 4 4
LPA/LPA2 -0.024 0.048 -9999 0 -10000 0 0
LPA/LPA1 -0.077 0.15 -9999 0 -0.36 66 66
HB-EGF/EGFR -0.41 0.25 -9999 0 -0.54 232 232
HBEGF -0.46 0.27 -9999 0 -0.61 230 230
mol:DAG 0.008 0.071 -9999 0 -0.47 2 2
cAMP biosynthetic process -0.028 0.13 -9999 0 -0.54 8 8
NFKB1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
GNB1 0.013 0.001 -9999 0 -10000 0 0
LYN 0.011 0.082 -9999 0 -0.45 1 1
GNAQ 0.001 0.055 -9999 0 -0.33 4 4
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 0.005 0.075 -9999 0 -0.64 4 4
LPAR1 -0.034 0.12 -9999 0 -0.69 6 6
IL8 -0.24 0.18 -9999 0 -0.49 62 62
PTK2 -0.021 0.12 -9999 0 -0.76 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.031 0.12 -9999 0 -0.35 10 10
EGFR -0.014 0.15 -9999 0 -0.8 10 10
PLCG1 -0.01 0.074 -9999 0 -0.38 4 4
PLD2 -0.021 0.12 -9999 0 -0.76 1 1
G12/G13 -0.059 0.12 -9999 0 -0.67 3 3
PI3K-beta -0.04 0.083 -9999 0 -0.59 2 2
cell migration -0.012 0.045 -9999 0 -10000 0 0
SLC9A3R2 0.011 0.047 -9999 0 -0.8 1 1
PXN -0.005 0.094 -9999 0 -0.44 1 1
HRAS/GTP -0.009 0.12 -9999 0 -0.46 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.61 0.35 -9999 0 -0.8 230 230
PRKCE 0.013 0.001 -9999 0 -10000 0 0
PRKCD 0.016 0.068 -9999 0 -0.46 1 1
Gi(beta/gamma) -0.012 0.12 -9999 0 -0.45 9 9
mol:LPA -0.037 0.082 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.033 0.086 -9999 0 -0.6 1 1
MAPKKK cascade -0.008 0.12 -9999 0 -0.44 8 8
contractile ring contraction involved in cytokinesis 0.003 0.063 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.057 0.14 -9999 0 -0.34 53 53
GNA15 0.001 0.055 -9999 0 -0.33 4 4
GNA12 0.008 0.066 -9999 0 -0.8 2 2
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT -0.14 0.18 -9999 0 -0.46 23 23
GNA11 0.001 0.055 -9999 0 -0.33 4 4
Rac1/GTP -0.004 0.096 -9999 0 -0.96 3 3
MMP2 -0.13 0.32 -9999 0 -0.72 66 66
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.17 0.3 -9999 0 -0.65 85 85
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.013 0 -9999 0 -10000 0 0
TCEB1 0.011 0.047 -9999 0 -0.8 1 1
HIF1A/p53 0.022 0.047 -9999 0 -10000 0 0
HIF1A 0.018 0.035 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.026 -9999 0 -10000 0 0
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.31 0.39 -9999 0 -0.77 124 124
ARNT/IPAS -0.13 0.22 -9999 0 -0.48 85 85
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.025 0.034 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.002 0.03 -9999 0 -0.53 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.025 0.034 -9999 0 -10000 0 0
PHD1-3/OS9 -0.036 0.13 -9999 0 -0.48 22 22
HIF1A/RACK1/Elongin B/Elongin C -0.007 0.029 -9999 0 -10000 0 0
VHL 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.025 0.034 -9999 0 -10000 0 0
EGLN3 -0.048 0.22 -9999 0 -0.8 23 23
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 0.007 0.065 -9999 0 -0.64 3 3
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.037 0.018 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.15 0.22 -9999 0 -0.43 100 100
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 0.012 0.06 -10000 0 -0.79 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.025 0.14 0.57 7 -10000 0 7
IL27/IL27R/JAK1 -0.073 0.17 -10000 0 -0.71 9 9
TBX21 -0.084 0.26 -10000 0 -0.72 24 24
IL12B -0.079 0.26 -10000 0 -0.81 33 33
IL12A -0.006 0.088 -10000 0 -0.48 10 10
IL6ST -0.004 0.099 -10000 0 -0.65 7 7
IL27RA/JAK1 -0.004 0.1 -10000 0 -0.57 9 9
IL27 -0.027 0.17 -10000 0 -0.82 13 13
TYK2 0.013 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.023 0.13 -10000 0 -0.63 6 6
T-helper 2 cell differentiation 0.025 0.14 0.57 7 -10000 0 7
T cell proliferation during immune response 0.025 0.14 0.57 7 -10000 0 7
MAPKKK cascade -0.025 0.14 -10000 0 -0.57 7 7
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 -0.049 0.22 -10000 0 -0.8 23 23
IL12RB1 -0.073 0.25 -10000 0 -0.8 32 32
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.14 0.33 -10000 0 -0.69 66 66
IL27/IL27R/JAK2/TYK2 -0.026 0.14 -10000 0 -0.57 7 7
positive regulation of T cell mediated cytotoxicity -0.025 0.14 -10000 0 -0.57 7 7
STAT1 (dimer) -0.16 0.29 0.52 1 -0.89 27 28
JAK2 0.012 0.007 -10000 0 -10000 0 0
JAK1 0.013 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.018 0.14 -10000 0 -0.54 7 7
T cell proliferation -0.05 0.18 -10000 0 -0.6 13 13
IL12/IL12R/TYK2/JAK2 -0.066 0.2 -10000 0 -0.61 24 24
IL17A -0.024 0.13 -10000 0 -0.63 6 6
mast cell activation 0.025 0.14 0.57 7 -10000 0 7
IFNG -0.013 0.048 -10000 0 -0.11 59 59
T cell differentiation -0.006 0.009 -10000 0 -0.025 28 28
STAT3 (dimer) -0.018 0.14 -10000 0 -0.54 7 7
STAT5A (dimer) -0.018 0.14 -10000 0 -0.65 3 3
STAT4 (dimer) -0.027 0.15 -10000 0 -0.7 4 4
STAT4 -0.002 0.11 -10000 0 -0.78 6 6
T cell activation -0.006 0.018 0.092 9 -10000 0 9
IL27R/JAK2/TYK2 -0.031 0.11 -10000 0 -0.6 6 6
GATA3 -0.005 0.15 -10000 0 -0.73 10 10
IL18 -0.004 0.088 -10000 0 -0.48 10 10
positive regulation of mast cell cytokine production -0.017 0.13 -10000 0 -0.53 7 7
IL27/EBI3 -0.03 0.16 -10000 0 -0.61 20 20
IL27RA -0.013 0.11 -10000 0 -0.62 9 9
IL6 -0.048 0.2 -10000 0 -0.66 28 28
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.013 0.062 -10000 0 -10000 0 0
IL1B -0.048 0.18 -10000 0 -0.61 29 29
EBI3 -0.007 0.11 -10000 0 -0.74 7 7
TNF -0.018 0.13 -10000 0 -0.58 15 15
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.013 0 -9999 0 -10000 0 0
EGFR -0.014 0.15 -9999 0 -0.8 10 10
EGF/EGFR -0.091 0.16 -9999 0 -0.49 11 11
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.089 0.15 -9999 0 -0.78 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.011 0.038 -9999 0 -0.64 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.14 0.27 -9999 0 -0.64 69 69
EGF/EGFR dimer/SHC -0.11 0.18 -9999 0 -0.42 78 78
mol:GDP -0.088 0.15 -9999 0 -0.77 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.007 0.065 -9999 0 -0.64 3 3
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.08 0.14 -9999 0 -0.72 1 1
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.081 0.14 -9999 0 -0.72 1 1
FRAP1 -0.054 0.16 -9999 0 -0.75 1 1
EGF/EGFR dimer -0.13 0.22 -9999 0 -0.49 78 78
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.006 0.054 -9999 0 -0.47 4 4
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR 0.003 0.083 -9999 0 -0.64 5 5
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.088 0.18 -9999 0 -0.42 63 63
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.05 0.17 -9999 0 -0.56 8 8
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.022 0.16 -9999 0 -0.8 12 12
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.34 0.4 -9999 0 -0.8 132 132
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.016 0.098 -9999 0 -0.61 8 8
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.011 0.047 -9999 0 -0.8 1 1
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.095 0.27 -9999 0 -0.8 39 39
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.1 0.19 -9999 0 -0.44 70 70
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.043 0.17 -9999 0 -0.59 9 9
MAP1B -0.01 0.054 -9999 0 -0.3 10 10
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.029 0.16 -9999 0 -0.72 2 2
RELN -0.11 0.26 -9999 0 -0.64 57 57
PAFAH/LIS1 -0.21 0.28 -9999 0 -0.53 132 132
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.064 0.11 -9999 0 -0.49 5 5
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.031 0.14 -9999 0 -0.61 4 4
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.054 0.18 -9999 0 -0.64 9 9
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.025 0 -9999 0 -10000 0 0
PAFAH1B3 0.013 0 -9999 0 -10000 0 0
PAFAH1B2 0.013 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.02 0.039 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.081 0.13 -9999 0 -0.56 9 9
LRP8 -0.008 0.13 -9999 0 -0.8 8 8
NDEL1/Katanin 60 -0.043 0.17 -9999 0 -0.59 9 9
P39/CDK5 -0.09 0.22 -9999 0 -0.82 9 9
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.037 0.16 -9999 0 -0.52 8 8
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.085 0.16 -9999 0 -0.56 12 12
RELN/VLDLR -0.085 0.16 -9999 0 -0.56 8 8
CDC42 0 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated 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
AKT1 0.065 0.2 -10000 0 -0.88 8 8
NCK1/PAK1/Dok-R -0.022 0.076 -10000 0 -0.42 8 8
NCK1/Dok-R -0.035 0.19 -10000 0 -1.1 8 8
PIK3CA 0.012 0.004 -10000 0 -10000 0 0
mol:beta2-estradiol -0.007 0.036 0.24 5 -10000 0 5
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.013 0.004 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.072 0.23 -10000 0 -0.83 26 26
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.031 0.17 -10000 0 -1 8 8
FN1 -0.44 0.4 -10000 0 -0.8 170 170
PLD2 0.048 0.21 -10000 0 -1.2 8 8
PTPN11 0.013 0 -10000 0 -10000 0 0
GRB14 -0.058 0.21 -10000 0 -0.66 32 32
ELK1 0.061 0.19 -10000 0 -1 8 8
GRB7 0.003 0.089 -10000 0 -0.76 4 4
PAK1 0.011 0.047 -10000 0 -0.8 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.37 0.34 -10000 0 -0.83 86 86
CDKN1A 0.067 0.18 -10000 0 -0.66 3 3
ITGA5 -0.27 0.39 -10000 0 -0.8 105 105
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.035 0.19 -10000 0 -1.1 8 8
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.068 0.16 -10000 0 -0.64 8 8
PLG 0.042 0.21 -10000 0 -1.2 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.048 0.18 -10000 0 -0.86 8 8
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0.004 -10000 0 -10000 0 0
ANGPT2 0.014 0.2 -10000 0 -0.61 18 18
BMX 0.013 0.25 -10000 0 -1.3 8 8
ANGPT1 0.022 0.21 -10000 0 -1.2 7 7
tube development 0.06 0.19 -10000 0 -0.75 4 4
ANGPT4 0.009 0.007 -10000 0 -10000 0 0
response to hypoxia 0.003 0.013 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.004 0.24 -10000 0 -1.2 8 8
alpha5/beta1 Integrin -0.22 0.29 -10000 0 -0.61 106 106
FGF2 -0.013 0.13 -10000 0 -0.68 11 11
STAT5A (dimer) 0.064 0.21 -10000 0 -0.86 3 3
mol:L-citrulline 0.068 0.16 -10000 0 -0.64 8 8
AGTR1 -0.047 0.19 -10000 0 -0.66 27 27
MAPK14 0.051 0.21 -10000 0 -1.1 8 8
Tie2/SHP2 -0.017 0.12 -10000 0 -1.2 3 3
TEK 0.03 0.15 -10000 0 -1.4 3 3
RPS6KB1 0.069 0.19 -10000 0 -0.85 8 8
Angiotensin II/AT1 -0.035 0.14 -10000 0 -0.5 27 27
Tie2/Ang1/GRB2 0.044 0.22 -10000 0 -1.2 8 8
MAPK3 0.056 0.19 -10000 0 -1 8 8
MAPK1 0.056 0.19 -10000 0 -1 8 8
Tie2/Ang1/GRB7 0.038 0.22 -10000 0 -1.2 8 8
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.046 0.22 -10000 0 -1.2 8 8
PI3K 0.06 0.21 -10000 0 -1 8 8
FES 0.051 0.21 -10000 0 -1.1 8 8
Crk/Dok-R -0.035 0.19 -10000 0 -1.1 8 8
Tie2/Ang1/ABIN2 0.044 0.22 -10000 0 -1.2 8 8
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.067 0.18 -10000 0 -0.78 8 8
STAT5A 0.014 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.069 0.19 -10000 0 -0.85 8 8
Tie2/Ang2 0.048 0.23 -10000 0 -1.1 3 3
Tie2/Ang1 0.042 0.23 -10000 0 -1.3 8 8
FOXO1 0.068 0.19 -10000 0 -0.79 8 8
ELF1 0.023 0.011 -10000 0 -10000 0 0
ELF2 0.045 0.21 -10000 0 -1.1 8 8
mol:Choline 0.05 0.2 -10000 0 -1.1 8 8
cell migration -0.1 0.084 -10000 0 -10000 0 0
FYN 0.057 0.21 -10000 0 -0.87 4 4
DOK2 0.011 0.038 -10000 0 -0.64 1 1
negative regulation of cell cycle 0.068 0.17 -10000 0 -0.59 3 3
ETS1 0.015 0.073 -10000 0 -0.78 2 2
PXN 0.077 0.16 -10000 0 -0.69 8 8
ITGB1 0.011 0.047 -10000 0 -0.8 1 1
NOS3 0.067 0.18 -10000 0 -0.74 8 8
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.017 0.17 -10000 0 -0.76 15 15
MAPKKK cascade 0.05 0.2 -10000 0 -1.1 8 8
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.045 0.22 -10000 0 -1.2 8 8
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.069 0.15 -10000 0 -0.58 8 8
mol:Phosphatidic acid 0.05 0.2 -10000 0 -1.1 8 8
mol:Angiotensin II 0 0.007 -10000 0 -10000 0 0
mol:NADP 0.068 0.16 -10000 0 -0.64 8 8
Rac1/GTP -0.038 0.14 -10000 0 -0.79 8 8
MMP2 -0.047 0.28 -10000 0 -1.2 8 8
Regulation of Androgen receptor activity

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
HDAC1 0.023 0.004 -9999 0 -10000 0 0
SMARCC1 0.01 0.011 -9999 0 -10000 0 0
REL 0.016 0.007 -9999 0 -10000 0 0
HDAC7 -0.061 0.17 -9999 0 -0.63 11 11
JUN 0.011 0.005 -9999 0 -10000 0 0
EP300 0.013 0.001 -9999 0 -10000 0 0
KAT2B -0.016 0.13 -9999 0 -0.64 13 13
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.009 0.11 -9999 0 -0.5 14 14
FOXO1 0.013 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.077 0.17 -9999 0 -0.64 14 14
MAP2K6 -0.023 0.14 -9999 0 -0.66 14 14
BRM/BAF57 -0.001 0.002 -9999 0 -10000 0 0
MAP2K4 0.008 0.008 -9999 0 -10000 0 0
SMARCA2 0.011 0.005 -9999 0 -10000 0 0
PDE9A -0.093 0.21 -9999 0 -1.3 8 8
NCOA2 0.004 0.075 -9999 0 -0.64 4 4
CEBPA 0.01 0.053 -9999 0 -0.64 2 2
EHMT2 0.011 0.005 -9999 0 -10000 0 0
cell proliferation -0.048 0.16 -9999 0 -0.54 5 5
NR0B1 -0.038 0.18 -9999 0 -0.8 16 16
EGR1 -0.013 0.12 -9999 0 -0.64 11 11
RXRs/9cRA -0.053 0.13 -9999 0 -0.38 42 42
AR/RACK1/Src -0.029 0.12 -9999 0 -0.52 10 10
AR/GR -0.044 0.15 -9999 0 -0.59 10 10
GNB2L1 0.013 0.003 -9999 0 -10000 0 0
PKN1 0.007 0.066 -9999 0 -0.8 2 2
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.011 0.045 -9999 0 -0.5 2 2
T-DHT/AR/TIF2/CARM1 -0.028 0.14 -9999 0 -0.58 11 11
SRC 0 0.096 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.31 0.47 -9999 0 -1.2 58 58
APPBP2 0.008 0.008 -9999 0 -10000 0 0
TRIM24 0.009 0.038 -9999 0 -0.64 1 1
T-DHT/AR/TIP60 -0.029 0.13 -9999 0 -0.55 11 11
TMPRSS2 -0.54 0.57 -9999 0 -1.1 145 145
RXRG -0.082 0.23 -9999 0 -0.66 42 42
mol:9cRA -0.001 0.003 -9999 0 -10000 0 0
RXRA 0.013 0.001 -9999 0 -10000 0 0
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.013 0.003 -9999 0 -10000 0 0
NR2C2 0.011 0.038 -9999 0 -0.64 1 1
KLK2 -0.022 0.17 -9999 0 -0.65 13 13
AR -0.058 0.17 -9999 0 -0.42 37 37
SENP1 0.013 0.001 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.018 0.012 -9999 0 -10000 0 0
SRY -0.043 0.18 -9999 0 -0.65 25 25
GATA2 0.008 0.066 -9999 0 -0.8 2 2
MYST2 0.014 0.001 -9999 0 -10000 0 0
HOXB13 -0.28 0.39 -9999 0 -0.81 105 105
T-DHT/AR/RACK1/Src -0.02 0.13 -9999 0 -0.53 10 10
positive regulation of transcription 0.008 0.066 -9999 0 -0.8 2 2
DNAJA1 0.008 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.004 -9999 0 -10000 0 0
NCOA1 0.017 0.008 -9999 0 -10000 0 0
SPDEF -0.24 0.32 -9999 0 -0.65 117 117
T-DHT/AR/TIF2 -0.01 0.11 -9999 0 -0.53 4 4
T-DHT/AR/Hsp90 -0.03 0.13 -9999 0 -0.56 10 10
GSK3B 0.008 0.007 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.011 0.1 -9999 0 -0.44 4 4
SIRT1 0.013 0.001 -9999 0 -10000 0 0
ZMIZ2 0.018 0.012 -9999 0 -10000 0 0
POU2F1 0.017 0.017 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.073 0.15 -9999 0 -0.54 19 19
CREBBP 0.013 0.003 -9999 0 -10000 0 0
SMARCE1 0.011 0.005 -9999 0 -10000 0 0
Ephrin A reverse 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
MAPKKK cascade -0.02 0.092 -9999 0 -0.44 14 14
EFNA5 -0.01 0.12 -9999 0 -0.64 11 11
FYN 0.003 0.1 -9999 0 -0.42 14 14
neuron projection morphogenesis -0.02 0.092 -9999 0 -0.44 14 14
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.02 0.092 -9999 0 -0.44 14 14
EPHA5 0 0.081 -9999 0 -0.8 3 3
Arf6 signaling events

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
CENTA1/KIF3B -0.009 0.061 -9999 0 -0.4 7 7
ARNO/beta Arrestin1-2 -0.025 0.088 -9999 0 -0.58 2 2
EGFR -0.014 0.15 -9999 0 -0.8 10 10
EPHA2 0.005 0.075 -9999 0 -0.64 4 4
USP6 0.013 0 -9999 0 -10000 0 0
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.13 0.22 -9999 0 -0.49 78 78
ARRB2 0.011 0.003 -9999 0 -10000 0 0
mol:GTP 0.021 0.018 -9999 0 -10000 0 0
ARRB1 0.009 0.053 -9999 0 -0.64 2 2
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR -0.005 0.11 -9999 0 -0.8 6 6
EGF -0.14 0.27 -9999 0 -0.64 69 69
somatostatin receptor activity 0 0 -9999 0 -0.001 6 6
ARAP2 0.009 0.053 -9999 0 -0.64 2 2
mol:GDP -0.011 0.076 -9999 0 -0.33 6 6
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 5 5
ITGA2B -0.04 0.2 -9999 0 -0.8 20 20
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.049 -9999 0 -0.48 1 1
ADAP1 0.013 0 -9999 0 -10000 0 0
KIF13B -0.002 0.098 -9999 0 -0.64 7 7
HGF/MET -0.019 0.099 -9999 0 -0.52 11 11
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.028 0.11 -9999 0 -0.34 7 7
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.11 0.18 -9999 0 -0.42 78 78
ADRB2 -0.038 0.18 -9999 0 -0.64 24 24
receptor agonist activity 0 0 -9999 0 0 7 7
actin filament binding 0 0 -9999 0 -0.001 6 6
SRC 0.013 0 -9999 0 -10000 0 0
ITGB3 -0.017 0.15 -9999 0 -0.76 12 12
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 5 5
ARF6/GDP 0.044 0.057 -9999 0 -10000 0 0
ARF6/GDP/GULP/ACAP1 -0.11 0.17 -9999 0 -0.43 39 39
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.049 0.15 -9999 0 -0.5 28 28
ACAP1 -0.003 0.11 -9999 0 -0.8 6 6
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0 0 -9999 0 -10000 0 0
EFNA1 0.011 0.047 -9999 0 -0.8 1 1
HGF -0.008 0.12 -9999 0 -0.7 9 9
CYTH3 0.012 0 -9999 0 -10000 0 0
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 7 7
endosomal lumen acidification 0 0 0 4 -0.001 6 10
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.16 0.29 -9999 0 -0.64 81 81
GNAQ/ARNO 0.014 0.008 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 -10000 0 0
MET 0.009 0.06 -9999 0 -0.72 2 2
GNA14 -0.095 0.24 -9999 0 -0.64 50 50
GNA15 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 5 5
GNA11 0.013 0 -9999 0 -10000 0 0
LHCGR 0.002 0.005 -9999 0 -10000 0 0
AGTR1 -0.048 0.19 -9999 0 -0.66 27 27
desensitization of G-protein coupled receptor protein signaling pathway 0 0 -9999 0 -10000 0 0
IPCEF1/ARNO -0.078 0.15 -9999 0 -0.72 1 1
alphaIIb/beta3 Integrin -0.063 0.19 -9999 0 -0.62 31 31
PDGFR-alpha 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
PDGFRA -0.007 0.11 -9999 0 -0.69 7 7
PDGF/PDGFRA/CRKL -0.014 0.083 -9999 0 -0.52 8 8
positive regulation of JUN kinase activity -0.009 0.056 -9999 0 -0.45 2 2
CRKL 0.011 0.047 -9999 0 -0.8 1 1
PDGF/PDGFRA/Caveolin-3 -0.12 0.22 -9999 0 -0.5 75 75
AP1 -0.17 0.37 -9999 0 -1 49 49
mol:IP3 0.006 0.084 -9999 0 -0.52 7 7
PLCG1 0.006 0.084 -9999 0 -0.52 7 7
PDGF/PDGFRA/alphaV Integrin -0.017 0.1 -9999 0 -0.63 8 8
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.084 -9999 0 -0.51 7 7
CAV3 -0.14 0.28 -9999 0 -0.66 69 69
CAV1 -0.065 0.24 -9999 0 -0.8 29 29
SHC/Grb2/SOS1 -0.009 0.056 -9999 0 -0.45 2 2
PDGF/PDGFRA/Shf -0.022 0.11 -9999 0 -0.56 12 12
FOS -0.12 0.39 -9999 0 -0.99 49 49
JUN -0.01 0.022 -9999 0 -10000 0 0
oligodendrocyte development -0.017 0.1 -9999 0 -0.63 8 8
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG 0.006 0.084 -9999 0 -0.52 7 7
PDGF/PDGFRA -0.007 0.11 -9999 0 -0.69 7 7
actin cytoskeleton reorganization -0.015 0.084 -9999 0 -0.49 9 9
SRF 0.026 0.01 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.01 0.063 -9999 0 -0.47 3 3
PDGF/PDGFRA/Crk/C3G -0.01 0.063 -9999 0 -0.47 3 3
JAK1 0.01 0.079 -9999 0 -0.5 7 7
ELK1/SRF 0.03 0.068 -9999 0 -0.49 1 1
SHB 0.009 0.053 -9999 0 -0.64 2 2
SHF -0.002 0.098 -9999 0 -0.64 7 7
CSNK2A1 0.01 0.022 -9999 0 -10000 0 0
GO:0007205 0.006 0.085 -9999 0 -0.52 7 7
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.009 0.056 -9999 0 -0.45 2 2
PDGF/PDGFRA/SHB -0.015 0.084 -9999 0 -0.49 9 9
PDGF/PDGFRA/Caveolin-1 -0.072 0.2 -9999 0 -0.6 36 36
ITGAV 0.006 0.076 -9999 0 -0.75 3 3
ELK1 0.008 0.089 -9999 0 -0.47 8 8
PIK3CA 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.012 0.076 -9999 0 -0.5 7 7
JAK-STAT cascade 0.01 0.079 -9999 0 -0.5 7 7
cell proliferation -0.022 0.11 -9999 0 -0.56 12 12
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.076 0.16 -9999 0 -0.4 50 50
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.011 0.047 -9999 0 -0.8 1 1
STAT1 (dimer)/Cbp/p300 -0.091 0.19 -9999 0 -0.71 15 15
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.012 0.024 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.07 0.094 -9999 0 -0.36 5 5
CaM/Ca2+ -0.07 0.14 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.061 0.23 -9999 0 -0.81 15 15
AKT1 -0.015 0.15 -9999 0 -10000 0 0
MAP2K1 -0.016 0.16 -9999 0 -10000 0 0
MAP3K11 -0.029 0.17 -9999 0 -10000 0 0
IFNGR1 0.008 0.015 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.18 0.24 -9999 0 -0.54 72 72
Rap1/GTP -0.054 0.11 -9999 0 -10000 0 0
CRKL/C3G -0.002 0.035 -9999 0 -0.61 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.083 0.17 -9999 0 -0.43 50 50
CEBPB 0.02 0.15 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.11 0.22 -9999 0 -0.9 10 10
STAT1 -0.06 0.23 -9999 0 -0.81 15 15
CALM1 0.014 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.14 0.32 -9999 0 -0.79 59 59
PIK3CA 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.087 0.2 -9999 0 -0.75 15 15
CEBPB/PTGES2/Cbp/p300 -0.034 0.066 -9999 0 -10000 0 0
mol:Ca2+ -0.075 0.15 -9999 0 -0.39 50 50
MAPK3 0.002 0.14 -9999 0 -10000 0 0
STAT1 (dimer) -0.094 0.13 -9999 0 -0.54 5 5
MAPK1 0.002 0.14 -9999 0 -10000 0 0
JAK2 0.008 0.015 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.008 0.015 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.03 0.12 -9999 0 -0.63 4 4
SMAD7 0.001 0.076 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.065 0.13 -9999 0 -10000 0 0
PI3K -0.068 0.14 -9999 0 -10000 0 0
IFNG -0.14 0.32 -9999 0 -0.79 59 59
apoptosis 0.013 0.1 -9999 0 -0.44 4 4
CAMK2G 0.014 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.12 0.27 -9999 0 -0.65 62 62
CAMK2B -0.16 0.29 -9999 0 -0.65 79 79
FRAP1 -0.008 0.14 -9999 0 -10000 0 0
PRKCD -0.01 0.15 -9999 0 -10000 0 0
RAP1B 0.011 0.047 -9999 0 -0.8 1 1
negative regulation of cell growth -0.07 0.094 -9999 0 -0.36 5 5
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0.001 -9999 0 -10000 0 0
IRF1 -0.02 0.19 -9999 0 -0.52 24 24
STAT1 (dimer)/PIASy -0.086 0.2 -9999 0 -0.75 15 15
SOCS1 -0.046 0.18 -9999 0 -0.65 25 25
mol:GDP -0.062 0.12 -9999 0 -10000 0 0
CASP1 0.001 0.078 -9999 0 -0.38 1 1
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.041 0.055 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.066 0.13 -9999 0 -10000 0 0
RAP1/GDP -0.055 0.11 -9999 0 -10000 0 0
CBL -0.03 0.16 -9999 0 -10000 0 0
MAP3K1 -0.028 0.17 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PIAS4 0.014 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.07 0.094 -9999 0 -0.36 5 5
PTPN11 -0.04 0.17 -9999 0 -0.39 50 50
CREBBP 0.014 0.001 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.028 0.14 -9999 0 -0.65 5 5
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 -0.03 0.18 -9999 0 -0.76 17 17
WNT4 -0.01 0.13 -9999 0 -0.69 10 10
FZD3 0.005 0.075 -9999 0 -0.64 4 4
WNT5A 0.004 0.08 -9999 0 -0.68 4 4
WNT11 -0.074 0.25 -9999 0 -0.76 34 34
ErbB2/ErbB3 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
USP8 0.02 0.006 -9999 0 -10000 0 0
RAS family/GTP -0.054 0.098 -9999 0 -0.63 1 1
NFATC4 -0.026 0.13 -9999 0 -0.5 2 2
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.013 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.074 0.14 -9999 0 -0.62 1 1
JUN 0.005 0.075 -9999 0 -0.28 1 1
HRAS 0.013 0.001 -9999 0 -10000 0 0
DOCK7 -0.045 0.15 -9999 0 -0.59 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.099 0.19 -9999 0 -0.46 61 61
AKT1 0.011 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.045 0.081 -9999 0 -0.36 4 4
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.057 0.17 -9999 0 -0.7 1 1
RAF1 -0.024 0.12 -9999 0 -0.61 1 1
ErbB2/ErbB3/neuregulin 2 -0.23 0.18 -9999 0 -0.56 5 5
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration 0.002 0.091 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.003 -9999 0 -10000 0 0
cell proliferation -0.15 0.28 -9999 0 -0.6 51 51
FOS -0.12 0.24 -9999 0 -0.51 49 49
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.074 0.14 -9999 0 -0.62 1 1
MAPK3 -0.11 0.23 -9999 0 -0.58 14 14
MAPK1 -0.11 0.23 -9999 0 -0.58 14 14
JAK2 -0.045 0.15 -9999 0 -0.59 1 1
NF2 -0.003 0.005 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.038 0.13 -9999 0 -0.7 1 1
NRG1 -0.15 0.32 -9999 0 -0.8 61 61
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.024 0.11 -9999 0 -0.43 1 1
MAPK9 -0.035 0.067 -9999 0 -10000 0 0
ERBB2 -0.004 0.051 -9999 0 -0.63 2 2
ERBB3 0.001 0.075 -9999 0 -0.64 4 4
SHC1 0.012 0.003 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.011 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0.001 0.003 -9999 0 -10000 0 0
RNF41 0.026 0.009 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.05 0.095 -9999 0 -0.39 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.004 0.043 -9999 0 -0.54 2 2
CHRNA1 -0.16 0.29 -9999 0 -0.54 98 98
myelination -0.017 0.13 -9999 0 -0.46 2 2
PPP3CB -0.042 0.14 -9999 0 -0.54 1 1
KRAS 0.013 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.05 0.099 -9999 0 -0.61 1 1
NRG2 -0.38 0.32 -9999 0 -0.64 184 184
mol:GDP -0.038 0.13 -9999 0 -0.69 1 1
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.029 0.13 -9999 0 -0.59 1 1
SRC 0.013 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.046 0.15 -9999 0 -0.58 1 1
MAP2K1 -0.097 0.2 -9999 0 -0.53 14 14
heart morphogenesis -0.074 0.14 -9999 0 -0.62 1 1
RAS family/GDP -0.049 0.097 -9999 0 -0.61 1 1
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.005 0.009 -9999 0 -10000 0 0
CHRNE 0.012 0.022 -9999 0 -0.22 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.011 0.003 -9999 0 -10000 0 0
nervous system development -0.074 0.14 -9999 0 -0.62 1 1
CDC42 0.013 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0 -9999 0 -10000 0 0
LAT2 -0.05 0.13 -9999 0 -0.47 7 7
AP1 -0.1 0.13 -9999 0 -0.44 24 24
mol:PIP3 -0.073 0.19 -9999 0 -0.54 12 12
IKBKB -0.027 0.12 -9999 0 -0.38 2 2
AKT1 -0.06 0.17 -9999 0 -0.59 6 6
IKBKG -0.027 0.12 -9999 0 -0.38 2 2
MS4A2 -0.01 0.12 -9999 0 -0.7 9 9
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
MAP3K1 -0.013 0.12 -9999 0 -0.44 2 2
mol:Ca2+ -0.052 0.15 -9999 0 -0.39 12 12
LYN 0.014 0.004 -9999 0 -10000 0 0
CBLB -0.049 0.13 -9999 0 -0.44 9 9
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.03 0.099 -9999 0 -10000 0 0
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.011 0.038 -9999 0 -0.64 1 1
PLD2 -0.099 0.19 -9999 0 -0.6 10 10
PTPN13 -0.042 0.13 -9999 0 -0.46 5 5
PTPN11 0.01 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.024 0.14 -9999 0 -0.36 6 6
SYK 0.011 0.038 -9999 0 -0.65 1 1
GRB2 0.013 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.12 0.16 -9999 0 -0.57 12 12
LAT -0.061 0.15 -9999 0 -0.51 14 14
PAK2 -0.024 0.12 -9999 0 -0.44 6 6
NFATC2 -0.087 0.18 -9999 0 -0.71 19 19
HRAS -0.035 0.13 -9999 0 -0.45 9 9
GAB2 0.009 0.053 -9999 0 -0.64 2 2
PLA2G1B 0.036 0.019 -9999 0 -10000 0 0
Fc epsilon R1 -0.16 0.22 -9999 0 -0.43 112 112
Antigen/IgE/Fc epsilon R1 -0.15 0.2 -9999 0 -0.39 112 112
mol:GDP -0.042 0.14 -9999 0 -0.47 9 9
JUN 0.013 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.092 0.24 -9999 0 -0.64 49 49
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.086 0.12 -9999 0 -0.46 9 9
CHUK -0.027 0.12 -9999 0 -0.38 2 2
KLRG1 -0.057 0.14 -9999 0 -0.49 9 9
VAV1 -0.055 0.14 -9999 0 -0.48 11 11
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.049 0.13 -9999 0 -0.44 9 9
negative regulation of mast cell degranulation -0.047 0.13 -9999 0 -0.45 9 9
BTK -0.076 0.11 -9999 0 -0.45 7 7
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.087 0.18 -9999 0 -0.66 10 10
GAB2/PI3K/SHP2 -0.11 0.15 -9999 0 -0.65 6 6
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.071 0.15 -9999 0 -0.63 6 6
RAF1 0.024 0.023 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.14 0.19 -9999 0 -0.64 14 14
FCER1G -0.002 0.1 -9999 0 -0.81 5 5
FCER1A -0.22 0.32 -9999 0 -0.65 106 106
Antigen/IgE/Fc epsilon R1/Fyn -0.14 0.19 -9999 0 -0.62 11 11
MAPK3 0.035 0.02 -9999 0 -10000 0 0
MAPK1 0.035 0.02 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.006 0.065 -9999 0 -0.6 2 2
DUSP1 -0.041 0.18 -9999 0 -0.64 25 25
NF-kappa-B/RelA -0.039 0.049 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.048 0.13 -9999 0 -0.44 7 7
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.068 0.099 -9999 0 -0.47 6 6
FER -0.049 0.13 -9999 0 -0.46 7 7
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.035 0.085 -9999 0 -0.42 12 12
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.042 0.14 -9999 0 -0.48 9 9
cytokine secretion -0.028 0.036 -9999 0 -10000 0 0
SPHK1 -0.053 0.14 -9999 0 -0.51 9 9
PTK2 -0.05 0.13 -9999 0 -0.46 7 7
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.12 0.16 -9999 0 -0.58 9 9
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.063 0.18 -9999 0 -0.52 9 9
MAP2K2 0.031 0.02 -9999 0 -10000 0 0
MAP2K1 0.031 0.02 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.081 0.11 -9999 0 -0.47 9 9
MAP2K4 0.019 0.009 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.15 0.2 -9999 0 -0.68 14 14
mol:Choline -0.098 0.19 -9999 0 -0.59 10 10
SHC/Grb2/SOS1 -0.069 0.097 -9999 0 -0.44 5 5
FYN 0.011 0.047 -9999 0 -0.8 1 1
DOK1 0.013 0 -9999 0 -10000 0 0
PXN -0.039 0.12 -9999 0 -0.43 6 6
HCLS1 -0.053 0.14 -9999 0 -0.46 12 12
PRKCB -0.051 0.15 -9999 0 -0.41 10 10
FCGR2B 0 0.091 -9999 0 -0.64 6 6
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.047 0.13 -9999 0 -0.46 9 9
LCP2 0.005 0.081 -9999 0 -0.8 3 3
PLA2G4A -0.063 0.16 -9999 0 -0.52 17 17
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.098 0.19 -9999 0 -0.59 10 10
IKK complex -0.004 0.095 -9999 0 -0.28 1 1
WIPF1 0.003 0.093 -9999 0 -0.8 4 4
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.015 0.094 -9999 0 -0.46 11 11
CRKL 0.011 0.047 -9999 0 -0.8 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.013 0 -9999 0 -10000 0 0
ITGA4 -0.014 0.15 -9999 0 -0.8 10 10
alpha4/beta7 Integrin/MAdCAM1 -0.038 0.13 -9999 0 -0.48 23 23
EPO -0.056 0.22 -9999 0 -0.8 25 25
alpha4/beta7 Integrin -0.022 0.11 -9999 0 -0.6 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.022 0.12 -9999 0 -0.61 11 11
EPO/EPOR (dimer) -0.065 0.19 -9999 0 -0.61 32 32
lamellipodium assembly 0.002 0.015 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 -0.039 0.11 -9999 0 -0.59 2 2
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.025 0.16 -9999 0 -0.8 13 13
cell adhesion -0.037 0.13 -9999 0 -0.48 23 23
CRKL/CBL -0.002 0.035 -9999 0 -0.61 1 1
ITGB1 0.011 0.047 -9999 0 -0.8 1 1
SRC -0.039 0.19 -9999 0 -0.5 39 39
ITGB7 0.011 0.038 -9999 0 -0.64 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.078 0.19 -9999 0 -0.54 44 44
p130Cas/Crk/Dock1 -0.058 0.14 -9999 0 -0.79 2 2
VCAM1 -0.078 0.25 -9999 0 -0.78 35 35
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.017 0.09 -9999 0 -0.48 11 11
BCAR1 -0.027 0.18 -9999 0 -0.46 39 39
EPOR -0.005 0.12 -9999 0 -0.8 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP 0.002 0.015 -9999 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 -0.005 0.12 -10000 0 -0.78 7 7
positive regulation of NF-kappaB transcription factor activity -0.037 0.14 -10000 0 -0.59 19 19
MAP2K4 0.011 0.099 -10000 0 -0.5 1 1
IKBKB 0.013 0 -10000 0 -10000 0 0
TNFRSF10B 0.013 0 -10000 0 -10000 0 0
TNFRSF10A 0.013 0 -10000 0 -10000 0 0
SMPD1 -0.006 0.037 -10000 0 -10000 0 0
IKBKG 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.018 0.15 -10000 0 -0.78 12 12
TRAIL/TRAILR2 -0.014 0.089 -10000 0 -0.59 7 7
TRAIL/TRAILR3 -0.027 0.12 -10000 0 -0.59 14 14
TRAIL/TRAILR1 -0.014 0.089 -10000 0 -0.59 7 7
TRAIL/TRAILR4 -0.037 0.14 -10000 0 -0.59 19 19
TRAIL/TRAILR1/DAP3/GTP -0.011 0.071 -10000 0 -0.49 6 6
IKK complex -0.025 0.062 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.011 0.093 -10000 0 -0.59 7 7
MAP3K1 -0.036 0.089 -10000 0 -0.54 1 1
TRAILR4 (trimer) -0.018 0.15 -10000 0 -0.77 12 12
TRADD 0.013 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.013 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.003 0.11 -10000 0 -0.54 1 1
CFLAR 0.013 0 -10000 0 -10000 0 0
MAPK1 0.011 0.093 -10000 0 -0.59 7 7
TRAIL/TRAILR1/FADD/TRADD/RIP -0.063 0.16 -10000 0 -0.46 42 42
mol:ceramide -0.006 0.037 -10000 0 -10000 0 0
FADD -0.084 0.26 -10000 0 -0.8 36 36
MAPK8 0.017 0.1 -10000 0 -0.5 2 2
TRAF2 0.008 0.066 -10000 0 -0.8 2 2
TRAILR3 (trimer) -0.005 0.12 -10000 0 -0.78 7 7
CHUK 0.013 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.074 0.19 -10000 0 -0.54 42 42
DAP3 0.013 0 -10000 0 -10000 0 0
CASP10 -0.051 0.16 0.28 9 -0.44 39 48
JNK cascade -0.037 0.14 -10000 0 -0.59 19 19
TRAIL (trimer) -0.005 0.12 -10000 0 -0.78 7 7
TNFRSF10C -0.005 0.12 -10000 0 -0.78 7 7
TRAIL/TRAILR1/DAP3/GTP/FADD -0.064 0.16 -10000 0 -0.46 42 42
TRAIL/TRAILR2/FADD -0.074 0.19 -10000 0 -0.54 42 42
cell death -0.006 0.037 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.11 -10000 0 -0.54 1 1
TRAILR2 (trimer) 0.013 0 -10000 0 -10000 0 0
CASP8 0 0.023 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.063 0.16 -10000 0 -0.46 42 42
Cellular roles of Anthrax toxin

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
ANTXR1 0.005 0.081 -10000 0 -0.8 3 3
ANTXR2 -0.008 0.13 -10000 0 -0.8 8 8
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.018 -10000 0 -0.096 11 11
monocyte activation -0.032 0.12 -10000 0 -0.28 49 49
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.003 0.015 -10000 0 -10000 0 0
MAP2K7 -0.003 0.015 -10000 0 -10000 0 0
MAP2K6 -0.019 0.075 -10000 0 -0.36 14 14
CYAA -0.001 0.091 -10000 0 -0.47 11 11
MAP2K4 -0.003 0.015 -10000 0 -10000 0 0
IL1B -0.029 0.14 -10000 0 -0.45 29 29
Channel -0.018 0.093 -10000 0 -0.5 11 11
NLRP1 -0.004 0.031 -10000 0 -0.48 1 1
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.022 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.018 0.096 11 -10000 0 11
MAPK3 -0.003 0.015 -10000 0 -10000 0 0
MAPK1 -0.003 0.015 -10000 0 -10000 0 0
PGR -0.049 0.12 -10000 0 -0.38 37 37
PA/Cellular Receptors -0.019 0.1 -10000 0 -0.54 11 11
apoptosis -0.003 0.018 -10000 0 -0.096 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0 0.087 -10000 0 -0.45 11 11
macrophage activation 0.019 0.017 -10000 0 -10000 0 0
TNF -0.025 0.17 -10000 0 -0.76 15 15
VCAM1 -0.032 0.12 -10000 0 -0.28 49 49
platelet activation -0.004 0.022 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.026 -10000 0 -10000 0 0
IL18 0.004 0.069 -10000 0 -0.34 11 11
negative regulation of macrophage activation -0.003 0.018 -10000 0 -0.096 11 11
LEF -0.004 0.018 -10000 0 -0.097 11 11
CASP1 -0.004 0.02 -10000 0 -0.22 1 1
mol:cAMP -0.004 0.022 -10000 0 -10000 0 0
necrosis -0.003 0.018 -10000 0 -0.096 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.017 0.088 -10000 0 -0.47 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -10000 0 -10000 0 0
HDAC4 0.013 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.012 0.14 0.61 16 -10000 0 16
CDKN1A 0.001 0.012 -10000 0 -10000 0 0
KAT2B -0.015 0.13 -10000 0 -0.64 13 13
BAX 0.013 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
FOXO4 0.023 0.027 -10000 0 -0.31 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT 0.005 0.047 -10000 0 -0.8 1 1
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.093 0.22 -10000 0 -0.5 66 66
PPARGC1A -0.21 0.31 -10000 0 -0.64 102 102
FHL2 0.009 0.053 -10000 0 -0.64 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0 -10000 0 -10000 0 0
HIST2H4A -0.012 0.14 -10000 0 -0.62 16 16
SIRT1/FOXO3a 0 0 -10000 0 -10000 0 0
SIRT1 0 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.007 0.04 -10000 0 -10000 0 0
apoptosis 0 0 -10000 0 -10000 0 0
SIRT1/PGC1A -0.14 0.19 -10000 0 -0.4 102 102
p53/SIRT1 -0.005 0.047 -10000 0 -0.47 3 3
SIRT1/FOXO4 -0.001 0.021 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.002 0.029 -10000 0 -10000 0 0
HIST1H1E 0.016 0.052 -10000 0 -0.28 9 9
SIRT1/p300 0 0 -10000 0 -10000 0 0
muscle cell differentiation 0.091 0.18 0.55 10 -10000 0 10
TP53 -0.006 0.064 -10000 0 -0.64 3 3
KU70/SIRT1/BAX 0 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.002 0.035 -10000 0 -0.61 1 1
ACSS2 0.022 0 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.091 0.18 -10000 0 -0.55 10 10
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.004 0.05 -9999 0 -0.62 2 2
PDGFRB -0.22 0.36 -9999 0 -0.8 85 85
SPHK1 -0.022 0.037 -9999 0 -0.37 1 1
mol:S1P -0.029 0.058 -9999 0 -0.44 4 4
S1P1/S1P/Gi -0.015 0.13 -9999 0 -0.46 7 7
GNAO1 0.007 0.061 -9999 0 -0.73 2 2
PDGFB-D/PDGFRB/PLCgamma1 -0.098 0.21 -9999 0 -0.58 11 11
PLCG1 -0.017 0.13 -9999 0 -0.46 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.22 0.36 -9999 0 -0.8 85 85
GNAI2 0.011 0.005 -9999 0 -10000 0 0
GNAI3 0.009 0.007 -9999 0 -10000 0 0
GNAI1 0.007 0.039 -9999 0 -0.65 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.014 0.046 -9999 0 -0.54 2 2
S1P1/S1P -0.038 0.068 -9999 0 -0.48 3 3
negative regulation of cAMP metabolic process -0.015 0.12 -9999 0 -0.45 7 7
MAPK3 -0.022 0.16 -9999 0 -0.56 7 7
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.009 0.047 -9999 0 -0.8 1 1
PLCB2 -0.001 0.081 -9999 0 -0.42 3 3
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.031 0.057 -9999 0 -0.4 3 3
receptor internalization -0.036 0.064 -9999 0 -0.44 3 3
PTGS2 -0.05 0.24 -9999 0 -0.6 47 47
Rac1/GTP -0.031 0.057 -9999 0 -0.4 3 3
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.009 0.048 -9999 0 -0.82 1 1
negative regulation of T cell proliferation -0.015 0.12 -9999 0 -0.45 7 7
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.008 0.11 -9999 0 -0.74 7 7
MAPK1 -0.022 0.16 -9999 0 -0.56 7 7
S1P1/S1P/PDGFB-D/PDGFRB -0.09 0.2 -9999 0 -0.54 11 11
ABCC1 0.004 0.081 -9999 0 -0.8 3 3
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.099 0.28 -9999 0 -0.71 47 47
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.04 0.12 -9999 0 -0.43 2 2
ATF2/c-Jun -0.007 0.094 -9999 0 -10000 0 0
MAPK11 -0.04 0.12 -9999 0 -0.4 7 7
MITF -0.041 0.16 -9999 0 -0.56 11 11
MAPKAPK5 -0.033 0.14 -9999 0 -0.49 7 7
KRT8 -0.1 0.22 -9999 0 -0.67 20 20
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.059 0.18 -9999 0 -0.65 7 7
CEBPB -0.033 0.14 -9999 0 -0.49 7 7
SLC9A1 -0.033 0.14 -9999 0 -0.49 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.027 0.14 -9999 0 -0.48 7 7
p38alpha-beta/MNK1 -0.033 0.15 -9999 0 -0.53 7 7
JUN -0.006 0.093 -9999 0 -10000 0 0
PPARGC1A -0.17 0.27 -9999 0 -0.73 39 39
USF1 -0.033 0.14 -9999 0 -0.49 7 7
RAB5/GDP/GDI1 -0.049 0.084 -9999 0 -0.41 2 2
NOS2 -0.11 0.31 -9999 0 -0.78 46 46
DDIT3 -0.041 0.16 -9999 0 -0.53 10 10
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.016 0.12 -9999 0 -0.45 2 2
p38alpha-beta/HBP1 -0.033 0.15 -9999 0 -0.53 7 7
CREB1 -0.029 0.15 -9999 0 -0.48 7 7
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.02 0.13 -9999 0 -0.53 2 2
RPS6KA4 -0.033 0.14 -9999 0 -0.49 7 7
PLA2G4A -0.037 0.15 -9999 0 -0.6 4 4
GDI1 -0.033 0.14 -9999 0 -0.49 7 7
TP53 -0.048 0.18 -9999 0 -0.64 9 9
RPS6KA5 -0.034 0.15 -9999 0 -0.49 7 7
ESR1 -0.055 0.18 -9999 0 -0.57 14 14
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.041 0.16 -9999 0 -0.54 9 9
MEF2A -0.033 0.14 -9999 0 -0.49 7 7
EIF4EBP1 -0.03 0.15 -9999 0 -0.48 7 7
KRT19 -0.16 0.23 -9999 0 -0.7 22 22
ELK4 -0.033 0.14 -9999 0 -0.49 7 7
ATF6 -0.033 0.14 -9999 0 -0.49 7 7
ATF1 -0.029 0.15 -9999 0 -0.48 7 7
p38alpha-beta/MAPKAPK2 -0.033 0.15 -9999 0 -0.53 7 7
p38alpha-beta/MAPKAPK3 -0.033 0.15 -9999 0 -0.53 7 7
Regulation of Telomerase

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
Telomerase catalytic core complex -0.14 0.29 -9999 0 -0.71 48 48
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.076 0.17 -9999 0 -0.47 49 49
IFNAR2 0.012 0.007 -9999 0 -10000 0 0
AKT1 -0.002 0.071 -9999 0 -0.43 1 1
ER alpha/Oestrogen -0.032 0.13 -9999 0 -0.58 17 17
NFX1/SIN3/HDAC complex 0.041 0.023 -9999 0 -10000 0 0
EGF -0.14 0.27 -9999 0 -0.64 69 69
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.015 0.012 -9999 0 -10000 0 0
TERT/c-Abl -0.15 0.26 -9999 0 -0.66 48 48
SAP18 0.011 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.18 0.34 -9999 0 -0.8 71 71
WRN 0.013 0 -9999 0 -10000 0 0
SP1 0.013 0.007 -9999 0 -10000 0 0
SP3 0.011 0.006 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.14 0.23 -9999 0 -0.71 15 15
Mad/Max -0.002 0.027 -9999 0 -0.47 1 1
TERT -0.15 0.3 -9999 0 -0.73 48 48
CCND1 -0.13 0.29 -9999 0 -0.88 14 14
MAX 0.011 0.006 -9999 0 -10000 0 0
RBBP7 0.011 0.006 -9999 0 -10000 0 0
RBBP4 0.011 0.006 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.011 0.006 -9999 0 -10000 0 0
Telomerase/911 0.022 0.044 -9999 0 -10000 0 0
CDKN1B -0.072 0.22 -9999 0 -0.51 59 59
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.011 0.006 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.011 0.006 -9999 0 -10000 0 0
JUN 0.012 0.006 -9999 0 -10000 0 0
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.006 -9999 0 -10000 0 0
FOS -0.094 0.24 -9999 0 -0.64 49 49
IFN-gamma/IRF1 -0.12 0.24 -9999 0 -0.6 59 59
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.011 0.047 -9999 0 -0.8 1 1
Telomerase 0.002 0.086 -9999 0 -0.4 4 4
IRF1 0.015 0.008 -9999 0 -10000 0 0
ESR1 -0.031 0.18 -9999 0 -0.75 17 17
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.025 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.046 0.025 -9999 0 -10000 0 0
HDAC1 0.011 0.006 -9999 0 -10000 0 0
HDAC2 0.013 0.007 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.023 0.047 -9999 0 -0.54 2 2
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.009 0.038 -9999 0 -0.64 1 1
MRE11A 0.013 0 -9999 0 -10000 0 0
HUS1 0.011 0.047 -9999 0 -0.8 1 1
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.14 0.25 -9999 0 -0.73 22 22
NR2F2 0.016 0.01 -9999 0 -10000 0 0
MAPK3 0.012 0.039 -9999 0 -0.64 1 1
MAPK1 0.012 0.039 -9999 0 -0.64 1 1
TGFB1/TGF beta receptor Type II 0.011 0.047 -9999 0 -0.8 1 1
NFKB1 0.013 0 -9999 0 -10000 0 0
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.013 0 -9999 0 -10000 0 0
EGFR -0.015 0.15 -9999 0 -0.81 10 10
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.13 0.22 -9999 0 -0.5 78 78
MYC 0.011 0.006 -9999 0 -10000 0 0
IL2 0 0.05 -9999 0 -0.84 1 1
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.011 0.047 -9999 0 -0.8 1 1
TRF2/BLM -0.002 0.033 -9999 0 -0.57 1 1
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.15 0.26 -9999 0 -0.66 44 44
SP1/HDAC2 0.019 0.014 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.14 0.23 -9999 0 -0.69 18 18
Smad3/Myc 0.018 0.042 -9999 0 -0.46 2 2
911 complex -0.002 0.03 -9999 0 -0.53 1 1
IFNG -0.14 0.32 -9999 0 -0.8 59 59
Telomerase/PinX1 -0.14 0.23 -9999 0 -0.7 16 16
Telomerase/AKT1/mTOR/p70S6K -0.001 0.08 -9999 0 -0.48 1 1
SIN3B 0.011 0.006 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.14 0.23 -9999 0 -0.7 16 16
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.14 0.23 -9999 0 -0.7 16 16
E2F1 -0.034 0.19 -9999 0 -0.81 17 17
ZNFX1 0.011 0.006 -9999 0 -10000 0 0
PIF1 -0.014 0.15 -9999 0 -0.8 10 10
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB -0.22 0.37 -9999 0 -0.8 85 85
alphaV beta3 Integrin -0.028 0.13 -9999 0 -0.61 14 14
PTK2 -0.023 0.081 -9999 0 -0.71 1 1
positive regulation of JNK cascade -0.009 0.041 -9999 0 -0.32 3 3
CDC42/GDP 0.044 0.069 -9999 0 -0.43 3 3
Rac1/GDP 0.046 0.069 -9999 0 -0.42 3 3
RAP1B 0.011 0.047 -9999 0 -0.8 1 1
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.011 0.038 -9999 0 -0.64 1 1
CDC42/GTP -0.011 0.05 -9999 0 -0.39 3 3
nectin-3/I-afadin -0.023 0.11 -9999 0 -0.58 12 12
RAPGEF1 0.043 0.075 -9999 0 -0.48 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.036 0.084 -9999 0 -0.56 3 3
PDGFB-D/PDGFRB -0.22 0.37 -9999 0 -0.8 85 85
TLN1 0.025 0.057 -9999 0 -0.45 1 1
Rap1/GTP -0.01 0.046 -9999 0 -0.39 1 1
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.002 0.028 -9999 0 -0.49 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.023 0.11 -9999 0 -0.58 12 12
PVR 0.011 0.047 -9999 0 -0.8 1 1
Necl-5(dimer) 0.011 0.047 -9999 0 -0.8 1 1
mol:GDP 0.043 0.081 -9999 0 -0.53 3 3
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
PI3K -0.14 0.21 -9999 0 -0.46 92 92
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.002 0.027 -9999 0 -0.47 1 1
positive regulation of lamellipodium assembly -0.015 0.049 -9999 0 -0.33 3 3
PVRL1 0.011 0.038 -9999 0 -0.64 1 1
PVRL3 -0.017 0.15 -9999 0 -0.76 12 12
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.009 0.053 -9999 0 -0.64 2 2
CLDN1 -0.012 0.13 -9999 0 -0.7 11 11
JAM-A/CLDN1 -0.032 0.11 -9999 0 -0.48 13 13
SRC -0.018 0.079 -9999 0 -0.63 3 3
ITGB3 -0.017 0.15 -9999 0 -0.76 12 12
nectin-1(dimer)/I-afadin/I-afadin -0.002 0.027 -9999 0 -0.47 1 1
FARP2 0.04 0.078 -9999 0 -0.52 3 3
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.021 0.1 -9999 0 -0.5 13 13
nectin-1/I-afadin -0.002 0.027 -9999 0 -0.47 1 1
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.021 0.1 -9999 0 -0.49 13 13
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.009 0.041 -9999 0 -0.32 3 3
alphaV/beta3 Integrin/Talin 0.017 0.11 -9999 0 -0.58 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.019 0.053 -9999 0 -0.39 1 1
VAV2 0.029 0.091 -9999 0 -0.53 3 3
RAP1/GDP -0.011 0.052 -9999 0 -0.46 1 1
ITGAV 0.006 0.076 -9999 0 -0.75 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.02 0.097 -9999 0 -0.5 12 12
nectin-3(dimer)/I-afadin/I-afadin -0.023 0.11 -9999 0 -0.58 12 12
Rac1/GTP -0.017 0.058 -9999 0 -0.41 3 3
PTPRM -0.011 0.054 -9999 0 -0.43 1 1
E-cadherin/beta catenin/alpha catenin -0.004 0.044 -9999 0 -0.64 1 1
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.035 0.12 -10000 0 -0.47 18 18
ER alpha/Gai/GDP/Gbeta gamma 0.024 0.094 -10000 0 -0.46 3 3
AKT1 0.015 0.13 -10000 0 -0.78 6 6
PIK3CA 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.011 0.13 -10000 0 -0.79 6 6
mol:Ca2+ -0.034 0.17 -10000 0 -0.65 5 5
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.029 0.12 -10000 0 -0.48 18 18
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.016 0.12 0.74 6 -10000 0 6
RhoA/GTP -0.02 0.083 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.024 0.086 -10000 0 -0.59 1 1
regulation of stress fiber formation -0.038 0.078 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.039 0.14 -10000 0 -0.52 23 23
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.025 0.1 -10000 0 -0.45 17 17
pseudopodium formation 0.038 0.078 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.027 0.11 -10000 0 -0.49 17 17
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.011 0.047 -10000 0 -0.8 1 1
GNAO1 0.009 0.06 -10000 0 -0.72 2 2
HRAS 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.025 0.11 -10000 0 -0.51 7 7
E2/ER beta (dimer) -0.014 0.091 -10000 0 -0.6 7 7
mol:GDP -0.03 0.11 -10000 0 -0.5 6 6
mol:NADP 0.025 0.11 -10000 0 -0.51 7 7
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.037 0.18 -10000 0 -0.68 5 5
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.045 0.18 -10000 0 -0.43 50 50
PLCB2 -0.045 0.18 -10000 0 -0.43 50 50
IGF1 -0.054 0.2 -10000 0 -0.67 30 30
mol:L-citrulline 0.025 0.11 -10000 0 -0.51 7 7
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.01 0.058 -10000 0 -0.57 2 2
JNK cascade -0.014 0.09 -10000 0 -0.6 7 7
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 -0.005 0.12 -10000 0 -0.78 7 7
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.029 0.18 -10000 0 -0.75 17 17
Gq family/GDP/Gbeta gamma -0.002 0.1 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.029 0.064 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.024 0.086 -10000 0 -0.59 1 1
GNAZ -0.004 0.11 -10000 0 -0.73 7 7
E2/ER alpha (dimer) -0.032 0.13 -10000 0 -0.57 17 17
STRN 0.011 0.038 -10000 0 -0.64 1 1
GNAL -0.06 0.21 -10000 0 -0.64 34 34
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.008 0.081 -10000 0 -0.52 7 7
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.011 0.038 -10000 0 -0.64 1 1
HBEGF -0.18 0.17 -10000 0 -0.45 62 62
cAMP biosynthetic process -0.068 0.15 -10000 0 -0.47 19 19
SRC 0.031 0.09 -10000 0 -0.55 1 1
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.028 0.097 -10000 0 -0.73 1 1
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.042 0.1 -10000 0 -0.6 2 2
Gs family/GTP -0.069 0.15 -10000 0 -0.48 19 19
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation 0.026 0.1 -10000 0 -0.49 7 7
mol:DAG -0.037 0.18 -10000 0 -0.68 5 5
Gs family/GDP/Gbeta gamma -0.053 0.12 -10000 0 -0.62 3 3
MSN 0.039 0.083 -10000 0 -10000 0 0
Gq family/GTP -0.084 0.17 -10000 0 -0.46 50 50
mol:PI-3-4-5-P3 0.012 0.12 -10000 0 -0.76 6 6
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.026 0.1 0.49 7 -10000 0 7
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.028 0.1 -10000 0 -0.77 1 1
NOS3 0.025 0.11 -10000 0 -0.54 7 7
GNA11 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade 0.037 0.11 -10000 0 -0.58 6 6
E2/ER alpha (dimer)/PELP1/Src -0.026 0.091 -10000 0 -0.55 2 2
ruffle organization 0.038 0.078 -10000 0 -10000 0 0
ROCK2 0.031 0.09 -10000 0 -10000 0 0
GNA14 -0.095 0.24 -10000 0 -0.64 50 50
GNA15 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.3 0.2 -10000 0 -0.64 20 20
MMP2 -0.052 0.19 -10000 0 -0.55 3 3
S1P3 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
PDGFRB -0.22 0.37 -9999 0 -0.8 85 85
mol:S1P 0.001 0.004 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.027 0.059 -9999 0 -0.56 1 1
GNAO1 0.01 0.061 -9999 0 -0.73 2 2
S1P/S1P3/G12/G13 -0.007 0.057 -9999 0 -0.5 3 3
AKT1 -0.07 0.11 -9999 0 -0.36 5 5
AKT3 0.039 0.11 -9999 0 -0.67 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.22 0.37 -9999 0 -0.8 85 85
GNAI2 0.015 0.002 -9999 0 -10000 0 0
GNAI3 0.015 0.002 -9999 0 -10000 0 0
GNAI1 0.013 0.038 -9999 0 -0.64 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.008 0.072 -9999 0 -0.71 3 3
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.034 0.081 -9999 0 -0.62 3 3
MAPK3 0.041 0.078 -9999 0 -0.59 3 3
MAPK1 0.041 0.078 -9999 0 -0.59 3 3
JAK2 0.036 0.1 -9999 0 -0.64 4 4
CXCR4 0.022 0.14 -9999 0 -0.55 13 13
FLT1 0.016 0.002 -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 0.078 -9999 0 -0.59 3 3
S1P/S1P3/Gi 0.034 0.082 -9999 0 -0.63 3 3
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.012 0.066 -9999 0 -0.57 3 3
VEGFA 0.014 0.047 -9999 0 -0.8 1 1
S1P/S1P2/Gi 0.035 0.056 -9999 0 -0.58 1 1
VEGFR1 homodimer/VEGFA homodimer 0.026 0.037 -9999 0 -0.61 1 1
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.019 0.12 -9999 0 -0.56 1 1
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ -0.002 0.11 -9999 0 -0.73 7 7
G12/G13 -0.004 0.05 -9999 0 -0.61 2 2
GNA14 -0.095 0.24 -9999 0 -0.64 50 50
GNA15 0.013 0 -9999 0 -10000 0 0
GNA12 0.008 0.066 -9999 0 -0.8 2 2
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.012 0.066 -9999 0 -0.57 3 3
Signaling events mediated by PRL

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
CCNE1 0.011 0.047 -10000 0 -0.8 1 1
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 -0.14 0.32 -10000 0 -0.8 58 58
CDKN1A 0.03 0.032 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.008 0.07 -10000 0 -0.61 4 4
mol:Ca2+ -0.074 0.18 0.37 3 -0.49 48 51
AGT -0.091 0.24 -10000 0 -0.65 48 48
CCNA2 0.032 0.079 -10000 0 -0.78 1 1
TUBA1B 0.013 0 -10000 0 -10000 0 0
EGR1 0.009 0.092 -10000 0 -0.46 11 11
CDK2/Cyclin E1 -0.005 0.031 -10000 0 -0.43 1 1
MAPK3 0.016 0.073 -10000 0 -0.61 4 4
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.073 -10000 0 -0.61 4 4
PTP4A1 0.027 0.072 -10000 0 -10000 0 0
PTP4A3 0.003 0.093 -10000 0 -0.8 4 4
PTP4A2 0.013 0 -10000 0 -10000 0 0
ITGB1 0.014 0.081 -10000 0 -0.61 5 5
SRC 0.013 0 -10000 0 -10000 0 0
RAC1 0.027 0.043 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.022 0.094 -10000 0 -10000 0 0
RABGGTA 0.013 0 -10000 0 -10000 0 0
BCAR1 0.005 0.042 0.37 4 -10000 0 4
RHOC 0.027 0.043 -10000 0 -10000 0 0
RHOA 0.027 0.043 -10000 0 -10000 0 0
cell motility 0.032 0.045 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.032 0.067 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.12 0.25 -10000 0 -0.61 62 62
ROCK1 0.032 0.046 -10000 0 -10000 0 0
RABGGTB 0.013 0 -10000 0 -10000 0 0
CDK2 0.013 0 -10000 0 -10000 0 0
mitosis 0.027 0.071 -10000 0 -10000 0 0
ATF5 -0.003 0.11 -10000 0 -0.8 6 6
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.004 0.12 0.75 7 -10000 0 7
PI3K Class IB/PDE3B -0.004 0.12 -10000 0 -0.76 7 7
PDE3B -0.004 0.12 -10000 0 -0.76 7 7
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.042 0.21 -9999 0 -1 12 12
MAP4K1 -0.012 0.14 -9999 0 -0.75 10 10
MAP3K8 0.013 0 -9999 0 -10000 0 0
PRKCB -0.005 0.12 -9999 0 -0.78 7 7
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.011 0.047 -9999 0 -0.8 1 1
MAP3K1 0.026 0.12 -9999 0 -0.56 10 10
JUN 0.026 0.086 -9999 0 -0.57 4 4
MAP3K7 0.026 0.12 -9999 0 -0.56 10 10
GRAP2 -0.007 0.12 -9999 0 -0.74 8 8
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.036 0.11 -9999 0 -0.53 10 10
LAT -0.008 0.13 -9999 0 -0.8 8 8
LCP2 0.005 0.081 -9999 0 -0.8 3 3
MAPK8 0.019 0.091 -9999 0 -0.51 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.018 0.12 -9999 0 -0.6 10 10
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.04 0.2 -9999 0 -1 10 10
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.011 0.047 -9999 0 -0.8 1 1
ITGB7 0.011 0.038 -9999 0 -0.64 1 1
ITGA4 -0.014 0.15 -9999 0 -0.8 10 10
alpha4/beta7 Integrin -0.022 0.11 -9999 0 -0.6 11 11
alpha4/beta1 Integrin -0.022 0.12 -9999 0 -0.61 11 11
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.009 0.044 -9999 0 -0.65 1 1
VDR 0.013 0 -9999 0 -10000 0 0
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.011 0.12 -9999 0 -0.45 2 2
RXRs/LXRs/DNA/Oxysterols 0.021 0.12 -9999 0 -0.52 2 2
MED1 0.011 0.047 -9999 0 -0.8 1 1
mol:9cRA 0.005 0.012 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.012 0.12 -9999 0 -0.55 4 4
RXRs/NUR77 -0.017 0.15 -9999 0 -0.44 9 9
RXRs/PPAR -0.11 0.18 -9999 0 -0.52 20 20
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.037 0.1 -9999 0 -10000 0 0
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.038 0.11 -9999 0 -0.35 9 9
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0.041 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.012 0.12 -9999 0 -0.55 4 4
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.014 0.14 -9999 0 -0.46 7 7
NR1H4 0.004 0.006 -9999 0 -10000 0 0
RXRs/LXRs/DNA 0.007 0.14 -9999 0 -10000 0 0
NR1H2 0.019 0.008 -9999 0 -10000 0 0
NR1H3 0.014 0.066 -9999 0 -0.79 2 2
RXRs/VDR/DNA/Vit D3 -0.009 0.13 -9999 0 -0.42 7 7
NR4A1 0 0.091 -9999 0 -0.64 6 6
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.001 0.095 -9999 0 -0.37 3 3
RXRG -0.076 0.23 -9999 0 -0.66 42 42
RXR alpha/CCPG 0.003 0.008 -9999 0 -10000 0 0
RXRA 0.019 0.008 -9999 0 -10000 0 0
RXRB 0.019 0.009 -9999 0 -10000 0 0
THRB -0.028 0.16 -9999 0 -0.64 19 19
PPARG -0.24 0.32 -9999 0 -0.64 116 116
PPARD 0.013 0 -9999 0 -10000 0 0
TNF 0.007 0.2 -9999 0 -0.75 15 15
mol:Oxysterols 0.005 0.01 -9999 0 -10000 0 0
cholesterol transport 0.021 0.12 -9999 0 -0.51 2 2
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.06 0.21 -9999 0 -0.64 34 34
RXRs/NUR77/BCL2 -0.017 0.11 -9999 0 -0.3 4 4
SREBF1 0.03 0.11 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA -0.014 0.14 -9999 0 -0.46 7 7
ABCA1 0.026 0.13 -9999 0 -0.84 2 2
RARs/THRs -0.057 0.14 -9999 0 -0.67 4 4
RXRs/FXR -0.015 0.14 -9999 0 -0.45 7 7
BCL2 0.004 0.08 -9999 0 -0.68 4 4
FAS signaling pathway (CD95)

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
SPTAN1 0.006 0.036 0.26 4 -10000 0 4
RFC1 0.006 0.036 0.26 4 -10000 0 4
PRKDC 0.006 0.036 0.26 4 -10000 0 4
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 -0.011 0.041 0.23 3 -10000 0 3
FASLG/FAS/FADD/FAF1 -0.05 0.12 -10000 0 -0.39 9 9
MAP2K4 0 0.12 -10000 0 -0.44 7 7
mol:ceramide -0.019 0.14 -10000 0 -0.48 8 8
GSN 0.006 0.036 0.26 4 -10000 0 4
FASLG/FAS/FADD/FAF1/Caspase 8 -0.019 0.12 -10000 0 -0.46 6 6
FAS 0.013 0.004 -10000 0 -10000 0 0
BID 0.003 0.045 -10000 0 -0.54 1 1
MAP3K1 0.012 0.077 -10000 0 -10000 0 0
MAP3K7 0.013 0.004 -10000 0 -10000 0 0
RB1 0.005 0.042 -10000 0 -0.39 1 1
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.02 0.092 -10000 0 -0.53 4 4
ARHGDIB 0.006 0.036 0.26 4 -10000 0 4
FADD -0.084 0.26 -10000 0 -0.8 36 36
actin filament polymerization -0.006 0.036 -10000 0 -0.26 4 4
NFKB1 -0.029 0.063 -10000 0 -10000 0 0
MAPK8 -0.005 0.16 -10000 0 -0.57 8 8
DFFA 0.006 0.036 0.26 4 -10000 0 4
DNA fragmentation during apoptosis 0.006 0.036 0.26 3 -10000 0 3
FAS/FADD/MET -0.066 0.18 -10000 0 -0.54 37 37
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.003 0.11 -10000 0 -0.8 6 6
FAF1 0.014 0.004 -10000 0 -10000 0 0
PARP1 0.006 0.036 0.26 4 -10000 0 4
DFFB 0.006 0.036 0.26 2 -10000 0 2
CHUK -0.024 0.054 -10000 0 -10000 0 0
FASLG -0.039 0.2 -10000 0 -0.75 21 21
FAS/FADD -0.073 0.2 -10000 0 -0.61 36 36
HGF -0.008 0.12 -10000 0 -0.7 9 9
LMNA 0.006 0.033 -10000 0 -10000 0 0
CASP6 0.006 0.036 0.26 4 -10000 0 4
CASP10 0.013 0.004 -10000 0 -10000 0 0
CASP3 0.008 0.042 0.3 4 -10000 0 4
PTPN13 0.007 0.065 -10000 0 -0.64 3 3
CASP8 0.007 0.052 0.37 6 -10000 0 6
IL6 -0.082 0.36 -10000 0 -1.2 28 28
MET 0.009 0.06 -10000 0 -0.72 2 2
ICAD/CAD 0.006 0.034 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.02 0.14 -10000 0 -0.49 8 8
activation of caspase activity by cytochrome c 0.003 0.045 -10000 0 -0.54 1 1
PAK2 0.006 0.035 0.25 3 -10000 0 3
BCL2 0.004 0.08 -10000 0 -0.68 4 4
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 0.013 0 -9999 0 -10000 0 0
VDR 0.013 0 -9999 0 -10000 0 0
Cbp/p300/PCAF -0.017 0.08 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.005 0.1 -9999 0 -0.49 6 6
KAT2B -0.015 0.13 -9999 0 -0.64 13 13
MAPK14 0.013 0 -9999 0 -10000 0 0
AKT1 0.018 0.12 -9999 0 -0.28 25 25
RAR alpha/9cRA/Cyclin H -0.018 0.053 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.001 0.11 -9999 0 -0.43 8 8
CDC2 0.001 0.001 -9999 0 -10000 0 0
response to UV 0.001 0.002 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.021 0.068 -9999 0 -0.52 2 2
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.004 0.14 -9999 0 -0.52 3 3
NCOA2 0.005 0.075 -9999 0 -0.64 4 4
NCOA3 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0 -9999 0 -10000 0 0
RARG 0.014 0.001 -9999 0 -10000 0 0
RAR gamma1/9cRA 0 0 -9999 0 -10000 0 0
MAPK3 0.014 0.001 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.01 0.053 -9999 0 -0.64 2 2
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.099 -9999 0 -10000 0 0
RARA 0.004 0.079 -9999 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.006 0.13 -9999 0 -0.53 9 9
PRKCA 0.014 0.047 -9999 0 -0.8 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.019 0.14 -9999 0 -0.53 3 3
RXRG -0.063 0.19 -9999 0 -0.41 64 64
RXRA 0.014 0.075 -9999 0 -10000 0 0
RXRB -0.008 0.11 -9999 0 -0.34 30 30
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RBP1 -0.15 0.33 -9999 0 -0.8 61 61
CRBP1/9-cic-RA -0.12 0.25 -9999 0 -0.62 61 61
RARB -0.058 0.21 -9999 0 -0.64 34 34
PRKCG -0.065 0.24 -9999 0 -0.8 29 29
MNAT1 0.013 0 -9999 0 -10000 0 0
RAR alpha/RXRs 0.01 0.14 -9999 0 -0.51 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.002 0.13 -9999 0 -0.5 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.11 -9999 0 -0.47 7 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.019 0.14 -9999 0 -0.53 3 3
positive regulation of DNA binding -0.018 0.051 -9999 0 -10000 0 0
NRIP1 -0.017 0.14 -9999 0 -1.2 1 1
RXRs/RARs -0.025 0.14 -9999 0 -0.43 12 12
RXRs/RXRs/DNA/9cRA -0.045 0.1 -9999 0 -0.43 8 8
PRKACA 0.013 0 -9999 0 -10000 0 0
CDK7 0.013 0 -9999 0 -10000 0 0
TFIIH 0 0 -9999 0 -10000 0 0
RAR alpha/9cRA -0.013 0.037 -9999 0 -10000 0 0
CCNH 0.013 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
RAR gamma2/9cRA 0 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.036 0.12 -10000 0 -0.69 4 4
UGCG -0.007 0.037 -10000 0 -0.59 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.011 0.13 -10000 0 -0.43 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.019 0.044 -10000 0 -0.58 1 1
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.025 0.083 -10000 0 -0.45 8 8
FRAP1 0.047 0.13 -10000 0 -0.52 8 8
FOXO3 0.055 0.12 -10000 0 -0.55 4 4
AKT1 0.048 0.12 -10000 0 -0.57 5 5
GAB2 0.01 0.053 -10000 0 -0.64 2 2
SMPD1 -0.005 0.015 -10000 0 -10000 0 0
SGMS1 -0.005 0.015 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.003 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation 0.038 0.056 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.024 0.009 -10000 0 -10000 0 0
RPS6KB1 0.006 0.069 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.003 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 -0.026 0.18 -10000 0 -0.8 16 16
PIK3R1 0.017 0.002 -10000 0 -10000 0 0
JAK1 0.017 0.002 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MYC 0.056 0.11 -10000 0 -0.57 1 1
MYB -0.11 0.39 -10000 0 -1.2 31 31
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.033 0.13 -10000 0 -0.55 10 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.063 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.033 0.13 -10000 0 -0.54 10 10
Rac1/GDP 0.028 0.01 -10000 0 -10000 0 0
T cell proliferation 0.043 0.12 -10000 0 -0.63 4 4
SHC1 0.014 0.002 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.022 -10000 0 -0.066 31 31
PRKCZ 0.042 0.13 -10000 0 -0.66 4 4
NF kappa B1 p50/RelA -0.023 0.082 -10000 0 -0.49 3 3
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.029 0.13 -10000 0 -0.54 12 12
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.085 0.27 -10000 0 -0.8 37 37
IL2RB 0 0.11 -10000 0 -0.8 6 6
TERT -0.16 0.34 -10000 0 -0.8 66 66
E2F1 -0.029 0.15 -10000 0 -0.43 31 31
SOS1 0.014 0.002 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP 0 0.011 0.032 31 -10000 0 31
PTPN11 0.014 0.002 -10000 0 -10000 0 0
IL2RG -0.012 0.15 -10000 0 -0.78 11 11
actin cytoskeleton organization 0.043 0.12 -10000 0 -0.63 4 4
GRB2 0.014 0.002 -10000 0 -10000 0 0
IL2 0.005 0.047 -10000 0 -0.8 1 1
PIK3CA 0.017 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.012 -10000 0 -10000 0 0
LCK -0.01 0.15 -10000 0 -0.8 10 10
BCL2 0.049 0.14 -10000 0 -0.78 5 5
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.031 0.03 -9999 0 -10000 0 0
epithelial cell differentiation -0.003 0.033 -9999 0 -10000 0 0
CYFIP2 0.009 0.053 -9999 0 -0.64 2 2
ENAH 0.066 0.042 -9999 0 -10000 0 0
EGFR -0.014 0.15 -9999 0 -0.8 10 10
EPHA2 0.005 0.075 -9999 0 -0.64 4 4
MYO6 0.037 0.04 -9999 0 -10000 0 0
CTNNB1 0.011 0.038 -9999 0 -0.64 1 1
ABI1/Sra1/Nap1 -0.003 0.032 -9999 0 -0.4 2 2
AQP5 -0.37 0.21 -9999 0 -0.49 228 228
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.038 0.034 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.12 -9999 0 -0.42 17 17
EGF -0.14 0.27 -9999 0 -0.64 69 69
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.14 0.22 -9999 0 -0.49 87 87
cortical microtubule organization -0.003 0.033 -9999 0 -10000 0 0
GO:0000145 0.037 0.033 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.033 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GDP -0.007 0.042 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.049 -9999 0 -0.48 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.05 0.036 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.038 0.035 -9999 0 -10000 0 0
ARF6/GTP -0.006 0.044 -9999 0 -0.44 1 1
CDH1 0.009 0.053 -9999 0 -0.64 2 2
EGFR/EGFR/EGF/EGF -0.084 0.14 -9999 0 -0.67 2 2
RhoA/GDP -0.003 0.03 -9999 0 -10000 0 0
actin cytoskeleton organization 0.044 0.038 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.013 0 -9999 0 -10000 0 0
IGF1 -0.054 0.2 -9999 0 -0.67 30 30
DIAPH1 -0.004 0.048 -9999 0 -0.6 2 2
Wnt receptor signaling pathway 0.003 0.033 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.007 0.042 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.044 0.039 -9999 0 -10000 0 0
EFNA1 0.011 0.047 -9999 0 -0.8 1 1
LPP 0.044 0.042 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.008 0.05 -9999 0 -10000 0 0
SEC6/SEC8 -0.003 0.026 -9999 0 -10000 0 0
MGAT3 0.005 0.12 -9999 0 -0.43 17 17
HGF/MET -0.015 0.076 -9999 0 -0.73 1 1
HGF -0.008 0.12 -9999 0 -0.7 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.031 0.03 -9999 0 -10000 0 0
actin cable formation 0.084 0.038 -9999 0 -10000 0 0
KIAA1543 0.019 0.11 -9999 0 -0.72 3 3
KIFC3 0.038 0.035 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.037 0.044 -9999 0 -0.43 1 1
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP -0.003 0.033 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.038 0.035 -9999 0 -10000 0 0
PIP5K1C 0.038 0.035 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 -0.006 0.036 -9999 0 -10000 0 0
adherens junction assembly 0.037 0.11 -9999 0 -0.67 3 3
IGF-1R heterotetramer/IGF1 -0.034 0.098 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET 0.009 0.06 -9999 0 -0.72 2 2
PLEKHA7 0.021 0.088 -9999 0 -0.64 1 1
mol:GTP -0.006 0.048 -9999 0 -0.48 1 1
establishment of epithelial cell apical/basal polarity 0.065 0.031 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.031 0.03 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.044 0.038 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.031 0.03 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.018 0.18 -9999 0 -0.56 10 10
MAP3K8 0.012 0.005 -9999 0 -10000 0 0
FOS 0 0.12 -9999 0 -0.46 9 9
PRKCA 0.01 0.047 -9999 0 -0.8 1 1
PTPN7 -0.029 0.18 -9999 0 -0.8 16 16
HRAS 0.013 0.001 -9999 0 -10000 0 0
PRKCB -0.006 0.12 -9999 0 -0.79 7 7
NRAS 0.013 0.001 -9999 0 -10000 0 0
RAS family/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.006 0.086 -9999 0 -0.38 7 7
MAP2K1 0.025 0.072 -9999 0 -0.43 3 3
ELK1 0.008 0.049 -9999 0 -0.84 1 1
BRAF -0.013 0.059 -9999 0 -0.42 3 3
mol:GTP -0.001 0.002 -9999 0 -0.006 49 49
MAPK1 0.006 0.086 -9999 0 -0.38 7 7
RAF1 -0.013 0.059 -9999 0 -0.42 3 3
KRAS 0.013 0.001 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.028 0.16 -9999 0 -0.65 19 19
GNB1/GNG2 -0.052 0.11 -9999 0 -0.58 5 5
mol:DAG -0.001 0.12 -9999 0 -0.66 2 2
PLCG1 -0.001 0.13 -9999 0 -0.7 2 2
YES1 -0.017 0.14 -9999 0 -0.61 5 5
FZD3 0.005 0.075 -9999 0 -0.64 4 4
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.049 0.1 -9999 0 -0.7 2 2
MAP3K7 -0.048 0.17 -9999 0 -0.6 4 4
mol:Ca2+ 0 0.12 -9999 0 -0.64 2 2
mol:IP3 -0.001 0.12 -9999 0 -0.66 2 2
NLK -0.005 0.008 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.06 0.18 -9999 0 -0.54 15 15
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.028 0.14 -9999 0 -0.65 5 5
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.017 0.14 -9999 0 -0.61 5 5
GO:0007205 0 0.12 -9999 0 -0.65 2 2
WNT6 -0.03 0.18 -9999 0 -0.76 17 17
WNT4 -0.01 0.13 -9999 0 -0.69 10 10
NFAT1/CK1 alpha -0.063 0.13 -9999 0 -0.64 7 7
GNG2 0.011 0.047 -9999 0 -0.8 1 1
WNT5A 0.004 0.08 -9999 0 -0.68 4 4
WNT11 -0.074 0.25 -9999 0 -0.76 34 34
CDC42 -0.007 0.13 -9999 0 -0.57 5 5
Ceramide 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
SPHK2 0.012 0.089 -10000 0 -0.61 6 6
MAP4K4 0.03 0.077 -10000 0 -0.43 3 3
BAG4 0.013 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.018 0.053 0.21 1 -0.41 1 2
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.024 0.17 -10000 0 -0.8 14 14
BAX -0.004 0.025 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.024 0.011 -10000 0 -10000 0 0
BAD -0.016 0.049 0.21 5 -10000 0 5
SMPD1 0.019 0.053 -10000 0 -0.26 2 2
RB1 -0.017 0.053 0.21 5 -0.36 1 6
FADD/Caspase 8 -0.012 0.17 -10000 0 -0.43 37 37
MAP2K4 -0.007 0.046 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.007 0.046 -10000 0 -10000 0 0
EGF -0.14 0.27 -10000 0 -0.64 69 69
mol:ceramide -0.027 0.053 0.22 5 -10000 0 5
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.012 0.089 -10000 0 -0.61 6 6
ASAH1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.017 0.053 0.21 5 -0.36 1 6
cell proliferation -0.038 0.087 -10000 0 -0.36 5 5
BID 0.019 0.055 -10000 0 -10000 0 0
MAP3K1 -0.016 0.049 0.21 5 -10000 0 5
EIF2A -0.001 0.057 -10000 0 -0.43 2 2
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.006 0.044 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.044 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.016 0.048 0.19 5 -10000 0 5
FADD -0.027 0.18 -10000 0 -0.46 38 38
KSR1 -0.016 0.049 0.21 5 -10000 0 5
MAPK8 -0.004 0.052 0.2 5 -0.26 3 8
PRKRA -0.016 0.049 0.22 2 -10000 0 2
PDGFA -0.003 0.11 -10000 0 -0.8 6 6
TRAF2 0.008 0.066 -10000 0 -0.8 2 2
IGF1 -0.054 0.2 -10000 0 -0.67 30 30
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.027 0.052 0.22 5 -10000 0 5
CTSD 0.013 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.019 0.1 -10000 0 -0.39 5 5
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.038 -10000 0 -0.64 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.012 0.089 -10000 0 -0.61 6 6
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.023 0.081 -10000 0 -0.46 3 3
TNFR1A/BAG4/TNF-alpha -0.024 0.11 -10000 0 -0.49 15 15
mol:Sphingosine-1-phosphate 0.012 0.089 -10000 0 -0.61 6 6
MAP2K1 0.002 0.044 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS -0.006 0.041 0.22 3 -10000 0 3
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0 0 -10000 0 -10000 0 0
EIF2AK2 -0.01 0.059 -10000 0 -0.46 2 2
TNF-alpha/TNFR1A/FAN -0.024 0.11 -10000 0 -0.49 15 15
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.035 0.046 -10000 0 -10000 0 0
MAP2K2 0.002 0.044 -10000 0 -10000 0 0
SMPD3 -0.006 0.11 -10000 0 -0.34 25 25
TNF -0.025 0.17 -10000 0 -0.76 15 15
PKC zeta/PAR4 -0.002 0.027 -10000 0 -0.47 1 1
mol:PHOSPHOCHOLINE 0.043 0.11 0.24 72 -10000 0 72
NF kappa B1/RelA/I kappa B alpha -0.001 0.019 -10000 0 -10000 0 0
AIFM1 -0.006 0.041 0.22 3 -10000 0 3
BCL2 0.004 0.08 -10000 0 -0.68 4 4
Paxillin-dependent events mediated by a4b1

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
CRKL 0.011 0.047 -10000 0 -0.8 1 1
Rac1/GDP 0.002 0.013 -10000 0 -10000 0 0
DOCK1 0.013 0 -10000 0 -10000 0 0
ITGA4 -0.014 0.15 -10000 0 -0.8 10 10
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.022 0.11 -10000 0 -0.6 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.019 0.099 -10000 0 -0.53 11 11
alpha4/beta7 Integrin/Paxillin -0.017 0.088 -10000 0 -0.48 10 10
lamellipodium assembly 0.002 0.014 -10000 0 -10000 0 0
PIK3CA 0.013 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
TLN1 0.011 0.047 -10000 0 -0.8 1 1
PXN 0.025 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP -0.015 0.076 -10000 0 -10000 0 0
cell adhesion -0.017 0.086 -10000 0 -0.44 12 12
CRKL/CBL -0.002 0.035 -10000 0 -0.61 1 1
alpha4/beta1 Integrin/Paxillin -0.017 0.09 -10000 0 -0.48 11 11
ITGB1 0.011 0.047 -10000 0 -0.8 1 1
ITGB7 0.011 0.038 -10000 0 -0.64 1 1
ARF6/GDP 0.002 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.066 0.16 -10000 0 -0.47 39 39
p130Cas/Crk/Dock1 0 0 -10000 0 -10000 0 0
VCAM1 -0.078 0.25 -10000 0 -0.78 35 35
alpha4/beta1 Integrin/Paxillin/Talin -0.018 0.087 -10000 0 -0.45 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 -0.016 0.084 -10000 0 -0.45 11 11
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.083 0.44 11 -10000 0 11
CBL 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.018 0.087 -10000 0 -0.45 12 12
Rac1/GTP 0.002 0.015 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.013 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.033 0.075 -9999 0 -0.5 2 2
NEF -0.006 0.045 -9999 0 -10000 0 0
NFKBIA 0.012 0.026 -9999 0 -10000 0 0
BIRC3 0.013 0.16 -9999 0 -0.74 14 14
CYCS 0.01 0.11 -9999 0 -0.53 3 3
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.031 0.19 -9999 0 -0.86 14 14
MAP2K7 0.012 0.094 -9999 0 -0.43 2 2
protein ubiquitination 0.031 0.096 -9999 0 -0.42 1 1
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.013 0 -9999 0 -10000 0 0
BID 0.002 0.11 -9999 0 -0.52 4 4
NF-kappa-B/RelA/I kappa B alpha -0.015 0.067 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.013 0 -9999 0 -10000 0 0
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD -0.084 0.26 -9999 0 -0.8 36 36
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.015 0.067 -9999 0 -10000 0 0
MAPK8 0.018 0.096 -9999 0 -0.44 2 2
APAF1 0.013 0 -9999 0 -10000 0 0
TRAF1 -0.008 0.13 -9999 0 -0.8 8 8
TRAF2 0.008 0.066 -9999 0 -0.8 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.006 0.11 -9999 0 -0.49 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.014 0.12 -9999 0 -0.48 3 3
CHUK 0.031 0.1 -9999 0 -0.46 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.053 0.14 -9999 0 -0.45 36 36
TCRz/NEF -0.05 0.17 -9999 0 -0.54 28 28
TNF -0.025 0.17 -9999 0 -0.76 15 15
FASLG -0.045 0.25 -9999 0 -0.81 27 27
NFKB1 0.012 0.026 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.024 0.11 -9999 0 -0.49 15 15
CASP6 -0.02 0.046 -9999 0 -10000 0 0
CASP7 0.041 0.13 -9999 0 -0.5 4 4
RELA 0.012 0.026 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.041 0.13 -9999 0 -0.5 4 4
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0 0 -9999 0 -10000 0 0
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.023 0.11 -9999 0 -0.48 2 2
APAF-1/Caspase 9 -0.039 0.1 -9999 0 -0.51 4 4
BCL2 0.021 0.1 -9999 0 -0.44 3 3
IL6-mediated signaling events

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
BCL2L1 0.001 0.22 -9999 0 -0.66 2 2
CRP -0.031 0.27 -9999 0 -0.77 17 17
cell cycle arrest -0.013 0.24 -9999 0 -0.71 8 8
TIMP1 0.01 0.2 -9999 0 -0.64 1 1
IL6ST 0 0.099 -9999 0 -0.64 7 7
Rac1/GDP 0.013 0.14 -9999 0 -0.58 7 7
AP1 -0.002 0.14 -9999 0 -0.65 2 2
GAB2 0.009 0.053 -9999 0 -0.64 2 2
TNFSF11 -0.078 0.32 -9999 0 -0.72 24 24
HSP90B1 0.035 0.052 -9999 0 -10000 0 0
GAB1 0.014 0.001 -9999 0 -10000 0 0
MAPK14 0.011 0.14 -9999 0 -0.63 6 6
AKT1 0.058 0.03 -9999 0 -10000 0 0
FOXO1 0.067 0.026 -9999 0 -10000 0 0
MAP2K6 -0.003 0.15 -9999 0 -0.64 6 6
mol:GTP 0 0.003 -9999 0 -10000 0 0
MAP2K4 0.02 0.16 -9999 0 -0.56 6 6
MITF 0.004 0.15 -9999 0 -0.68 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.013 0 -9999 0 -10000 0 0
A2M 0.02 0.039 -9999 0 -0.65 1 1
CEBPB 0.02 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.025 0.07 -9999 0 -0.39 2 2
STAT3 -0.015 0.25 -9999 0 -0.76 7 7
STAT1 -0.027 0.098 -9999 0 -0.35 23 23
CEBPD 0.001 0.22 -9999 0 -0.66 2 2
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K 0 0.002 -9999 0 -10000 0 0
JUN 0.013 0.001 -9999 0 -10000 0 0
PIAS3/MITF 0.01 0.14 -9999 0 -0.64 6 6
MAPK11 0.011 0.14 -9999 0 -0.63 6 6
STAT3 (dimer)/FOXO1 0.045 0.21 -9999 0 -10000 0 0
GRB2/SOS1/GAB family -0.031 0.093 -9999 0 -0.58 4 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.001 0.13 -9999 0 -0.64 5 5
GRB2 0.014 0.001 -9999 0 -10000 0 0
JAK2 0.013 0 -9999 0 -10000 0 0
LBP -0.1 0.38 -9999 0 -0.9 47 47
PIK3R1 0.015 0 -9999 0 -10000 0 0
JAK1 0.015 0.005 -9999 0 -10000 0 0
MYC 0.001 0.22 -9999 0 -0.66 2 2
FGG -0.024 0.26 -9999 0 -0.76 15 15
macrophage differentiation -0.013 0.24 -9999 0 -0.71 8 8
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.04 0.13 -9999 0 -0.57 8 8
JUNB 0 0.21 -9999 0 -10000 0 0
FOS -0.093 0.24 -9999 0 -0.64 49 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.002 0.14 -9999 0 -0.54 9 9
STAT1/PIAS1 -0.002 0.14 -9999 0 -0.54 7 7
GRB2/SOS1/GAB family/SHP2/PI3K 0.041 0.035 -9999 0 -10000 0 0
STAT3 (dimer) -0.015 0.25 -9999 0 -0.74 8 8
PRKCD 0.026 0.18 -9999 0 -0.66 2 2
IL6R 0.013 0.038 -9999 0 -0.65 1 1
SOCS3 0.016 0.14 -9999 0 -0.84 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.02 0.069 -9999 0 -0.41 4 4
Rac1/GTP -0.051 0.11 -9999 0 -0.58 7 7
HCK 0.003 0.084 -9999 0 -0.72 4 4
MAPKKK cascade 0.039 0.07 -9999 0 -0.56 2 2
bone resorption -0.072 0.31 -9999 0 -0.68 24 24
IRF1 0.001 0.22 -9999 0 -0.66 3 3
mol:GDP 0.006 0.15 -9999 0 -0.62 7 7
SOS1 0.012 0.005 -9999 0 -10000 0 0
VAV1 0.006 0.15 -9999 0 -0.63 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.011 0.13 -9999 0 -0.69 5 5
PTPN11 -0.001 0.016 -9999 0 -10000 0 0
IL6/IL6RA -0.029 0.16 -9999 0 -0.51 28 28
gp130 (dimer)/TYK2/TYK2/LMO4 0.015 0.067 -9999 0 -0.41 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 0.015 0.067 -9999 0 -0.41 1 1
IL6 -0.048 0.2 -9999 0 -0.67 28 28
PIAS3 0.013 0 -9999 0 -10000 0 0
PTPRE 0.011 0.013 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
RAC1 0.014 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.007 0.13 -9999 0 -0.65 5 5
LMO4 0.015 0.011 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.1 0.17 -9999 0 -0.71 7 7
MCL1 0.066 0.025 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.04 0.11 -10000 0 -0.46 1 1
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.001 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.002 0.031 -10000 0 -0.54 1 1
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.042 0.12 -10000 0 -0.38 34 34
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 0.011 0.03 0.094 34 -10000 0 34
GNAL -0.06 0.21 -10000 0 -0.64 34 34
GNG2 0.011 0.047 -10000 0 -0.8 1 1
CRH 0.001 0.003 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.032 -10000 0 -0.38 2 2
MAPK11 0.009 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.14 0.31 -9999 0 -1.3 1 1
PLK1 0.08 0.082 -9999 0 -0.69 1 1
BIRC5 0.073 0.11 -9999 0 -0.68 4 4
HSPA1B 0.14 0.31 -9999 0 -1.3 1 1
MAP2K1 0.043 0.037 -9999 0 -10000 0 0
BRCA2 0.14 0.32 -9999 0 -1.3 2 2
FOXM1 0.13 0.35 -9999 0 -2.1 1 1
XRCC1 0.14 0.31 -9999 0 -1.3 1 1
FOXM1B/p19 -0.18 0.26 -9999 0 -1.1 6 6
Cyclin D1/CDK4 0.082 0.36 -9999 0 -1 4 4
CDC2 0.14 0.32 -9999 0 -1.4 1 1
TGFA 0.095 0.36 -9999 0 -1 4 4
SKP2 0.14 0.31 -9999 0 -1.3 1 1
CCNE1 0.016 0.047 -9999 0 -0.78 1 1
CKS1B 0.14 0.31 -9999 0 -1.5 1 1
RB1 -0.049 0.1 -9999 0 -0.67 2 2
FOXM1C/SP1 0.13 0.31 -9999 0 -1.7 1 1
AURKB 0.08 0.082 -9999 0 -0.72 1 1
CENPF 0.14 0.31 -9999 0 -1.3 1 1
CDK4 0.023 0.017 -9999 0 -10000 0 0
MYC 0.14 0.28 -9999 0 -1.1 1 1
CHEK2 0.041 0.057 -9999 0 -0.71 1 1
ONECUT1 0.081 0.38 -9999 0 -1.1 6 6
CDKN2A -0.32 0.38 -9999 0 -0.78 124 124
LAMA4 0.12 0.35 -9999 0 -1.1 4 4
FOXM1B/HNF6 0.076 0.4 -9999 0 -1.2 6 6
FOS 0.006 0.54 -9999 0 -1.1 49 49
SP1 0.015 0.001 -9999 0 -10000 0 0
CDC25B 0.13 0.32 -9999 0 -1.3 1 1
response to radiation 0.025 0.035 -9999 0 -10000 0 0
CENPB 0.14 0.31 -9999 0 -1.3 1 1
CENPA 0.14 0.32 -9999 0 -1.2 2 2
NEK2 0.14 0.32 -9999 0 -1.3 2 2
HIST1H2BA 0.13 0.31 -9999 0 -1.3 1 1
CCNA2 0.016 0.049 -9999 0 -0.82 1 1
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.14 0.33 -9999 0 -1.7 1 1
CCNB2 0.14 0.31 -9999 0 -1.5 1 1
CCNB1 0.14 0.32 -9999 0 -1.4 1 1
ETV5 0.14 0.32 -9999 0 -1.3 1 1
ESR1 0.11 0.36 -9999 0 -1.1 5 5
CCND1 0.086 0.38 -9999 0 -1.1 5 5
GSK3A 0.039 0.033 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.045 0.064 -9999 0 -0.52 2 2
CDK2 0.019 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.03 0.04 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.072 0.18 -9999 0 -1.5 1 1
GAS1 0.14 0.33 -9999 0 -1.2 4 4
MMP2 0.072 0.38 -9999 0 -1 6 6
RB1/FOXM1C 0.1 0.35 -9999 0 -1.4 1 1
CREBBP 0.013 0 -9999 0 -10000 0 0
p38 MAPK signaling 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
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 -0.004 0.043 -9999 0 -0.54 2 2
ATM 0.013 0 -9999 0 -10000 0 0
MAP2K3 0.018 0.044 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.021 0.063 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.003 0.083 -9999 0 -0.64 5 5
TXN 0.009 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
GADD45A 0.011 0.047 -9999 0 -0.8 1 1
GADD45B 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.013 0 -9999 0 -10000 0 0
MAP3K6 0.011 0.038 -9999 0 -0.64 1 1
MAP3K7 0.013 0 -9999 0 -10000 0 0
MAP3K4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.002 0.027 -9999 0 -0.47 1 1
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.008 0.066 -9999 0 -0.8 2 2
RAC1/OSM/MEKK3/MKK3 -0.006 0.012 -9999 0 -10000 0 0
TRAF6 0.009 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.16 0.29 -9999 0 -0.65 79 79
CCM2 0.013 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.11 0.18 -9999 0 -0.41 79 79
MAPK11 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.096 0.16 -9999 0 -0.37 79 79
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.017 0.023 -9999 0 -0.37 1 1
TAOK2 0.019 0 -9999 0 -10000 0 0
TAOK3 0.019 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.013 0 -9999 0 -10000 0 0
MAP3K10 0.011 0.047 -9999 0 -0.8 1 1
MAP3K3 0.013 0 -9999 0 -10000 0 0
TRX/ASK1 0.017 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.007 0.05 -9999 0 -0.46 1 1
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.031 0.12 -10000 0 -0.57 1 1
CRKL 0.006 0.13 -10000 0 -0.48 1 1
mol:DAG 0.018 0.12 -10000 0 -0.47 1 1
HRAS 0.037 0.12 -10000 0 -10000 0 0
MAPK8 -0.012 0.15 -10000 0 -0.49 1 1
RAP1A 0.008 0.13 -10000 0 -0.48 1 1
GAB1 0.008 0.13 -10000 0 -0.48 1 1
MAPK14 -0.01 0.15 -10000 0 -0.49 1 1
EPO -0.053 0.22 -10000 0 -0.8 25 25
PLCG1 0.017 0.12 -10000 0 -0.49 1 1
EPOR/TRPC2/IP3 Receptors -0.005 0.12 -10000 0 -0.79 7 7
RAPGEF1 0.013 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.054 0.16 -10000 0 -0.5 33 33
GAB1/SHC/GRB2/SOS1 -0.034 0.097 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.043 0.19 -10000 0 -0.6 32 32
IRS2 0.005 0.13 -10000 0 -0.48 1 1
STAT1 -0.003 0.16 -10000 0 -0.63 2 2
STAT5B 0.022 0.12 -10000 0 -0.54 1 1
cell proliferation -0.002 0.14 -10000 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.033 0.096 -10000 0 -0.66 1 1
TEC -0.012 0.16 -10000 0 -0.72 4 4
SOCS3 0.011 0.038 -10000 0 -0.64 1 1
STAT1 (dimer) -0.002 0.16 -10000 0 -0.62 2 2
JAK2 0.012 0.012 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.01 0.14 -10000 0 -0.51 1 1
EPO/EPOR -0.043 0.19 -10000 0 -0.6 32 32
LYN 0.015 0.002 -10000 0 -10000 0 0
TEC/VAV2 -0.019 0.18 -10000 0 -0.79 5 5
elevation of cytosolic calcium ion concentration -0.005 0.12 -10000 0 -0.79 7 7
SHC1 0.013 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.017 0.17 -10000 0 -0.5 32 32
mol:IP3 0.018 0.12 -10000 0 -0.47 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.039 0.11 -10000 0 -0.74 1 1
SH2B3 0.009 0.048 -10000 0 -0.79 1 1
NFKB1 -0.01 0.15 -10000 0 -0.46 3 3
EPO/EPOR (dimer)/JAK2/SOCS3 -0.027 0.083 0.27 1 -10000 0 1
PTPN6 -0.001 0.14 -10000 0 -0.51 1 1
TEC/VAV2/GRB2 -0.054 0.16 -10000 0 -0.76 5 5
EPOR -0.005 0.12 -10000 0 -0.79 7 7
INPP5D 0.011 0.038 -10000 0 -0.64 1 1
mol:GDP -0.035 0.099 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
PLCG2 0.013 0 -10000 0 -10000 0 0
CRKL/CBL/C3G -0.025 0.11 -10000 0 -10000 0 0
VAV2 -0.009 0.16 -10000 0 -0.7 3 3
CBL 0.008 0.13 -10000 0 -0.48 1 1
SHC/Grb2/SOS1 -0.037 0.1 -10000 0 -10000 0 0
STAT5A 0.022 0.12 -10000 0 -0.54 1 1
GRB2 0.013 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.04 0.13 -10000 0 -0.65 1 1
LYN/PLCgamma2 0 0 -10000 0 -10000 0 0
PTPN11 0.013 0 -10000 0 -10000 0 0
BTK 0.006 0.13 -10000 0 -0.48 1 1
BCL2 0.025 0.15 -10000 0 -0.85 4 4
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.025 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.041 0 -9999 0 -10000 0 0
CDKN1A 0.041 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.013 0 -9999 0 -10000 0 0
FOXO3 0.041 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0.013 0 -9999 0 -10000 0 0
AKT3 0.011 0.052 -9999 0 -0.36 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.039 0.028 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.013 0 -9999 0 -10000 0 0
RAF1 0.013 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.041 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
AKT1/RAF1 0.04 0 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.041 0 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
TBC1D4 0.027 0 -9999 0 -10000 0 0
MAP3K5 0.013 0 -9999 0 -10000 0 0
MAPKAP1 0.013 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.048 0.009 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
AKT1S1 0.041 0 -9999 0 -10000 0 0
CASP9 0.041 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.047 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.02 0 -9999 0 -10000 0 0
CHUK 0.041 0 -9999 0 -10000 0 0
BAD/BCL-XL 0.054 0 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.019 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.064 0.014 -9999 0 -10000 0 0
PDPK1 0.013 0 -9999 0 -10000 0 0
MDM2 0.041 0 -9999 0 -10000 0 0
MAPKKK cascade -0.039 0 -9999 0 -10000 0 0
MDM2/Cbp/p300 0 0 -9999 0 -10000 0 0
TSC1/TSC2 0.048 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
glucose import -0.14 0.19 -9999 0 -0.35 133 133
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.035 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.14 0.19 -9999 0 -0.35 133 133
GSK3A 0.041 0 -9999 0 -10000 0 0
FOXO1 0.041 0 -9999 0 -10000 0 0
GSK3B 0.041 0 -9999 0 -10000 0 0
SFN 0.011 0.038 -9999 0 -0.64 1 1
G1/S transition of mitotic cell cycle 0.048 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.052 0.014 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
KPNA1 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
RHEB 0.013 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.01 0.053 -9999 0 -0.64 2 2
ELF1 -0.019 0.11 -9999 0 -10000 0 0
CCNA2 0.011 0.047 -9999 0 -0.8 1 1
PIK3CA 0.014 0 -9999 0 -10000 0 0
JAK3 -0.029 0.18 -9999 0 -0.8 16 16
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.035 0.13 -9999 0 -0.57 9 9
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.02 0.029 -9999 0 -0.33 2 2
IL2RA -0.056 0.24 -9999 0 -0.7 37 37
IL2RB -0.002 0.11 -9999 0 -0.8 6 6
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.015 0.15 -9999 0 -0.79 11 11
G1/S transition of mitotic cell cycle 0.037 0.073 -9999 0 -0.67 1 1
PTPN11 0.014 0 -9999 0 -10000 0 0
CCND2 0.028 0.067 -9999 0 -0.78 2 2
LCK -0.013 0.15 -9999 0 -0.8 10 10
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.003 0.047 -9999 0 -0.8 1 1
CDK6 0 0.1 -9999 0 -0.8 5 5
CCND3 0.045 0.12 -9999 0 -0.59 4 4
IGF1 pathway

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
NCK2 0.013 0 -9999 0 -10000 0 0
PTK2 0.013 0 -9999 0 -10000 0 0
CRKL -0.007 0.11 -9999 0 -0.39 6 6
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0.013 0 -9999 0 -10000 0 0
IRS1/Crk -0.006 0.11 -9999 0 -0.37 5 5
IGF-1R heterotetramer/IGF1/PTP1B -0.038 0.12 -9999 0 -0.47 5 5
AKT1 0.02 0.093 -9999 0 -10000 0 0
BAD 0.028 0.088 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.006 0.11 -9999 0 -0.37 5 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.032 0.098 -9999 0 -0.37 5 5
RAF1 0.032 0.085 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.03 0.091 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.036 0.11 -9999 0 -0.36 30 30
PIK3CA 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.02 0.093 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.027 0.076 -9999 0 -10000 0 0
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.026 0.078 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.029 0.089 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.006 0.025 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.032 0.098 -9999 0 -0.37 5 5
Crk/p130 Cas/Paxillin -0.028 0.085 -9999 0 -10000 0 0
IGF1R 0.006 0.025 -9999 0 -10000 0 0
IGF1 -0.054 0.21 -9999 0 -0.67 30 30
IRS2/Crk 0.001 0.1 -9999 0 -10000 0 0
PI3K -0.03 0.09 -9999 0 -10000 0 0
apoptosis -0.033 0.079 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD 0.004 0.13 -9999 0 -0.39 25 25
RAF1/14-3-3 E 0.038 0.077 -9999 0 -10000 0 0
BAD/14-3-3 0.034 0.083 -9999 0 -10000 0 0
PRKCZ 0.019 0.094 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.021 0.062 -9999 0 -10000 0 0
PTPN1 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.004 0.13 -9999 0 -0.42 25 25
BCAR1 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.034 0.1 -9999 0 -0.43 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.006 0.11 -9999 0 -0.37 5 5
GRB10 0.011 0.047 -9999 0 -0.8 1 1
PTPN11 -0.006 0.11 -9999 0 -0.37 5 5
IRS1 -0.016 0.11 -9999 0 -0.36 30 30
IRS2 -0.008 0.11 -9999 0 -0.36 7 7
IGF-1R heterotetramer/IGF1 -0.05 0.15 -9999 0 -0.5 30 30
GRB2 0.013 0 -9999 0 -10000 0 0
PDPK1 0.011 0.097 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKD1 -0.004 0.14 -9999 0 -0.42 29 29
SHC1 0.013 0 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.05 0.12 -9999 0 -0.74 1 1
TC10/GTP -0.048 0.11 -9999 0 -0.72 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0 0 -9999 0 -10000 0 0
HRAS 0.013 0 -9999 0 -10000 0 0
APS homodimer 0.011 0.047 -9999 0 -0.8 1 1
GRB14 -0.058 0.21 -9999 0 -0.66 32 32
FOXO3 -0.007 0.046 -9999 0 -0.77 1 1
AKT1 0.021 0.1 -9999 0 -10000 0 0
INSR 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.011 0.047 -9999 0 -0.8 1 1
SORBS1 -0.092 0.24 -9999 0 -0.64 49 49
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.039 0 -9999 0 -10000 0 0
CAV1 -0.018 0.15 -9999 0 -0.47 29 29
CBL/APS/CAP/Crk-II/C3G -0.054 0.13 -9999 0 -0.78 1 1
Insulin Receptor/Insulin/IRS1/NCK2 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.042 0 -9999 0 -10000 0 0
RPS6KB1 0.029 0.097 -9999 0 -10000 0 0
PARD6A 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.007 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.025 0.074 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.015 -9999 0 -10000 0 0
Insulin Receptor 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0 0 -9999 0 -10000 0 0
PRKCI -0.007 0.021 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.032 0.093 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.006 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 0.021 0.1 -9999 0 -10000 0 0
PRKCZ -0.009 0.036 -9999 0 -0.52 1 1
SH2B2 0.011 0.047 -9999 0 -0.8 1 1
SHC/SHIP 0.035 0.02 -9999 0 -10000 0 0
F2RL2 -0.29 0.4 -9999 0 -0.8 114 114
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.059 0.14 -9999 0 -0.83 1 1
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.002 0.028 -9999 0 -0.5 1 1
INPP5D 0.028 0.021 -9999 0 -0.34 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.005 0.059 -9999 0 -1 1 1
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 0.013 0 -9999 0 -10000 0 0
p62DOK/RasGAP 0 0.006 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.028 0.021 -9999 0 -0.34 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 0.025 0.1 -9999 0 -10000 0 0
PTPRA 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.037 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.17 0.22 -9999 0 -0.46 113 113
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.005 0.081 -9999 0 -0.8 3 3
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.019 0.043 -9999 0 -0.28 6 6
GNAO1 0.009 0.06 -9999 0 -0.72 2 2
mol:Sphinganine-1-P 0.019 0.063 -9999 0 -0.61 3 3
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.007 0.044 -9999 0 -0.44 2 2
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 -0.004 0.05 -9999 0 -0.61 2 2
S1PR3 0.006 0.071 -9999 0 -0.7 3 3
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.005 0.034 -9999 0 -10000 0 0
S1PR5 0.011 0.038 -9999 0 -0.64 1 1
S1PR4 -0.035 0.19 -9999 0 -0.8 18 18
GNAI1 0.011 0.038 -9999 0 -0.64 1 1
S1P/S1P5/G12 -0.008 0.051 -9999 0 -0.47 2 2
S1P/S1P3/Gq -0.011 0.12 -9999 0 -0.49 2 2
S1P/S1P4/Gi 0.019 0.088 -9999 0 -0.54 2 2
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ -0.004 0.11 -9999 0 -0.73 7 7
GNA14 -0.095 0.24 -9999 0 -0.64 50 50
GNA15 0.013 0 -9999 0 -10000 0 0
GNA12 0.008 0.066 -9999 0 -0.8 2 2
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.013 0 -9999 0 -10000 0 0
ABCC1 0.005 0.081 -9999 0 -0.8 3 3
Circadian rhythm 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
chromatin modification 0 0.003 -9999 0 -10000 0 0
CLOCK 0.017 0 -9999 0 -10000 0 0
TIMELESS/CRY2 0.047 0.01 -9999 0 -10000 0 0
DEC1/BMAL1 -0.077 0.2 -9999 0 -0.61 38 38
ATR 0.013 0 -9999 0 -10000 0 0
NR1D1 0.046 0.012 -9999 0 -10000 0 0
ARNTL 0.017 0 -9999 0 -10000 0 0
TIMELESS 0.046 0.012 -9999 0 -10000 0 0
NPAS2 0.009 0.075 -9999 0 -0.64 4 4
CRY2 0.013 0 -9999 0 -10000 0 0
mol:CO -0.015 0 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME 0.015 0 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.041 0.049 -9999 0 -10000 0 0
BMAL1/CLOCK 0.027 0.085 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0 0.003 -9999 0 -10000 0 0
mol:NADPH 0.015 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.047 0.01 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.092 0.27 -9999 0 -0.8 38 38
Aurora A signaling

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
Aurora A/GADD45A -0.005 0.046 -9999 0 -0.53 1 1
BIRC5 0.003 0.093 -9999 0 -0.8 4 4
NFKBIA 0.028 0.039 -9999 0 -10000 0 0
CPEB1 -0.075 0.23 -9999 0 -0.67 39 39
AKT1 0.028 0.039 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.003 0.032 -9999 0 -10000 0 0
NDEL1/TACC3 -0.006 0.047 -9999 0 -0.46 2 2
GADD45A 0.011 0.047 -9999 0 -0.8 1 1
GSK3B 0.013 0.004 -9999 0 -10000 0 0
PAK1/Aurora A -0.005 0.046 -9999 0 -0.53 1 1
MDM2 0.013 0 -9999 0 -10000 0 0
JUB 0.013 0 -9999 0 -10000 0 0
TPX2 0.012 0.089 -9999 0 -0.62 6 6
TP53 -0.005 0.039 -9999 0 -0.32 3 3
DLG7 0.017 0.039 -9999 0 -0.29 4 4
AURKAIP1 0.013 0 -9999 0 -10000 0 0
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.006 0.05 -9999 0 -0.48 2 2
G2/M transition of mitotic cell cycle -0.003 0.032 -9999 0 -10000 0 0
AURKA 0.02 0.046 -9999 0 -0.34 4 4
AURKB -0.003 0.026 -9999 0 -0.28 2 2
CDC25B -0.013 0.065 -9999 0 -0.32 10 10
G2/M transition checkpoint -0.003 0.032 -9999 0 -10000 0 0
mRNA polyadenylation -0.053 0.13 -9999 0 -0.39 39 39
Aurora A/CPEB -0.053 0.13 -9999 0 -0.39 39 39
Aurora A/TACC1/TRAP/chTOG -0.004 0.034 -9999 0 -10000 0 0
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication -0.005 0.046 -9999 0 -0.53 1 1
regulation of centrosome cycle -0.006 0.046 -9999 0 -0.45 2 2
spindle assembly -0.004 0.034 -9999 0 -10000 0 0
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.008 0.067 -9999 0 -0.55 4 4
CENPA -0.005 0.034 -9999 0 -0.36 2 2
Aurora A/PP2A -0.004 0.035 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.033 0.035 -9999 0 -10000 0 0
negative regulation of DNA binding 0.025 0.043 -9999 0 -0.32 3 3
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.003 0.032 -9999 0 -10000 0 0
mitotic prometaphase 0 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.046 -9999 0 -0.34 4 4
TACC1 0.011 0.038 -9999 0 -0.64 1 1
TACC3 0.008 0.066 -9999 0 -0.8 2 2
Aurora A/Antizyme1 -0.003 0.031 -9999 0 -10000 0 0
Aurora A/RasGAP -0.004 0.035 -9999 0 -10000 0 0
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.004 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.002 0.03 -9999 0 -0.53 1 1
Importin alpha/Importin beta/TPX2 0.012 0.089 -9999 0 -0.61 6 6
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.022 0.079 -9999 0 -0.48 6 6
PAK1 0.011 0.047 -9999 0 -0.8 1 1
CKAP5 0.013 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.017 0.14 -10000 0 -0.64 13 13
regulation of axonogenesis -0.025 0.029 -10000 0 -10000 0 0
myoblast fusion 0.02 0.069 0.32 13 -10000 0 13
mol:GTP -0.01 0.039 -10000 0 -0.26 1 1
regulation of calcium-dependent cell-cell adhesion -0.021 0.064 0.41 4 -10000 0 4
ARF1/GTP -0.007 0.027 -10000 0 -10000 0 0
mol:GM1 0.003 0.032 -10000 0 -10000 0 0
mol:Choline 0.024 0.028 -10000 0 -10000 0 0
lamellipodium assembly -0.019 0.07 -10000 0 -0.32 13 13
MAPK3 0.018 0.059 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.022 0.065 -10000 0 -0.41 4 4
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.02 0.069 -10000 0 -0.32 13 13
ARF1/GDP 0.01 0.07 -10000 0 -0.51 1 1
ARF6 0.007 0.022 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 0.008 0.065 -10000 0 -0.64 3 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.059 -10000 0 -10000 0 0
actin filament bundle formation 0.017 0.061 0.51 1 -10000 0 1
KALRN -0.03 0.099 -10000 0 -0.37 18 18
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.017 0.062 -10000 0 -0.51 1 1
NME1 0.012 0.047 -10000 0 -0.8 1 1
Rac1/GDP -0.017 0.062 -10000 0 -0.51 1 1
substrate adhesion-dependent cell spreading -0.01 0.039 -10000 0 -0.26 1 1
cortical actin cytoskeleton organization -0.019 0.071 -10000 0 -0.32 13 13
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.01 0.039 -10000 0 -0.26 1 1
ARF6/GTP -0.01 0.039 -10000 0 -0.26 1 1
RhoA/GTP -0.007 0.027 -10000 0 -10000 0 0
mol:GDP -0.019 0.071 -10000 0 -0.32 13 13
ARF6/GTP/RAB11FIP3/RAB11A -0.004 0.021 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0.015 0.032 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.019 0.07 -10000 0 -0.32 13 13
ruffle organization 0.025 0.029 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.01 0.039 -10000 0 -0.26 1 1
PLD2 0.015 0.032 -10000 0 -10000 0 0
PIP5K1A 0.025 0.029 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.024 0.028 -10000 0 -10000 0 0
Rac1/GTP -0.019 0.071 -10000 0 -0.32 13 13
HIF-2-alpha transcription factor network

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
MMP14 -0.003 0.089 -10000 0 -0.67 5 5
oxygen homeostasis 0 0.017 -10000 0 -10000 0 0
TCEB2 0.013 0 -10000 0 -10000 0 0
TCEB1 0.011 0.047 -10000 0 -0.8 1 1
VHL/Elongin B/Elongin C/HIF2A -0.02 0.075 -10000 0 -10000 0 0
EPO -0.015 0.26 -10000 0 -0.7 16 16
FIH (dimer) 0.012 0.017 -10000 0 -10000 0 0
APEX1 0.015 0.014 -10000 0 -10000 0 0
SERPINE1 -0.24 0.38 -10000 0 -0.77 33 33
FLT1 0.009 0.036 -10000 0 -10000 0 0
ADORA2A 0 0.22 -10000 0 -0.86 2 2
germ cell development -0.004 0.23 -10000 0 -0.81 4 4
SLC11A2 0.003 0.22 -10000 0 -1 1 1
BHLHE40 0.003 0.22 -10000 0 -1 1 1
HIF1AN 0.012 0.017 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.054 0.098 -10000 0 -0.5 4 4
ETS1 0.025 0.066 -10000 0 -0.79 2 2
CITED2 -0.005 0.11 -10000 0 -1 3 3
KDR 0.007 0.052 -10000 0 -0.65 1 1
PGK1 0.003 0.22 -10000 0 -1 1 1
SIRT1 0.013 0.002 -10000 0 -10000 0 0
response to hypoxia -0.001 0.004 -10000 0 -10000 0 0
HIF2A/ARNT -0.007 0.25 -10000 0 -0.88 4 4
EPAS1 0.012 0.13 -10000 0 -0.43 5 5
SP1 0.022 0.003 -10000 0 -10000 0 0
ABCG2 -0.005 0.23 -10000 0 -0.88 3 3
EFNA1 0.002 0.23 -10000 0 -1.3 1 1
FXN 0.002 0.22 -10000 0 -0.99 1 1
POU5F1 -0.006 0.24 -10000 0 -0.86 4 4
neuron apoptosis 0.006 0.24 0.84 4 -10000 0 4
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 -0.049 0.22 -10000 0 -0.8 23 23
EGLN2 0.012 0.017 -10000 0 -10000 0 0
EGLN1 0.012 0.017 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.002 0.03 -10000 0 -0.53 1 1
VHL 0.013 0 -10000 0 -10000 0 0
ARNT 0.015 0.014 -10000 0 -10000 0 0
SLC2A1 -0.007 0.24 -10000 0 -0.87 8 8
TWIST1 -0.007 0.24 -10000 0 -0.83 7 7
ELK1 0.019 0.047 -10000 0 -0.8 1 1
HIF2A/ARNT/Cbp/p300 -0.045 0.09 -10000 0 -0.61 1 1
VEGFA 0.002 0.23 -10000 0 -0.99 2 2
CREBBP 0.013 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.017 0.14 -9999 0 -0.64 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.018 0.05 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.011 0.047 -9999 0 -0.8 1 1
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.011 0.047 -9999 0 -0.8 1 1
p38 alpha/TAB1 -0.02 0.045 -9999 0 -10000 0 0
PRKG1 -0.008 0.12 -9999 0 -0.71 9 9
DUSP8 0.013 0 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.028 0.07 -9999 0 -0.42 5 5
apoptosis -0.02 0.043 -9999 0 -10000 0 0
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.041 0.18 -9999 0 -0.64 25 25
PAK1 0.011 0.047 -9999 0 -0.8 1 1
SRC 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.001 0.02 -9999 0 -10000 0 0
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.019 0.1 -9999 0 -0.39 5 5
BLK -0.12 0.3 -9999 0 -0.77 53 53
HCK 0.004 0.084 -9999 0 -0.72 4 4
MAP2K3 0.011 0.038 -9999 0 -0.64 1 1
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.011 0.047 -9999 0 -0.8 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.028 0.073 -9999 0 -10000 0 0
positive regulation of innate immune response 0.027 0.11 -9999 0 -0.41 4 4
LCK -0.014 0.15 -9999 0 -0.8 10 10
p38alpha-beta/MKP7 0.032 0.1 -9999 0 -0.39 3 3
p38alpha-beta/MKP5 0.031 0.11 -9999 0 -0.4 1 1
PGK/cGMP -0.016 0.093 -9999 0 -0.54 9 9
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.007 0.14 -9999 0 -0.51 5 5
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.023 0.16 -9999 0 -0.78 13 13
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.035 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG -0.039 0.19 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.028 -9999 0 -0.48 1 1
CaM/Ca2+ -0.03 0.18 -9999 0 -10000 0 0
HIF1A 0.022 0 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.004 0.16 -9999 0 -10000 0 0
PLCG1 -0.039 0.19 -9999 0 -10000 0 0
NOS3 -0.002 0.16 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO -0.001 0.15 -9999 0 -10000 0 0
FLT1 0.033 0 -9999 0 -10000 0 0
PGF -0.12 0.3 -9999 0 -0.8 49 49
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.038 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.006 0.15 -9999 0 -10000 0 0
endothelial cell proliferation -0.019 0.16 -9999 0 -10000 0 0
mol:Ca2+ -0.039 0.19 -9999 0 -10000 0 0
MAPK3 -0.019 0.17 -9999 0 -10000 0 0
MAPK1 -0.019 0.17 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.12 0.3 -9999 0 -0.8 49 49
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.065 0.24 -9999 0 -0.8 29 29
VEGFA homodimer 0.011 0.047 -9999 0 -0.8 1 1
VEGFR1 homodimer/VEGFA homodimer 0.033 0.032 -9999 0 -0.52 1 1
platelet activating factor biosynthetic process -0.01 0.16 -9999 0 -10000 0 0
PI3K -0.071 0.16 -9999 0 -10000 0 0
PRKCA -0.029 0.18 -9999 0 -10000 0 0
PRKCB -0.038 0.19 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer -0.055 0.2 -9999 0 -0.52 49 49
VEGFA 0.011 0.047 -9999 0 -0.8 1 1
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.039 0.19 -9999 0 -10000 0 0
RASA1 0.044 0 -9999 0 -10000 0 0
NRP2 0.011 0.047 -9999 0 -0.8 1 1
VEGFR1 homodimer 0.033 0 -9999 0 -10000 0 0
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.035 0.2 -9999 0 -0.73 7 7
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.07 0.16 -9999 0 -10000 0 0
mol:L-citrulline -0.001 0.15 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.001 0.025 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.027 -9999 0 -10000 0 0
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.066 0.15 -9999 0 -10000 0 0
PDPK1 -0.019 0.17 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.027 -9999 0 -10000 0 0
mol:NADP -0.001 0.15 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.001 0.025 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.033 0.032 -9999 0 -0.52 1 1
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.009 0.06 -9999 0 -0.72 2 2
CDC42/GTP -0.02 0.07 -9999 0 -0.51 2 2
PLCG1 0.02 0.084 -9999 0 -0.53 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 -0.004 0.05 -9999 0 -0.61 2 2
cell migration -0.02 0.069 -9999 0 -0.5 2 2
S1PR5 0.011 0.038 -9999 0 -0.64 1 1
S1PR4 -0.035 0.19 -9999 0 -0.8 18 18
MAPK3 0.02 0.084 -9999 0 -0.53 2 2
MAPK1 0.02 0.084 -9999 0 -0.53 2 2
S1P/S1P5/Gi 0.029 0.053 -9999 0 -0.47 1 1
GNAI1 0.011 0.038 -9999 0 -0.64 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.049 -9999 0 -0.49 3 3
RHOA 0.003 0.12 -9999 0 -0.45 20 20
S1P/S1P4/Gi 0.012 0.089 -9999 0 -0.56 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.004 0.11 -9999 0 -0.73 7 7
S1P/S1P4/G12/G13 -0.032 0.12 -9999 0 -0.49 20 20
GNA12 0.008 0.066 -9999 0 -0.8 2 2
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.033 0.043 -9999 0 -10000 0 0
STMN1 0.024 0.052 -9999 0 -0.62 2 2
Aurora B/RasGAP/Survivin 0.017 0.082 -9999 0 -0.63 4 4
Chromosomal passenger complex/Cul3 protein complex 0.035 0.046 -9999 0 -0.4 2 2
BIRC5 0.005 0.094 -9999 0 -0.81 4 4
DES -0.3 0.26 -9999 0 -0.55 154 154
Aurora C/Aurora B/INCENP 0.019 0.051 -9999 0 -0.45 3 3
Aurora B/TACC1 0.013 0.042 -9999 0 -0.47 2 2
Aurora B/PP2A 0.016 0.039 -9999 0 -0.61 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.018 0.01 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.001 -9999 0 -10000 0 0
NDC80 0.018 0.083 -9999 0 -0.62 5 5
Cul3 protein complex -0.004 0.039 -9999 0 -0.4 3 3
KIF2C 0.01 0.034 -9999 0 -0.32 2 2
PEBP1 0.014 0.002 -9999 0 -10000 0 0
KIF20A 0.012 0.002 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.016 0.039 -9999 0 -0.61 1 1
SEPT1 0 0.1 -9999 0 -0.8 5 5
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.033 0.027 -9999 0 -0.38 1 1
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.002 -9999 0 -10000 0 0
H3F3B 0.021 0.022 -9999 0 -0.36 1 1
AURKB 0.019 0.049 -9999 0 -0.81 1 1
AURKC 0.009 0.06 -9999 0 -0.72 2 2
CDCA8 0.013 0.047 -9999 0 -0.81 1 1
cytokinesis -0.019 0.05 -9999 0 -0.56 2 2
Aurora B/Septin1 0.019 0.082 -9999 0 -0.46 7 7
AURKA -0.001 0.1 -9999 0 -0.8 5 5
INCENP 0.015 0.002 -9999 0 -10000 0 0
KLHL13 0.011 0.038 -9999 0 -0.64 1 1
BUB1 0.012 0.002 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.017 0.077 -9999 0 -0.59 4 4
EVI5 0.015 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.004 0.037 -9999 0 -0.49 1 1
SGOL1 0.013 0 -9999 0 -10000 0 0
CENPA 0.025 0.063 -9999 0 -0.51 3 3
NCAPG 0.013 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.016 0.039 -9999 0 -0.61 1 1
NCAPD2 0.005 0.081 -9999 0 -0.8 3 3
Aurora B/PP1-gamma 0.016 0.039 -9999 0 -0.61 1 1
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH 0.005 0.081 -9999 0 -0.8 3 3
NPM1 0.011 0.027 -9999 0 -0.42 1 1
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.009 0.053 -9999 0 -0.64 2 2
mitotic prometaphase 0.001 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.039 -9999 0 -0.61 1 1
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.004 0.041 -9999 0 -0.48 2 2
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.011 0.027 -9999 0 -0.42 1 1
MYLK 0.017 0.043 -9999 0 -0.36 4 4
KIF23 0.014 0.001 -9999 0 -10000 0 0
VIM 0.026 0.037 -9999 0 -0.61 1 1
RACGAP1 0.014 0.001 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.011 0.027 -9999 0 -0.42 1 1
Chromosomal passenger complex 0.036 0.05 -9999 0 -0.51 2 2
Chromosomal passenger complex/EVI5 0.046 0.097 -9999 0 -0.88 2 2
TACC1 0.011 0.038 -9999 0 -0.64 1 1
PPP2R5D 0.013 0 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.004 0.044 -9999 0 -0.54 2 2
CRKL 0.033 0.054 -9999 0 -0.42 1 1
mol:PIP3 -0.024 0.003 -9999 0 -10000 0 0
AKT1 0 0.002 -9999 0 -10000 0 0
PTK2B 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.04 0.052 -9999 0 -0.4 1 1
RANBP10 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.016 0.084 -9999 0 -0.44 11 11
MAP3K5 0.043 0.059 -9999 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.014 0.075 -9999 0 -0.48 4 4
AP1 -0.067 0.15 -9999 0 -0.41 49 49
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
apoptosis -0.092 0.26 -9999 0 -0.69 49 49
STAT3 (dimer) 0.036 0.054 -9999 0 -10000 0 0
GAB1/CRKL/SHP2/PI3K -0.007 0.038 -9999 0 -10000 0 0
INPP5D 0.011 0.038 -9999 0 -0.64 1 1
CBL/CRK 0.041 0.045 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.013 0 -9999 0 -10000 0 0
PTEN 0.013 0 -9999 0 -10000 0 0
ELK1 0.001 0.022 -9999 0 -0.25 2 2
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.005 0.027 -9999 0 -10000 0 0
PAK1 0.007 0.027 -9999 0 -0.47 1 1
HGF/MET/RANBP10 -0.016 0.084 -9999 0 -0.44 11 11
HRAS 0.029 0.073 -9999 0 -0.64 1 1
DOCK1 0.04 0.052 -9999 0 -0.4 1 1
GAB1 0.028 0.049 -9999 0 -10000 0 0
CRK 0.035 0.047 -9999 0 -10000 0 0
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.016 0.083 -9999 0 -0.5 7 7
JUN 0.013 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.008 0.043 -9999 0 -0.29 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
cell morphogenesis 0.066 0.059 -9999 0 -10000 0 0
GRB2/SHC -0.006 0.035 -9999 0 -10000 0 0
FOS -0.092 0.24 -9999 0 -0.64 49 49
GLMN 0 0 -9999 0 -10000 0 0
cell motility 0.001 0.022 -9999 0 -0.25 2 2
HGF/MET/MUC20 -0.016 0.085 -9999 0 -0.45 11 11
cell migration -0.007 0.034 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
MET/RANBP10 -0.004 0.044 -9999 0 -0.54 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.03 0.056 -9999 0 -10000 0 0
MET/MUC20 -0.004 0.045 -9999 0 -0.55 2 2
RAP1B 0.046 0.055 -9999 0 -10000 0 0
RAP1A 0.047 0.049 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.016 0.084 -9999 0 -0.44 11 11
RAF1 0.037 0.069 -9999 0 -0.6 1 1
STAT3 0.037 0.054 -9999 0 -10000 0 0
cell proliferation 0.048 0.071 -9999 0 -10000 0 0
RPS6KB1 0.012 0.018 -9999 0 -10000 0 0
MAPK3 -0.005 0.019 -9999 0 -0.26 1 1
MAPK1 -0.005 0.019 -9999 0 -0.26 1 1
RANBP9 0.013 0 -9999 0 -10000 0 0
MAPK8 0.057 0.067 -9999 0 -0.5 2 2
SRC 0.037 0.053 -9999 0 -10000 0 0
PI3K -0.006 0.035 -9999 0 -10000 0 0
MET/Glomulin 0.009 0.041 -9999 0 -0.49 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
MAP2K1 0.044 0.065 -9999 0 -0.54 1 1
MET 0.009 0.06 -9999 0 -0.72 2 2
MAP4K1 0.036 0.062 -9999 0 -10000 0 0
PTK2 0.013 0 -9999 0 -10000 0 0
MAP2K2 0.044 0.065 -9999 0 -0.54 1 1
BAD 0.008 0.002 -9999 0 -10000 0 0
MAP2K4 0.05 0.056 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.007 0.04 -9999 0 -10000 0 0
INPPL1 0.013 0 -9999 0 -10000 0 0
PXN 0.013 0 -9999 0 -10000 0 0
SH3KBP1 0.013 0 -9999 0 -10000 0 0
HGS 0.017 0.043 -9999 0 -10000 0 0
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.008 0.12 -9999 0 -0.7 9 9
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
PTPRJ 0.013 0 -9999 0 -10000 0 0
NCK/PLCgamma1 0.025 0.044 -9999 0 -10000 0 0
PDPK1 -0.01 0.002 -9999 0 -10000 0 0
HGF/MET/SHIP -0.017 0.092 -9999 0 -0.48 11 11
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0.001 -9999 0 -10000 0 0
HDAC2 0.013 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.013 0.073 -9999 0 -0.41 10 10
forebrain development -0.008 0.14 -9999 0 -0.46 7 7
GNAO1 0.008 0.06 -9999 0 -0.72 2 2
SMO/beta Arrestin2 0.003 0.084 -9999 0 -0.47 9 9
SMO -0.006 0.11 -9999 0 -0.64 9 9
ARRB2 0.013 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.055 0.033 -9999 0 -10000 0 0
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.012 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0.005 0.013 -9999 0 -10000 0 0
GNAI1 0.01 0.038 -9999 0 -0.64 1 1
XPO1 0.015 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.051 0.097 -9999 0 -0.5 2 2
SAP30 0.013 0.001 -9999 0 -10000 0 0
mol:GDP -0.006 0.11 -9999 0 -0.64 9 9
MIM/GLI2A 0.011 0.026 -9999 0 -10000 0 0
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.012 0.005 -9999 0 -10000 0 0
GLI2 0.031 0.059 -9999 0 -10000 0 0
GLI3 0.05 0.036 -9999 0 -10000 0 0
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.013 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.011 0.047 -9999 0 -0.8 1 1
Gi family/GTP 0.021 0.079 -9999 0 -0.49 3 3
SIN3B 0.013 0.001 -9999 0 -10000 0 0
SIN3A 0.013 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.058 0.038 -9999 0 -10000 0 0
GLI2/Su(fu) 0.038 0.065 -9999 0 -10000 0 0
FOXA2 -0.089 0.22 -9999 0 -0.64 41 41
neural tube patterning -0.008 0.14 -9999 0 -0.46 7 7
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.024 0.047 -9999 0 -0.4 1 1
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 0.011 0.026 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.008 0.14 -9999 0 -0.46 7 7
SUFU 0.02 0.052 -9999 0 -0.44 1 1
LGALS3 0.013 0 -9999 0 -10000 0 0
catabolic process 0.068 0.05 -9999 0 -10000 0 0
GLI3A/CBP -0.019 0.11 -9999 0 -10000 0 0
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.009 0.14 -9999 0 -0.48 7 7
RAB23 0.008 0.066 -9999 0 -0.8 2 2
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.013 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.024 0.047 -9999 0 -0.4 1 1
GNAZ -0.005 0.11 -9999 0 -0.73 7 7
RBBP4 0.013 0.001 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.035 0.055 -9999 0 -10000 0 0
STK36 0.015 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.028 0.072 -9999 0 -0.44 3 3
PTCH1 0.002 0.13 -9999 0 -10000 0 0
MIM/GLI1 -0.024 0.19 -9999 0 -0.64 9 9
CREBBP -0.019 0.11 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.052 0.014 -9999 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 0.036 0.075 -9999 0 -0.4 2 2
BAG4 0.013 0 -9999 0 -10000 0 0
BAD 0.03 0.028 -9999 0 -10000 0 0
NFKBIA 0.013 0 -9999 0 -10000 0 0
BIRC3 -0.024 0.17 -9999 0 -0.8 14 14
BAX 0.03 0.028 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.013 0.021 -9999 0 -0.095 3 3
IKBKB 0.043 0.072 -9999 0 -10000 0 0
MAP2K2 0.043 0.03 -9999 0 -10000 0 0
MAP2K1 0.043 0.03 -9999 0 -10000 0 0
SMPD1 0.019 0.021 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 -0.009 0.16 -9999 0 -0.62 5 5
MAP2K4 0.037 0.028 -9999 0 -10000 0 0
protein ubiquitination 0.045 0.073 -9999 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.048 0.033 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
RAF1 0.037 0.03 -9999 0 -10000 0 0
CRADD 0.014 0 -9999 0 -10000 0 0
mol:ceramide 0.022 0.03 -9999 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.014 0 -9999 0 -10000 0 0
MAP3K1 0.03 0.029 -9999 0 -10000 0 0
TRADD 0.014 0 -9999 0 -10000 0 0
RELA/p50 0.013 0 -9999 0 -10000 0 0
MAPK3 0.045 0.03 -9999 0 -10000 0 0
MAPK1 0.045 0.03 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD -0.018 0.17 -9999 0 -0.44 38 38
KSR1 0.03 0.03 -9999 0 -10000 0 0
MAPK8 0.041 0.039 -9999 0 -0.35 1 1
TRAF2 0.008 0.066 -9999 0 -0.8 2 2
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.043 0.072 -9999 0 -10000 0 0
TNF R/SODD 0 0 -9999 0 -10000 0 0
TNF -0.024 0.17 -9999 0 -0.76 15 15
CYCS 0.032 0.029 -9999 0 -10000 0 0
IKBKG 0.043 0.072 -9999 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.029 0.078 -9999 0 -0.42 3 3
RELA 0.013 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
AIFM1 0.032 0.029 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.024 0.11 -9999 0 -0.49 15 15
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.028 0.021 -9999 0 -10000 0 0
NSMAF 0.036 0.074 -9999 0 -0.4 2 2
response to hydrogen peroxide 0 0 -9999 0 -10000 0 0
BCL2 0.004 0.08 -9999 0 -0.68 4 4
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.062 0.018 -10000 0 -10000 0 0
NFATC2 0.034 0.047 -10000 0 -0.3 1 1
NFATC3 0.024 0.026 -10000 0 -0.43 1 1
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.015 0.076 -10000 0 -0.47 2 2
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.042 0.11 -10000 0 -0.55 7 7
BCL2/BAX -0.007 0.058 -10000 0 -0.51 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.001 0.003 -10000 0 -10000 0 0
BAX 0.013 0 -10000 0 -10000 0 0
MAPK14 0.014 0.002 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.021 0.072 -10000 0 -0.55 1 1
Calcineurin A alpha-beta B1/BCL2 0.004 0.08 -10000 0 -0.68 4 4
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.021 0.071 0.54 1 -10000 0 1
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.014 0 -10000 0 -10000 0 0
SFN 0.011 0.038 -10000 0 -0.64 1 1
MAP3K8 0.014 0.002 -10000 0 -10000 0 0
NFAT4/CK1 alpha -0.001 0.014 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.01 0.048 -10000 0 -10000 0 0
CABIN1 0.015 0.077 -10000 0 -0.48 2 2
CALM1 0.014 0.002 -10000 0 -10000 0 0
RAN 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.04 0.2 -10000 0 -0.8 20 20
mol:Ca2+ 0.001 0.003 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.036 0.14 -10000 0 -0.61 18 18
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 0.01 0.053 -10000 0 -0.64 2 2
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0 0.019 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0 0.001 -10000 0 -10000 0 0
CASP3 0.014 0.002 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.002 0.018 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.046 0.013 -10000 0 -10000 0 0
PRKCB -0.005 0.12 -10000 0 -0.78 7 7
PRKCE 0.013 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.029 0.024 -10000 0 -0.38 1 1
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.038 -10000 0 -0.64 1 1
PRKCA 0.011 0.047 -10000 0 -0.8 1 1
PRKCG -0.069 0.24 -10000 0 -0.8 29 29
PRKCQ -0.001 0.1 -10000 0 -0.72 6 6
FKBP38/BCL2 -0.007 0.058 -10000 0 -0.51 4 4
EP300 0.014 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.064 0.033 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.022 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.035 0.13 -10000 0 -0.53 20 20
NFATc/ERK1 0.067 0.017 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.042 0.12 -10000 0 -0.55 7 7
NR4A1 0.056 0.1 -10000 0 -0.61 6 6
GSK3B 0.014 0.002 -10000 0 -10000 0 0
positive T cell selection 0.024 0.026 -10000 0 -0.43 1 1
NFAT1/CK1 alpha -0.007 0.026 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.014 0.002 -10000 0 -10000 0 0
AKAP5 -0.035 0.19 -10000 0 -0.8 18 18
MEF2D 0.014 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.066 0.019 -10000 0 -10000 0 0
CREBBP 0.014 0.002 -10000 0 -10000 0 0
BCL2 0.004 0.08 -10000 0 -0.68 4 4
TCGA08_rtk_signaling

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
PDGFRA -0.003 0.11 -9999 0 -0.69 7 7
HRAS 0.013 0 -9999 0 -10000 0 0
EGFR -0.014 0.15 -9999 0 -0.8 10 10
AKT 0.037 0.051 -9999 0 -0.3 6 6
FOXO3 0.013 0 -9999 0 -10000 0 0
AKT1 0.013 0 -9999 0 -10000 0 0
FOXO1 0.013 0 -9999 0 -10000 0 0
AKT3 -0.003 0.11 -9999 0 -0.8 6 6
FOXO4 0.009 0.053 -9999 0 -0.64 2 2
MET 0.009 0.06 -9999 0 -0.72 2 2
PIK3CA 0.013 0 -9999 0 -10000 0 0
PIK3CB 0.013 0 -9999 0 -10000 0 0
NRAS 0.013 0 -9999 0 -10000 0 0
PIK3CG -0.025 0.17 -9999 0 -0.77 15 15
PIK3R3 0.011 0.038 -9999 0 -0.64 1 1
PIK3R2 0.013 0 -9999 0 -10000 0 0
NF1 0.013 0 -9999 0 -10000 0 0
RAS 0.019 0.043 -9999 0 -10000 0 0
ERBB2 0.008 0.066 -9999 0 -0.8 2 2
proliferation/survival/translation -0.031 0.027 -9999 0 -10000 0 0
PI3K 0.025 0.052 -9999 0 -0.25 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
KRAS 0.013 0 -9999 0 -10000 0 0
FOXO 0.048 0.03 -9999 0 -10000 0 0
AKT2 0.013 0 -9999 0 -10000 0 0
PTEN 0.013 0 -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 0 -9999 0 -10000 0 0
DAPP1 0.008 0.098 -9999 0 -0.39 2 2
Src family/SYK family/BLNK-LAT/BTK-ITK -0.01 0.17 -9999 0 -0.75 9 9
mol:DAG 0.026 0.09 -9999 0 -0.31 8 8
HRAS 0.014 0 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
ARF5/GDP 0.042 0.036 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
PLCG1 0.013 0 -9999 0 -10000 0 0
ARF5 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP 0 0 -9999 0 -10000 0 0
ADAP1 0 0 -9999 0 -10000 0 0
ARAP3 0 0 -9999 0 -10000 0 0
INPPL1 0.013 0 -9999 0 -10000 0 0
PREX1 0.013 0 -9999 0 -10000 0 0
ARHGEF6 0.009 0.053 -9999 0 -0.64 2 2
ARHGEF7 0.013 0 -9999 0 -10000 0 0
ARF1 0.013 0 -9999 0 -10000 0 0
NRAS 0.014 0 -9999 0 -10000 0 0
FYN 0.011 0.047 -9999 0 -0.8 1 1
ARF6 0.013 0 -9999 0 -10000 0 0
FGR 0.011 0.047 -9999 0 -0.8 1 1
mol:Ca2+ 0.026 0.049 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.007 0.065 -9999 0 -0.64 3 3
ZAP70 -0.022 0.16 -9999 0 -0.74 14 14
mol:IP3 0.029 0.066 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
ARF1/GDP 0.042 0.036 -9999 0 -10000 0 0
RhoA/GDP -0.001 0.007 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
BLNK -0.056 0.2 -9999 0 -0.64 32 32
actin cytoskeleton reorganization 0.067 0.031 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PLEKHA2 0.031 0.024 -9999 0 -0.39 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
PTEN 0 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.029 0.18 -9999 0 -0.65 14 14
BLK -0.12 0.3 -9999 0 -0.77 53 53
PDPK1 0.013 0 -9999 0 -10000 0 0
CYTH1 0 0 -9999 0 -10000 0 0
HCK 0.004 0.084 -9999 0 -0.72 4 4
CYTH3 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
KRAS 0.014 0 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.002 0.027 -9999 0 -0.47 1 1
SGK1 -0.002 0.029 -9999 0 -0.51 1 1
INPP5D 0.011 0.038 -9999 0 -0.64 1 1
mol:GDP 0.036 0.038 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
SYK 0.011 0.038 -9999 0 -0.64 1 1
ARF6/GDP -0.001 0.007 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP 0 0 -9999 0 -10000 0 0
VAV1 0.003 0.083 -9999 0 -0.64 5 5
mol:PI-3-4-P2 0.023 0.028 -9999 0 -0.47 1 1
RAS family/GTP/PI3K Class I 0 0 -9999 0 -10000 0 0
PLEKHA1 0.031 0.024 -9999 0 -10000 0 0
Rac1/GDP 0.042 0.036 -9999 0 -10000 0 0
LAT -0.008 0.13 -9999 0 -0.8 8 8
Rac1/GTP 0.037 0.052 -9999 0 -10000 0 0
ITK -0.015 0.073 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.024 0.12 -9999 0 -0.45 8 8
LCK -0.014 0.15 -9999 0 -0.8 10 10
BTK -0.001 0.024 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.27 0.32 -10000 0 -0.64 133 133
CLTC 0.034 0.017 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.029 0.001 -10000 0 -10000 0 0
Dynamin 2/GTP -0.002 0.028 -10000 0 -0.49 1 1
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.03 0.018 -10000 0 -10000 0 0
CPE 0.015 0.055 -10000 0 -0.54 3 3
CTNNB1 0.011 0.038 -10000 0 -0.64 1 1
membrane fusion 0 0 -10000 0 -10000 0 0
CTNND1 0.033 0.028 -10000 0 -0.45 1 1
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0.007 -10000 0 -10000 0 0
TSHR 0.008 0.078 -10000 0 -0.54 6 6
INS 0.013 0.002 -10000 0 -10000 0 0
BIN1 0 0.1 -10000 0 -0.8 5 5
mol:Choline 0 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.032 -10000 0 -0.54 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.028 -10000 0 -0.48 1 1
JUP 0.03 0.018 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.008 0.062 -10000 0 -0.49 5 5
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.029 0.023 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.047 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.029 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.027 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.026 0.011 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.015 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.047 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.033 0.028 -10000 0 -0.45 1 1
NME1 0.019 0.032 -10000 0 -0.54 1 1
clathrin coat assembly 0.034 0.017 -10000 0 -10000 0 0
IL2RA 0.001 0.082 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.14 -10000 0 -0.51 1 1
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.036 0.007 -10000 0 -10000 0 0
SDC1 0.031 0.011 -10000 0 -10000 0 0
ARF6/GDP 0.017 0.032 -10000 0 -0.54 1 1
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.003 0.03 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
endocytosis 0.008 0.062 0.48 5 -10000 0 5
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.013 0.098 -10000 0 -0.58 1 1
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.013 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.025 0.029 -10000 0 -0.48 1 1
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.024 0.077 -10000 0 -10000 0 0
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.027 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.005 0.054 -9999 0 -0.52 3 3
E-cadherin/beta catenin -0.005 0.046 -9999 0 -0.47 3 3
CTNNB1 0.011 0.038 -9999 0 -0.64 1 1
JUP 0.011 0.038 -9999 0 -0.64 1 1
CDH1 0.009 0.053 -9999 0 -0.64 2 2
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.09 0.024 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 0 0 -9999 0 -10000 0 0
NFKBIA 0.051 0 -9999 0 -10000 0 0
BIRC2 -0.003 0.11 -9999 0 -0.8 6 6
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG -0.004 0.026 -9999 0 -10000 0 0
IKK complex/A20 -0.02 0.077 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.051 0.031 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.003 0.019 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 0.013 0 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.013 0 -9999 0 -10000 0 0
cIAP1/UbcH5C -0.012 0.085 -9999 0 -0.61 6 6
ATM 0.013 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.028 0.12 -9999 0 -0.57 15 15
TRAF6 0.013 0 -9999 0 -10000 0 0
PRKCA 0.011 0.047 -9999 0 -0.8 1 1
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.025 0.17 -9999 0 -0.76 15 15
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.051 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex -0.003 0.022 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.004 0.029 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.002 0.027 -9999 0 -0.48 1 1
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC5 0 0 -9999 0 -10000 0 0
GATA2/HDAC5 -0.004 0.05 -9999 0 -0.61 2 2
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.024 0.17 -9999 0 -0.79 14 14
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -9999 0 -10000 0 0
GATA2 0.008 0.066 -9999 0 -0.8 2 2
HDAC4/RFXANK 0 0 -9999 0 -10000 0 0
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.013 0 -9999 0 -10000 0 0
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.002 0.035 -9999 0 -0.61 1 1
Histones 0.032 0.052 -9999 0 -10000 0 0
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 -0.04 0.2 -9999 0 -0.8 20 20
Tubulin/HDAC6 -0.002 0.03 -9999 0 -0.53 1 1
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.011 0.005 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.002 0.035 -9999 0 -0.61 1 1
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.034 0.13 -9999 0 -0.52 20 20
HDAC4/ER alpha -0.032 0.13 -9999 0 -0.56 17 17
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.032 0.052 -9999 0 -10000 0 0
cell motility -0.002 0.03 -9999 0 -0.53 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.013 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.029 0.18 -9999 0 -0.75 17 17
HDAC6/HDAC11 -0.002 0.027 -9999 0 -0.47 1 1
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.002 0.11 -9999 0 -0.75 6 6
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.008 0.057 -9999 0 -10000 0 0
GNG2 0.011 0.047 -9999 0 -0.8 1 1
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A 0.011 0.047 -9999 0 -0.8 1 1
HDAC11 0.011 0.038 -9999 0 -0.64 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.013 0 -9999 0 -10000 0 0
nuclear import 0 0 -9999 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.012 0.007 -10000 0 -10000 0 0
BUB1B 0.023 0.023 -10000 0 -10000 0 0
PLK1 0.018 0.02 -10000 0 -0.16 1 1
PLK1S1 0.015 0.018 -10000 0 -0.17 2 2
KIF2A 0.026 0.018 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.018 0.02 -10000 0 -0.16 1 1
GOLGA2 0.013 0 -10000 0 -10000 0 0
Hec1/SPC24 0.015 0.091 -10000 0 -0.47 10 10
WEE1 0.023 0.024 -10000 0 -10000 0 0
cytokinesis 0.034 0.021 -10000 0 -10000 0 0
PP2A-alpha B56 0 0.007 -10000 0 -10000 0 0
AURKA 0.014 0.028 -10000 0 -0.19 5 5
PICH/PLK1 0.027 0.076 -10000 0 -0.38 10 10
CENPE 0.026 0.018 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.026 0.018 -10000 0 -10000 0 0
PPP2CA 0.013 0 -10000 0 -10000 0 0
FZR1 0.013 0 -10000 0 -10000 0 0
TPX2 0.012 0.029 -10000 0 -0.18 6 6
PAK1 0.01 0.047 -10000 0 -0.8 1 1
SPC24 -0.003 0.11 -10000 0 -0.8 6 6
FBXW11 0.013 0 -10000 0 -10000 0 0
CLSPN 0.012 0.034 -10000 0 -0.2 7 7
GORASP1 0.013 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -0.017 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.01 0.01 -10000 0 -0.07 1 1
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.013 5 5
STAG2 0.013 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0 0.007 -10000 0 -10000 0 0
spindle elongation 0.018 0.02 -10000 0 -0.16 1 1
ODF2 0.013 0.002 -10000 0 -10000 0 0
BUB1 -0.001 0.009 -10000 0 -10000 0 0
TPT1 0.016 0.01 -10000 0 -10000 0 0
CDC25C 0.015 0.028 -10000 0 -0.24 3 3
CDC25B -0.013 0.14 -10000 0 -0.8 10 10
SGOL1 0.012 0.007 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.013 0.069 -10000 0 -0.39 10 10
CDC14B 0.011 0.029 -10000 0 -0.49 1 1
CDC20 0.003 0.093 -10000 0 -0.8 4 4
PLK1/PBIP1 -0.005 0.04 -10000 0 -0.48 2 2
mitosis 0 0.005 0.04 5 -0.021 2 7
FBXO5 0.022 0.018 -10000 0 -10000 0 0
CDC2 0.001 0.003 -10000 0 -0.016 10 10
NDC80 0.003 0.093 -10000 0 -0.8 4 4
metaphase plate congression 0.017 0.012 -10000 0 -10000 0 0
ERCC6L -0.012 0.065 -10000 0 -0.36 10 10
NLP/gamma Tubulin 0.015 0.011 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.016 0.01 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.013 0.001 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 0.031 0.017 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.009 -10000 0 -10000 0 0
RAB1A 0.013 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.018 0.044 -10000 0 -0.46 2 2
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.019 -10000 0 -10000 0 0
microtubule-based process 0.024 0.018 -10000 0 -10000 0 0
Golgi organization 0.018 0.02 -10000 0 -0.16 1 1
Cohesin/SA2 -0.002 0.012 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A 0.013 0 -10000 0 -10000 0 0
APC/C/CDC20 0.017 0.064 -10000 0 -0.52 4 4
PPP2R1A 0.013 0 -10000 0 -10000 0 0
chromosome segregation -0.005 0.04 -10000 0 -0.47 2 2
PRC1 0.013 0 -10000 0 -10000 0 0
ECT2 0.021 0.053 -10000 0 -0.48 3 3
C13orf34 0.019 0.043 -10000 0 -0.46 2 2
NUDC 0.017 0.012 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.023 0.022 -10000 0 -10000 0 0
spindle assembly 0.018 0.016 -10000 0 -10000 0 0
spindle stabilization 0.015 0.018 -10000 0 -0.17 2 2
APC/C/HCDH1 0.017 0.025 -10000 0 -0.41 1 1
MKLP2/PLK1 0.024 0.018 -10000 0 -10000 0 0
CCNB1 0.014 0.003 -10000 0 -10000 0 0
PPP1CB 0.013 0.001 -10000 0 -10000 0 0
BTRC 0.013 0 -10000 0 -10000 0 0
ROCK2 0.024 0.03 -10000 0 -0.44 1 1
TUBG1 0.016 0.01 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.013 0.068 -10000 0 -0.38 10 10
MLF1IP 0.009 0.052 -10000 0 -0.63 2 2
INCENP 0.013 0.001 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.007 0.04 0.42 1 -10000 0 1
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.049 -10000 0 -0.49 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.009 0.06 -10000 0 -0.72 2 2
RhoA/GTP -0.007 0.041 -10000 0 -0.43 1 1
negative regulation of cAMP metabolic process 0.029 0.053 -10000 0 -0.47 1 1
GNAZ -0.004 0.11 -10000 0 -0.73 7 7
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.008 0.066 -10000 0 -0.8 2 2
S1PR5 0.011 0.038 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.029 0.053 -10000 0 -0.47 1 1
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.011 0.038 -10000 0 -0.64 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.028 0.13 -9999 0 -0.61 14 14
AKT1 0.093 0.038 -9999 0 -10000 0 0
PTK2B 0.038 0.11 -9999 0 -0.62 1 1
VEGFR2 homodimer/Frs2 0.031 0.066 -9999 0 -0.54 4 4
CAV1 -0.065 0.24 -9999 0 -0.8 29 29
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.008 0.062 -9999 0 -0.55 1 1
endothelial cell proliferation 0.099 0.054 -9999 0 -10000 0 0
mol:Ca2+ 0.058 0.046 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.004 0.039 -9999 0 -10000 0 0
RP11-342D11.1 0.049 0.046 -9999 0 -0.5 1 1
CDH5 0.011 0.047 -9999 0 -0.8 1 1
VEGFA homodimer -0.002 0.027 -9999 0 -0.48 1 1
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.009 0.06 -9999 0 -0.72 2 2
HRAS/GDP -0.003 0.033 -9999 0 -10000 0 0
SH2D2A -0.086 0.27 -9999 0 -0.8 37 37
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.005 0.035 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.061 0.16 -9999 0 -0.59 2 2
VEGFR1 homodimer 0.013 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.004 0.037 -9999 0 -10000 0 0
GRB10 0.057 0.061 -9999 0 -0.71 1 1
PTPN11 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.011 0.047 -9999 0 -0.8 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.006 0.047 -9999 0 -10000 0 0
HRAS 0.013 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.043 0.06 -9999 0 -0.48 1 1
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.005 0.081 -9999 0 -0.8 3 3
oxygen and reactive oxygen species metabolic process -0.003 0.039 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0 0.1 -9999 0 -0.8 5 5
Nck/Pak -0.002 0.035 -9999 0 -0.61 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.005 0.05 -9999 0 -0.55 1 1
mol:GDP -0.003 0.036 -9999 0 -10000 0 0
mol:NADP 0.079 0.047 -9999 0 -10000 0 0
eNOS/Hsp90 0.081 0.045 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.059 0.046 -9999 0 -10000 0 0
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.009 0.053 -9999 0 -0.64 2 2
VEGFA 0.013 0.047 -9999 0 -0.8 1 1
VEGFC -0.088 0.27 -9999 0 -0.8 38 38
FAK1/Vinculin 0.064 0.073 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.023 0.099 -9999 0 -0.66 1 1
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.023 0.02 -9999 0 -10000 0 0
mol:L-citrulline 0.079 0.047 -9999 0 -10000 0 0
ITGAV 0.006 0.076 -9999 0 -0.75 3 3
PIK3CA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.008 0.058 -9999 0 -0.52 1 1
VEGFR2 homodimer/VEGFA homodimer -0.004 0.044 -9999 0 -0.55 1 1
VEGFR2/3 heterodimer 0.028 0.09 -9999 0 -0.63 5 5
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.062 0.047 -9999 0 -0.49 1 1
VEGFR2 homodimer 0.037 0.043 -9999 0 -0.7 1 1
FLT1 0.013 0 -9999 0 -10000 0 0
NEDD4 0.016 0.004 -9999 0 -10000 0 0
MAPK3 0.062 0.049 -9999 0 -10000 0 0
MAPK1 0.062 0.049 -9999 0 -10000 0 0
VEGFA145/NRP2 -0.004 0.049 -9999 0 -0.61 2 2
VEGFR1/2 heterodimer 0.037 0.037 -9999 0 -0.61 1 1
KDR 0.037 0.043 -9999 0 -0.7 1 1
VEGFA165/NRP1/VEGFR2 homodimer -0.005 0.046 -9999 0 -0.49 1 1
SRC 0.013 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.064 0.049 -9999 0 -10000 0 0
PI3K -0.004 0.034 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.004 0.042 -9999 0 -0.55 1 1
FES 0.059 0.047 -9999 0 -0.51 1 1
GAB1 -0.003 0.032 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.004 0.042 -9999 0 -0.55 1 1
CTNNB1 0.011 0.038 -9999 0 -0.64 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.043 0.12 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Yes -0.004 0.042 -9999 0 -0.55 1 1
PI3K/GAB1 0.094 0.039 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.009 0.059 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.068 0.18 -9999 0 -1.4 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.059 0.047 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.06 0.16 -9999 0 -0.59 2 2
PTK2 0.059 0.077 -9999 0 -10000 0 0
EDG1 0.049 0.046 -9999 0 -0.5 1 1
mol:DAG 0.059 0.046 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.037 -9999 0 -10000 0 0
MAP2K3 0.063 0.057 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.005 0.056 -9999 0 -0.72 1 1
PLCG1 0.059 0.047 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.006 0.046 -9999 0 -10000 0 0
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.004 0.042 -9999 0 -0.55 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.004 0.042 -9999 0 -0.55 1 1
cell migration 0.087 0.066 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.032 -9999 0 -10000 0 0
FYN 0.011 0.047 -9999 0 -0.8 1 1
VEGFB/NRP1 -0.004 0.038 -9999 0 -0.47 1 1
mol:NO 0.079 0.047 -9999 0 -10000 0 0
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.003 0.033 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.056 0.062 -9999 0 -0.71 1 1
VHL 0.013 0 -9999 0 -10000 0 0
ITGB3 -0.017 0.15 -9999 0 -0.76 12 12
NOS3 0.081 0.051 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Sck -0.007 0.058 -9999 0 -0.59 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.064 0.052 -9999 0 -10000 0 0
PRKCB 0.055 0.082 -9999 0 -10000 0 0
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.048 0.046 -9999 0 -0.5 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.004 0.042 -9999 0 -0.55 1 1
VEGFA165/NRP2 -0.004 0.049 -9999 0 -0.61 2 2
MAPKKK cascade -0.004 0.045 -9999 0 -0.58 1 1
NRP2 0.011 0.047 -9999 0 -0.8 1 1
VEGFC homodimer -0.088 0.27 -9999 0 -0.8 38 38
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.064 0.073 -9999 0 -10000 0 0
MAP3K13 0.056 0.056 -9999 0 -10000 0 0
PDPK1 0.085 0.039 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.029 0.086 -9999 0 -0.43 10 10
KLHL20 -0.01 0.037 -9999 0 -0.29 1 1
CYFIP2 0.009 0.053 -9999 0 -0.64 2 2
Rac1/GDP 0.06 0.038 -9999 0 -10000 0 0
ENAH 0.04 0.053 -9999 0 -0.48 3 3
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.011 0.047 -9999 0 -0.8 1 1
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.011 0.038 -9999 0 -0.64 1 1
CDC42/GTP -0.003 0.026 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.026 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.005 0.04 -9999 0 -10000 0 0
RAPGEF1 0.054 0.046 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.005 0.05 -9999 0 -0.5 3 3
CRK 0.048 0.05 -9999 0 -0.44 3 3
E-cadherin/gamma catenin/alpha catenin -0.004 0.049 -9999 0 -0.58 2 2
alphaE/beta7 Integrin -0.002 0.027 -9999 0 -0.47 1 1
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.002 0.028 -9999 0 -0.49 1 1
DLG1 0.04 0.053 -9999 0 -0.48 3 3
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.018 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.005 0.045 -9999 0 -0.49 1 1
PI3K -0.003 0.023 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.004 0.056 -9999 0 -0.67 2 2
TIAM1 0.007 0.065 -9999 0 -0.64 3 3
E-cadherin(dimer)/Ca2+ -0.003 0.033 -9999 0 -10000 0 0
AKT1 -0.002 0.013 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.009 0.053 -9999 0 -0.64 2 2
RhoA/GDP 0.06 0.038 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.028 -9999 0 -0.2 1 1
CDC42/GDP 0.06 0.038 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.024 0.038 -9999 0 -0.42 2 2
ITGB7 0.011 0.038 -9999 0 -0.64 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.003 0.035 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.003 0.034 -9999 0 -0.34 3 3
mol:GDP 0.057 0.043 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0.038 -9999 0 -0.64 1 1
p120 catenin/RhoA/GDP -0.003 0.028 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.03 0.047 -9999 0 -0.24 7 7
NME1 0.011 0.047 -9999 0 -0.8 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.04 0.053 -9999 0 -0.48 3 3
regulation of cell-cell adhesion -0.003 0.023 -9999 0 -10000 0 0
WASF2 -0.004 0.013 -9999 0 -10000 0 0
Rap1/GTP -0.003 0.03 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.004 0.046 -9999 0 -0.67 1 1
CCND1 0.034 0.058 -9999 0 -0.31 7 7
VAV2 0.041 0.075 -9999 0 -10000 0 0
RAP1/GDP -0.001 0.032 -9999 0 -10000 0 0
adherens junction assembly 0.04 0.051 -9999 0 -0.46 3 3
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.005 0.047 -9999 0 -0.64 1 1
E-cadherin/beta catenin -0.003 0.034 -9999 0 -0.41 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.04 0.053 -9999 0 -0.48 3 3
PIK3CA 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.016 0.06 -9999 0 -0.5 1 1
E-cadherin/beta catenin/alpha catenin -0.004 0.039 -9999 0 -0.4 3 3
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.005 0.051 -9999 0 -0.51 3 3
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.052 0.03 -10000 0 -0.41 1 1
adherens junction organization 0.043 0.052 -10000 0 -0.5 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.044 0.081 -10000 0 -10000 0 0
FMN1 0.034 0.078 -10000 0 -0.6 2 2
mol:IP3 -0.002 0.027 -10000 0 -0.43 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.037 0.047 -10000 0 -0.66 1 1
CTNNB1 0.011 0.037 -10000 0 -0.64 1 1
AKT1 0.05 0.034 -10000 0 -0.46 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.042 0.059 -10000 0 -0.52 3 3
CTNND1 0.015 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.044 -10000 0 -0.6 1 1
VASP 0.044 0.045 -10000 0 -0.62 1 1
ZYX 0.044 0.045 -10000 0 -0.62 1 1
JUB 0.044 0.045 -10000 0 -0.62 1 1
EGFR(dimer) 0.028 0.094 -10000 0 -0.44 11 11
E-cadherin/beta catenin-gamma catenin -0.005 0.052 -10000 0 -0.49 3 3
mol:PI-3-4-5-P3 -0.003 0.031 -10000 0 -0.49 1 1
PIK3CA 0.014 0.001 -10000 0 -10000 0 0
PI3K -0.003 0.032 -10000 0 -0.5 1 1
FYN 0.052 0.053 -10000 0 -0.6 1 1
mol:Ca2+ -0.002 0.026 -10000 0 -0.42 1 1
JUP 0.011 0.037 -10000 0 -0.64 1 1
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG -0.002 0.027 -10000 0 -0.43 1 1
CDH1 0.009 0.053 -10000 0 -0.64 2 2
RhoA/GDP 0.044 0.081 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.044 0.044 -10000 0 -0.6 1 1
SRC 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR -0.014 0.15 -10000 0 -0.8 10 10
CASR 0.044 0.053 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.023 -10000 0 -10000 0 0
AKT2 0.05 0.034 -10000 0 -0.46 1 1
actin cable formation 0.041 0.076 -10000 0 -0.57 2 2
apoptosis 0.002 0.028 0.44 1 -10000 0 1
CTNNA1 0.015 0.001 -10000 0 -10000 0 0
mol:GDP 0.037 0.086 -10000 0 -0.43 1 1
PIP5K1A 0.044 0.045 -10000 0 -0.62 1 1
PLCG1 -0.002 0.027 -10000 0 -0.44 1 1
Rac1/GTP -0.016 0.076 -10000 0 -0.4 11 11
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.011 0.038 -9999 0 -0.64 1 1
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.045 0.015 -9999 0 -10000 0 0
SMAD3/SMAD4 0.05 0.017 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.023 -9999 0 -0.4 1 1
SMAD2/SMAD2/SMAD4 -0.001 0.017 -9999 0 -10000 0 0
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.021 0.022 -9999 0 -0.35 1 1
MAP3K1 0.013 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.006 0.054 -9999 0 -0.47 4 4
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 0.007 0.065 -9999 0 -0.64 3 3
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.013 0 -9999 0 -10000 0 0
KPNA2 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.005 0.046 -10000 0 -0.47 3 3
ATM 0.013 0 -10000 0 -10000 0 0
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.013 0 -10000 0 -10000 0 0
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.028 0 -10000 0 -10000 0 0
protein ubiquitination -0.005 0.04 -10000 0 -0.44 1 1
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.013 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.004 0.038 -10000 0 -0.56 1 1
FANCF 0.009 0.053 -10000 0 -0.64 2 2
BRCA1 0.013 0 -10000 0 -10000 0 0
CCNE1 0.011 0.047 -10000 0 -0.8 1 1
CDK2/Cyclin E1 -0.002 0.035 -10000 0 -0.61 1 1
FANCG 0.008 0.066 -10000 0 -0.8 2 2
BRCA1/BACH1/BARD1 -0.005 0.046 -10000 0 -0.47 3 3
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA 0.011 0.047 -10000 0 -0.8 1 1
DNA repair 0.074 0.056 -10000 0 -0.49 1 1
BRCA1/BARD1/ubiquitin -0.005 0.046 -10000 0 -0.47 3 3
BARD1/DNA-PK -0.003 0.035 -10000 0 -10000 0 0
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.005 0.046 0.47 3 -10000 0 3
BRCA1/BARD1/CTIP/M/R/N Complex 0.041 0.03 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.004 0.039 -10000 0 -10000 0 0
BRCA1/BARD1/P53 -0.007 0.049 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.004 0.039 -10000 0 -0.4 3 3
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 0.007 0.065 -10000 0 -0.64 3 3
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.004 0.039 -10000 0 -0.4 3 3
BRCA1/BARD1/UbcH7 -0.004 0.039 -10000 0 -0.4 3 3
BRCA1/BARD1/RAD51/PCNA -0.005 0.044 -10000 0 -0.48 1 1
BARD1/DNA-PK/P53 -0.006 0.045 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.005 0.046 -10000 0 -0.47 3 3
BRCA1/BARD1/CTIP -0.003 0.035 -10000 0 -10000 0 0
FA complex 0.039 0.041 -10000 0 -0.5 1 1
BARD1/EWS -0.005 0.046 -10000 0 -0.47 3 3
RBBP8 0.025 0 -10000 0 -10000 0 0
TP53 0.007 0.065 -10000 0 -0.64 3 3
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.007 0.049 -10000 0 -10000 0 0
BRCA1/BARD1 -0.005 0.041 -10000 0 -0.44 1 1
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.005 0.047 -10000 0 -0.48 3 3
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.011 0.047 -10000 0 -0.8 1 1
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.005 0.046 -10000 0 -0.47 3 3
EWSR1 0.013 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.013 0 -9999 0 -9999 0 0
PLK4 0.013 0 -9999 0 -9999 0 0
regulation of centriole replication 0.025 0 -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 0.013 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.004 0.044 -9999 0 -0.49 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.001 0.012 -9999 0 -10000 0 0
AURKB 0.011 0.047 -9999 0 -0.8 1 1
AURKC 0.009 0.06 -9999 0 -0.72 2 2
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.081 0.094 -10000 0 -0.41 1 1
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.057 0.14 0.3 6 -0.45 1 7
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 0.025 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.018 0.14 -10000 0 -0.8 10 10
PRKCI 0.013 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.035 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.038 -10000 0 -0.64 1 1
TRIP10 0.013 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.05 0.014 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 -0.064 0.15 0.3 6 -0.51 1 7
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.028 0 -10000 0 -10000 0 0
SFN 0.011 0.038 -10000 0 -0.64 1 1
LNPEP 0.013 0 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -9999 0 -9999 0 0
MKNK1 0.013 0 -9999 0 -9999 0 0
mol:PIP3 0 0 -9999 0 -9999 0 0
FRAP1 0.017 0 -9999 0 -9999 0 0
AKT1 0 0 -9999 0 -9999 0 0
INSR 0.013 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0 -9999 0 -9999 0 0
TSC2 0.013 0 -9999 0 -9999 0 0
RHEB/GDP 0 0 -9999 0 -9999 0 0
TSC1 0.014 0 -9999 0 -9999 0 0
Insulin Receptor/IRS1 0.017 0 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0.013 0 -9999 0 -9999 0 0
RPS6KB1 0.031 0 -9999 0 -9999 0 0
MAP3K5 0.011 0 -9999 0 -9999 0 0
PIK3R1 0.014 0 -9999 0 -9999 0 0
apoptosis 0.011 0 -9999 0 -9999 0 0
mol:LY294002 0 0 -9999 0 -9999 0 0
EIF4B 0.037 0 -9999 0 -9999 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0 0 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -9999 0 -9999 0 0
KIAA1303 0 0 -9999 0 -9999 0 0
PI3K 0.026 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.035 0 -9999 0 -9999 0 0
FKBP1A 0.014 0 -9999 0 -9999 0 0
RHEB/GTP 0 0 -9999 0 -9999 0 0
mol:Amino Acids 0 0 -9999 0 -9999 0 0
FKBP12/Rapamycin 0 0 -9999 0 -9999 0 0
PDPK1 0 0 -9999 0 -9999 0 0
EIF4E 0.013 0 -9999 0 -9999 0 0
ASK1/PP5C 0.023 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0 -9999 0 -9999 0 0
TSC1/TSC2 0 0 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RPS6 0.013 0 -9999 0 -9999 0 0
PPP5C 0.013 0 -9999 0 -9999 0 0
EIF4G1 0.013 0 -9999 0 -9999 0 0
IRS1 0.009 0 -9999 0 -9999 0 0
INS 0 0 -9999 0 -9999 0 0
PTEN 0.013 0 -9999 0 -9999 0 0
PDK2 0 0 -9999 0 -9999 0 0
EIF4EBP1 0.009 0.039 -9999 0 -9999 0 0
PIK3CA 0.014 0 -9999 0 -9999 0 0
PPP2R5D 0.024 0 -9999 0 -9999 0 0
peptide biosynthetic process 0.019 0 -9999 0 -9999 0 0
RHEB 0.014 0 -9999 0 -9999 0 0
EIF4A1 0.013 0 -9999 0 -9999 0 0
mol:Rapamycin 0 0 -9999 0 -9999 0 0
EEF2 0.019 0 -9999 0 -9999 0 0
eIF4E/4E-BP1 0.016 0.034 -9999 0 -9999 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.019 0.085 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.015 0.065 -9999 0 -10000 0 0
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones -0.008 0.037 -9999 0 -10000 0 0
YY1/LSF 0.021 0.057 -9999 0 -10000 0 0
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.015 0.064 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 -0.01 0.045 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA 0.028 0.063 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.01 0.045 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.052 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.031 0.057 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.008 0.066 -9999 0 -0.8 2 2
GATA1 0.011 0.005 -9999 0 -10000 0 0
Mad/Max -0.002 0.027 -9999 0 -0.47 1 1
NuRD/MBD3 Complex/GATA1/Fog1 0.063 0.002 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.013 0 -9999 0 -10000 0 0
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA 0.018 0.058 -9999 0 -10000 0 0
KAT2B -0.015 0.13 -9999 0 -0.64 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.047 0 -9999 0 -10000 0 0
SIN3 complex 0 0 -9999 0 -10000 0 0
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.013 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.017 0.054 -9999 0 -10000 0 0
YY1/HDAC2 0.021 0.057 -9999 0 -10000 0 0
YY1/HDAC1 0.021 0.057 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.052 0 -9999 0 -10000 0 0
PPARG -0.14 0.17 -9999 0 -0.69 5 5
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.01 0.045 -9999 0 -10000 0 0
MBD3L2 -0.002 0.046 -9999 0 -0.8 1 1
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.055 0.012 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 0.018 0.058 -9999 0 -10000 0 0
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.019 0.068 -9999 0 -10000 0 0
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.011 0.038 -9999 0 -0.64 1 1
STAT3 0.028 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.009 0.044 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 -0.009 0.044 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.028 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.058 -9999 0 -10000 0 0
histone deacetylation 0.052 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.009 0.039 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.013 0.064 -9999 0 -0.58 2 2
GATA1/HDAC1 0 0 -9999 0 -10000 0 0
GATA1/HDAC3 -0.01 0.045 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.028 0.12 -9999 0 -0.57 15 15
SIN3/HDAC complex/Mad/Max 0.051 0.013 -9999 0 -10000 0 0
NuRD Complex 0.061 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.008 0.036 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 0 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.025 0.17 -9999 0 -0.76 15 15
negative regulation of cell growth 0.051 0.013 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.052 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.016 0.069 -9999 0 -0.35 4 4
SIN3/HDAC complex/NCoR1 0.05 0 -9999 0 -10000 0 0
TFCP2 0.013 0 -9999 0 -10000 0 0
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.013 0 -9999 0 -10000 0 0
MBD2 0.013 0 -9999 0 -10000 0 0
FoxO family signaling

Figure 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
G6PC 0.043 0.012 -9999 0 -10000 0 0
PLK1 0.12 0.1 -9999 0 -0.74 1 1
CDKN1B 0.15 0.046 -9999 0 -10000 0 0
FOXO3 0.12 0.1 -9999 0 -0.57 1 1
KAT2B -0.001 0.13 -9999 0 -0.63 13 13
FOXO1/SIRT1 0.009 0.024 -9999 0 -10000 0 0
CAT 0.11 0.12 -9999 0 -1.2 1 1
CTNNB1 0.011 0.038 -9999 0 -0.64 1 1
AKT1 0.03 0.01 -9999 0 -10000 0 0
FOXO1 0.046 0.009 -9999 0 -10000 0 0
MAPK10 0.028 0.08 -9999 0 -0.45 1 1
mol:GTP 0.003 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.049 -9999 0 -10000 0 0
response to oxidative stress 0.018 0.01 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.003 0.069 -9999 0 -0.54 1 1
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.016 0.001 -9999 0 -10000 0 0
BCL2L11 0.044 0.024 -9999 0 -10000 0 0
FOXO1/SKP2 0.047 0.007 -9999 0 -10000 0 0
mol:GDP 0.018 0.01 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
GADD45A 0.13 0.055 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.083 0.011 -9999 0 -10000 0 0
MST1 0.02 0.071 -9999 0 -0.68 3 3
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.064 0.019 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.044 0.031 -9999 0 -10000 0 0
MAPK9 0.046 0.005 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.005 0.017 -9999 0 -10000 0 0
SOD2 0.16 0.054 -9999 0 -10000 0 0
RBL2 0.12 0.072 -9999 0 -10000 0 0
RAL/GDP 0.035 0.011 -9999 0 -10000 0 0
CHUK 0.027 0.009 -9999 0 -10000 0 0
Ran/GTP 0.015 0.001 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.045 0.008 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.016 0.26 -9999 0 -0.89 21 21
SKP2 0.013 0 -9999 0 -10000 0 0
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.027 0.009 -9999 0 -10000 0 0
CCNB1 0.12 0.094 -9999 0 -10000 0 0
FOXO1-3a-4/beta catenin 0.006 0.03 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.046 0.007 -9999 0 -10000 0 0
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.025 0.038 -9999 0 -0.63 1 1
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.002 -9999 0 -10000 0 0
ZFAND5 0.11 0.044 -9999 0 -10000 0 0
SFN 0.011 0.038 -9999 0 -0.64 1 1
CDK2 0.014 0.002 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.078 0.031 -9999 0 -10000 0 0
CREBBP 0.014 0.002 -9999 0 -10000 0 0
FBXO32 0.11 0.14 -9999 0 -1.3 2 2
BCL6 0.12 0.072 -9999 0 -10000 0 0
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.028 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.046 -9999 0 -0.46 1 1
NFKBIA 0.023 0.052 -9999 0 -0.54 1 1
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0 -9999 0 -10000 0 0
ARRB2 0.019 0 -9999 0 -10000 0 0
REL 0.013 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.028 0 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.022 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.025 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.047 -9999 0 -0.43 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.048 0.045 -9999 0 -0.45 1 1
SRC 0.013 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.031 0.047 -9999 0 -0.43 1 1
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.011 0.038 -9999 0 -0.64 1 1
I kappa B alpha/PIK3R1 0.029 0.049 -9999 0 -0.51 1 1
cell death -0.006 0.034 -9999 0 -0.43 1 1
NF kappa B1 p105/c-Rel 0.028 0 -9999 0 -10000 0 0
LCK -0.014 0.15 -9999 0 -0.8 10 10
BCL3 0.013 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0 0 -9999 0 -9999 0 0
HDAC4 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.013 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.019 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.031 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.013 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.013 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0 0 -9999 0 -9999 0 0
RANGAP1 0.013 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.024 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.013 0 -9999 0 -9999 0 0
UBE2I 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.013 0 -9999 0 -9999 0 0
PIAS1 0.013 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0 -9999 0 -10000 0 0
AP2 -0.002 0.035 -9999 0 -0.61 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.028 0 -9999 0 -10000 0 0
CD4 0.009 0.06 -9999 0 -0.72 2 2
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.03 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.011 0.047 -9999 0 -0.8 1 1
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.028 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.03 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.036 0.024 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.048 -9999 0 -0.48 3 3
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.013 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 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.003 0.036 -9999 0 -0.45 2 2
NFKB1 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.004 0.05 -9999 0 -0.61 2 2
RELB 0.008 0.066 -9999 0 -0.8 2 2
NFKB2 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.004 0.043 -9999 0 -0.54 2 2
regulation of B cell activation -0.004 0.043 -9999 0 -0.53 2 2
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 303 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.IQ.7632 TCGA.IQ.7631 TCGA.IQ.7630 TCGA.HD.7917
109_MAP3K5 0.06 0.06 0.06 0.06
47_PPARGC1A 0.013 0.013 0.013 0.013
105_BMP4 0.013 0.013 0.013 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 0.013 0.013 0.013
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR -0.35 -0.35 -0.35 -0.35
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.019 0.019
84_STAT5B -0.071 -0.22 -0.031 0.049
84_STAT5A -0.071 -0.22 -0.031 0.049
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/HNSC-TP/2398224/0.mRNAseq_preprocessor.Finished/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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